Genetic associations of protein-coding variants in human disease.

Genome-wide association studies (GWAS) have identified thousands of genetic variants linked to the risk of human disease. However, GWAS have so far remained largely underpowered in relation to identifying associations in the rare and low-frequency allelic spectrum and have lacked the resolution to trace causal mechanisms to underlying genes1. Here we combined whole-exome sequencing in 392,814 UK Biobank participants with imputed genotypes from 260,405 FinnGen participants (653,219 total individuals) to conduct association meta-analyses for 744 disease endpoints across the protein-coding allelic frequency spectrum, bridging the gap between common and rare variant studies. We identified 975 associations, with more than one-third being previously unreported. We demonstrate population-level relevance for mutations previously ascribed to causing single-gene disorders, map GWAS associations to likely causal genes, explain disease mechanisms, and systematically relate disease associations to levels of 117 biomarkers and clinical-stage drug targets. Combining sequencing and genotyping in two population biobanks enabled us to benefit from increased power to detect and explain disease associations, validate findings through replication and propose medical actionability for rare genetic variants. Our study provides a compendium of protein-coding variant associations for future insights into disease biology and drug discovery

Cellular and molecular study of a few aspects of atrial fibrillation and long QT syndrome : role of connexins 40 and 43, the transcription factor PITX2c and the potassium channel encoded by KCNH2

La fibrillation atriale (FA) est l'arythmie cardiaque soutenue la plus fréquente chez les adultes. Elle est associée à une augmentation du risque d'accident vasculaire cérébral, d'insuffisance cardiaque et de la mortalité. Un mécanisme de torsades auriculaires a été décrit chez des patients atteints du syndrome du QT long congénital (SQTL). Malgré une littérature très riche sur le sujet, les mécanismes impliqués dans la genèse et le maintien de ces arythmies restent mal connus et constituent un obstacle dans le diagnostic et la prise en charge de ces maladies. Dans la première partie de ce travail, nous avons abordé l'histologie et la distribution des connexines (Cxs) chez deux groupes de patients avec et sans FA par une approche de microscopie confocale. Nous avons ainsi décrit d'une part un réseau entre fibroblastes et myocytes communiquant via les Cx 40 et 43 et d'autre part la présence de myofibroblastes, d'une forte fibrose et d'un remodelage des Cx 40 et 43 dans le tissu de patients FA. Par ailleurs, pour identifier de nouvelles mutations impliquées dans ces arythmies, nous avons étudié une cohorte de 60 patients atteints de FA. Les recherches génétiques et l'étude fonctionnelle nous ont permis d'associer 5 nouvelles mutations: P41S et M207V (PITX2), G277E (Cx 40) A253V (Cx 43) et P1034H (KCNH2) à la FA. Celles-ci semblent jouer un rôle clé dans la constitution du substrat arythmogène. Enfin, dans la dernière partie, nous avons exploré l'impact électrophysiologique d'un variant de KCNH2, R148W, trouvé tout d'abord chez un enfant décédé de mort subite pendant le sommeil, puis chez plusieurs membres de la famille, dont certains présentent un intervalle QT allongé. Ce variant, exprimé dans les ovocytes de Xénope et étudié en voltage-clamp, réduit le courant de 29% et pourrait alors prédisposer à la survenue de torsades de pointes et expliquer en partie l'allongement du QTc. Outre les nouveaux variants géniques découverts, ce travail est le premier à associer un gain de fonction du facteur de croissance PITX2c en relation avec la FA. Le remodelage histologique des Cx et les variants nucléotidiques touchant les gènes GJA1, GJA5, PITX2 et KCNH2 pourraient ainsi participer à l'étiologie de la FA et du QT longAtrial fibrillation (AF) is the most common sustained arrhythmia in adults. It is associated with an increased risk of stroke, heart failure and mortality. A mechanism of atrial torsades has been described in patients with congenital long QT syndrome (LQTS). Despite the already existing body of literature, the mechanisms involved in the genesis and maintenance of these arrhythmias remain poorly understood and constitute an obstacle in diagnosis and management of these diseases. In the first part of this work, we discussed the histology of connexins (Cxs) and their distribution in two groups of patients (with and without FA), by confocal microscopy approach. We have described a network of fibroblasts and myocytes communicating across Cx 40 and 43 and the presence of myofibroblasts, of a strong fibrosis and of a remodeling of Cx 40 and 43 distribution in the tissue of AF patients. In addition, to identify new mutations involved in these arrhythmias, we studied a cohort of 60 patients with AF. Genetic investigations and functional study enabled us to associate five novel mutations with AF: M207V and P41S (PITX2), G277E (Cx 40) A253V (Cx 43) and P1034H (KCNH2). These mutations likely play a key role in the formation of the arrhythmogenic substrate. Finally, we explored the electrophysiological impact of a KCNH2 variant, R148W, initially found in a child who died suddenly during sleep and subsequently disclosed in several family members, some with a long QT interval. When expressed in Xenopus oocytes and studied in voltage-clamp, this variant reduces the current by 29%, which might predispose to torsades de pointes and partly explain the QTc prolongation. In addition to these newly discovered gene variants, this work is the first to report a gain-of-function mutation of the transcription factor PITX2c in AF. Histological remodeling of Cxs and the nucleotide variants affecting GJA1, GJA5, PITX2 and KCNH2 might thus participate in the etiology of AF and LQT

