ARIA-EAACI statement on asthma and COVID-19 (June 2, 2020)

Non peer reviewe

Cabbage and fermented vegetables : From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19

Large differences in COVID-19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS-CoV-2 binds to its receptor, the angiotensin-converting enzyme 2 (ACE2). As a result of SARS-CoV-2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT(1)R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID-19. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT(1)R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof-of-concept of dietary manipulations that may enhance Nrf2-associated antioxidant effects, helpful in mitigating COVID-19 severity.Peer reviewe

Nrf2-interacting nutrients and COVID-19 : time for research to develop adaptation strategies

There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPAR gamma:Peroxisome proliferator-activated receptor, NF kappa B: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2 alpha:Elongation initiation factor 2 alpha). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT(1)R axis (AT(1)R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity

Function of NIPBL in the cardiac development

Le complexe cohésine est requis dans l’organisation 3D du génome qui contribue à réguler l’expression des gènes en modulant l’interaction entre les éléments de régulation tels que les promoteurs et les enhancers. Cette dynamique est notamment essentielle pour la régulation de l’expression des gènes clés de l’identité cellulaire. Le Syndrome de Cornelia de Lange (SCdL) est une maladie congénitale rare affectant jusqu’à 1/45 000 naissances. Cette pathologie est le plus souvent associée à une mutation de NIPBL, qui a pour fonction de charger le complexe cohésine sur l’ADN. Le phénotype des patients atteints du SCdL est très hétérogène et cette pathologie affecte de multiples organes dont le cœur. La première partie de ma thèse porte sur les défauts valvulaires des patients. Aucune étude rapportant les caractéristiques des valves cardiaques des souris Nipbl+/- a été publiée, alors même que les défauts liés aux valves sont courants chez les patients SCdL. Nous avons montré que les souris Nipbl+/- présentent un épaississement des cuspides de la valve aortique ainsi qu’un retard de septation de la voie d’éjection. Dans une deuxième partie nous nous sommes interrogés sur le rôle de NIPBL durant la cardiogenèse. Nous avons réalisé des expériences d’immunoprecipitation de chromatine pour comprendre le lien entre NIPBL et les gènes dérégules en l’absence de Nipbl que nous avons identifié dans les progéniteurs cardiaques par une analyse de type transcriptome en cellule unique. Enfin la dernière partie de ma thèse porte sur la génération de lignées de poissons zèbre déficientes en nipbl, permettant d’élargir le panel de modèles SCdL disponibles pour l’étude de cette pathologie.The cohesin complex, a large ring able to encircled DNA, is required for establishing 3D genome structure. By forming DNA loops, this complex is directly involved in the cis-regulation of gene expression by enabling interactions between the regulatory elements such as enhancers and promoters. These dynamics are essential for the regulation of key cell identity genes. Cornelia de Lange Syndrome (CdLS) is a congenital disease affecting up to 1/45 000 live births. This disease is mostly associated with mutations in NIPBL, which loads the cohesin complex onto the DNA. CdLS is a multi-systemic disorder, affecting the heart in various ways. The first part of my thesis is on valve defects, that are often observes in CdLS patients but had not been studied in the mice models of CdLS. We reported that Nipbl+/- mice present a thickening of the aortic cuspid valve and a delayed septation of the outflow tract. In the second part, we study the function of NIPBL in cardiogenesis. We perform chromatin immunoprecipitation (ChIP) experiments to understand the link between NIPBL and genes deregulated by the absence of Nipbl identified by single cell transcriptomic analysis in cardiac progenitors. Finally, we used CRISPR-cas9 technology to generate a nipbl+/- zebrafish to increase the panel of CdLS models available

Nipbl Haploinsufficiency Leads to Delayed Outflow Tract Septation and Aortic Valve Thickening

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms242115564/s1.International audienceCornelia de Lange Syndrome (CdLS) patients, who frequently carry a mutation in NIPBL, present an increased incidence of outflow tract (OFT)-related congenital heart defects (CHDs). Nipbl+/- mice recapitulate a number of phenotypic traits of CdLS patients, including a small body size and cardiac defects, but no study has specifically focused on the valves. Here, we show that adult Nipbl+/- mice present aortic valve thickening, a condition that has been associated with stenosis. During development, we observed that OFT septation and neural crest cell condensation was delayed in Nipbl+/- embryos. However, we did not observe defects in the deployment of the main lineages contributing to the semilunar valves. Indeed, endocardial endothelial-to-mesenchymal transition (EndMT), analysed via outflow tract explants, and neural crest migration, analysed via genetic lineage tracing, did not significantly differ in Nipbl+/- mice and their wild-type littermates. Our study provides the first direct evidence for valve formation defects in Nipbl+/- mice and points to specific developmental defects as an origin for valve disease in patients

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function.

Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here, we demonstrate that the male-specific lethal (MSL)-complex-mediated histone H4 acetylation at lysine 16 (H4K16ac) is enriched at TEs in human embryonic stem cells (hESCs) and cancer cells. This in turn activates transcription of subsets of full-length long interspersed nuclear elements (LINE1s, L1s) and endogenous retrovirus (ERV) long terminal repeats (LTRs). Furthermore, we show that the H4K16ac-marked L1 and LTR subfamilies display enhancer-like functions and are enriched in genomic locations with chromatin features associated with active enhancers. Importantly, such regions often reside at boundaries of topologically associated domains and loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac-marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape at specific genomic locations by maintaining an active chromatin landscape at TEs

H4K16ac activates the transcription of transposable elements and contributes to their cis -regulatory function

Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here, we demonstrate that the male-specific lethal (MSL)-complex-mediated histone H4 acetylation at lysine 16 (H4K16ac) is enriched at TEs in human embryonic stem cells (hESCs) and cancer cells. This in turn activates transcription of subsets of full-length long interspersed nuclear elements (LINE1s, L1s) and endogenous retrovirus (ERV) long terminal repeats (LTRs). Furthermore, we show that the H4K16ac-marked L1 and LTR subfamilies display enhancer-like functions and are enriched in genomic locations with chromatin features associated with active enhancers. Importantly, such regions often reside at boundaries of topologically associated domains and loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac-marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape at specific genomic locations by maintaining an active chromatin landscape at TEs

Impact of diets enriched with omega-3 fatty acids or antioxidants on Belgian blue bull semen

Improving bull semen quality and quantity is an important issue for artificial insemination (AI) centers. Spermatogenesis is influenced by many factors, including genetics and nutrition. The objective of the study was to evaluate the impact on blood and semen parameters of enriching the diet of Belgian blue bulls with 1. Omega-3 fatty acids: concentrate enriched with extruded linseed (Linamix, Dumoulin) providing an omega-3 concentration of 14g/kg instead of 3.7 and extra vitamin E to prevent lipid peroxidation (160mg/kg instead of 50) = O3 diet; 2. Antioxidants :concentrate supplemented with 47mg/kg betacarotene, 200mg/kg encapsulated grape extracts rich in polyphenols (Nor-Grape BP-0, Nor-Feed), 600 mg/kg melon extracts rich in superoxide dismutase (Melofeed, Lallemand) and 1mg/kg selenium instead of 0.8 = AX diet; 3. in comparison with the basic concentrate without enrichment = CT diet. After at least one month of receiving the CT diet, 24 Belgian blue bulls (1 to 9 years old) housed in the AI center of Inovéo (Ciney, Belgium) were randomly assigned to 3 groups. Each group received successively the three diets (basic diet + 1.25kg concentrate per 100 kg BW per day) for a period of 4 months in a different order. At the end of each 4-month period, specific analysis were conducted on semen (volume, concentration and computer assisted sperm analysis for motility and morphological parameters; fatty acid profiles analysis using gas chromatography) and blood samples (concentration in selenium, vitamin A and vitamin E). Statistical analysis was performed using a mixed model for repeated measurements with diet, period of the year and their interaction as fixed effects. A majority of the measured parameters was influenced by the period of sampling. As expected, blood concentrations in selenium and vitamin A were on average higher with the AX diet (p=0.0011 and 0.034, respectively), while the vitamin E concentrations were higher with the O3 diet by comparison with the two other diets (p<0.0001). A higher semen concentration was found with the AX diet by comparison with the CT diet (mean: 1.45 vs 1.28 billion spz/ml; p=0.037). The proportion of motile spz also tended to be higher for the AX by comparison to the CT regime (mean: 60.6 vs 56.1%; p=0.098). No significant difference was observed for the semen parameters between the AX and the O3 diet or between the O3 and the CT diet. The diet did not significantly influence the other measured sperm characteristics, including the proportion of progressive spermatozoa. The proportion of saturated, monounsaturated or polyunsaturated fatty acids in sperm cells was similar between diets. However, the O3 diet significantly increased the proportion of docosahexaenoic acid (DHA; p=0.0001) and its precursor alpha-linolenic acid (ALA; p=0.0009) by comparison with the two other diets. A high DHA content in sperm membranes usually correlates with a better sperm quality, which was not demonstrated in the present study. In conclusion, the diet enriched in linseed increased the DHA content of the sperm, while supplementing the diet with a cocktail of natural antioxidants had a positive impact on semen concentration and motility

Key recommendations for primary care from the 2022 Global Initiative for Asthma (GINA) update

The Global Initiative for Asthma (GINA) was established in 1993 by the World Health Organization and the US National Heart Lung and Blood Institute to improve asthma awareness, prevention and management worldwide. GINA develops and publishes evidence-based, annually updated resources for clinicians. GINA guidance is adopted by national asthma guidelines in many countries, adapted to fit local healthcare systems, practices, and resource availability. GINA is independent of industry, funded by the sale and licensing of its materials. This review summarizes key practical guidance for primary care from the 2022 GINA strategy report. It provides guidance on confirming the diagnosis of asthma using spirometry or peak expiratory flow. GINA recommends that all adults, adolescents and most children with asthma should receive inhaled corticosteroid (ICS)-containing therapy to reduce the risk of severe exacerbations, either taken regularly, or (for adults and adolescents with “mild” asthma) as combination ICS–formoterol taken as needed for symptom relief. For patients with moderate–severe asthma, the preferred regimen is maintenance-and-reliever therapy (MART) with ICS–formoterol. Asthma treatment is not “one size fits all”; GINA recommends individualized assessment, adjustment, and review of treatment. As many patients with difficult-to-treat or severe asthma are not referred early for specialist review, we provide updated guidance for primary care on diagnosis, further investigation, optimization and treatment of severe asthma across secondary and tertiary care. While the GINA strategy has global relevance, we recognize that there are special considerations for its adoption in low- and middle-income countries, particularly the current poor access to inhaled medications

Regulatory de novo mutations underlying intellectual disability

The genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood. We sequenced 63 whole genomes from 21 ID probands and their unaffected parents. In addition, we analysed 30 previously sequenced genomes from exome-negative ID probands. We found that regulatory DNMs were selectively enriched in fetal brain-specific enhancers as compared with adult brain enhancers. DNM-containing enhancers were associated with genes that show preferential expression in the prefrontal cortex. Furthermore, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1, and POU3F3). Most of the DNMs from ID probands showed allele-specific enhancer activity when tested using luciferase assay. Using CRISPR-mediated mutation and editing of epigenomic marks, we show that DNMs at regulatory elements affect the expression of putative target genes. Our results, therefore, provide new evidence to indicate that DNMs in fetal brain-specific enhancers play an essential role in the aetiology of ID.This work was funded by grants from the Wellcome Trust Institute Strategic Support and National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, Institute for Translational Medicine and Therapeutics (P70888) obtained by SS Atanur. J Ferrer and MG De Vas’s work was funded by grants from the Wellcome Trust (WT101033 to J Ferrer), Medical Research Council (MR/L02036X/1 to J Ferrer), and European Research Council Advanced Grant (789055 to J Ferrer). MM Pradeepa’s lab is funded by the UKRI/MRC (MR/T000783/1), and Barts charity (MGU0475) grants. TN Khan was partially supported by the Government of Pakistan under the PSDP project “Development of National University of Medical Sciences (NUMS), Rawalpindi.