Effects of antimony and arsenic on antioxidant enzyme activities of two steppic plant species in an old antimony mining area

The present work was undertaken to determine strategies and antioxidant enzyme activities involved in the adaptation of two wild steppic plants (Hedysarum pallidum Desf. and Lygeum spartum L.) to the toxic environment of the abandoned antimony mining area of Djebel Hamimat (Algeria). For this purpose, soils and plants were collected in different zones coinciding with a Sb and As concentrations gradient in the soil. Antimony (Sb) and arsenic (As) were analyzed by ICP-OES in the soils and the aboveground parts and roots of the plants. Malondialdehyde (MDA) and antioxidant enzyme activities were measured by spectrometry. Results show levels of Sb and As exceptionally high in most soil and plant samples. The two species accumulate differently Sb and As in their above and belowground parts. MDA levels, in the two parts of both species, increase significantly with increasing soil Sb and As concentrations, but they are significantly higher in H. pallidum than in L. spartum. The activities of antioxidant enzymes differ significantly according to the soil metalloid concentrations, the plant species considered and the plant part. Apart from superoxide dismutase (SOD) whose activity is, overall, higher in H. pallidum than in L. spartum, the activities of all the other enzymes studied (glutathione S-transferase (GST), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX)) are generally higher in L. spartum than in H. pallidum. For both species, APX and GST are overall more active in the upper parts than in the roots, while it is the reverse for SOD and CAT. POD is more active in the upper parts than in the roots of L. spartum and the reverse applies to H. pallidum. It appears that the two studied plant species use different tolerance strategies to protect themselves against elevated As and Sb concentrations

Effect of Zinc on the Growth and the Antioxidant System of Lens Culinaris Cultivated on Agar Medium

This study aimed to analyze the impact of Zn on the growth and the antioxidant response of Lens culinaris. For this purpose, the seeds were germinated for 6 days in an MS/2 culture medium with different Zn concentrations. Malondialdehyde (MDA), total protein contents, and antioxidant enzymes activities were measured in both parts of the plant by spectrometry. The results showed that from the Zn concentration of 250 µM, the growth of lentils is inversely proportional to the concentration of Zn in the culture medium. The variations in the level of MDA are not very significant, but at 10 000 μM of Zn in the medium, the level becomes very important, whilst the total protein content decreased. Besides, the evaluation of enzymatic activities indicated that the decline of peroxidase (POD) is concomitant with the increase in glutathione peroxidase (GPx) and that glutathione S-transferase (GST), as well as catalase (CAT) reach their maximum activities at 10 000 µM and 3000 µM of Zn in upper parts and roots, respectively. These findings revealed that MDA is a real indicator of oxidative stress in Lens culinaris and that this plant is tolerant to the presence of Zn in the culture medium by developing a powerful antioxidant system, but beyond a certain concentration its antioxidant system becomes ineffective and the plant enters a stress state

The variant hERG/R148W associated with LQTS is a mutation that reduces current density on co-expression with the WT

International audienceBackground: A variant of the ether-à-go-go related channel (hERG), p.Arg148Trp (R148W) was found at heterozygous state in two infants who died from sudden infant death syndrome (SIDS), one with documented prolonged QTc and Torsade de Pointes (TdP), and in an adult woman with QTc > 500 ms, atrio-ventricular block and TdP. This variant was previously reported in cases of severe ventricular arrhythmia but very rarely in control subjects. Its classification as mutation or polymorphism awaited electrophysiological characterization. Methods: The properties of this N-terminal, proximal domain, hERG variant were explored in Xenopus oocytes injected with the same amount of RNA encoding for either hERG/WT or hERG/R148W or their equimolar mixture. The human ventricular cell (TNNP) model was used to test the effects of changes in hERG current.Results: R148W alone produced a current similar to the WT (369±76 nA (mean±SEM), n=13 versus 342±55 nA in WT, n=13), while the coexpression of 1/2 WT + 1/2 R148W lowered the current by 29 % versus WT (243±35 nA, n=13, p<0.05). The voltage dependencies of steady-state activation and inactivation were not changed in the variant alone or in coexpression with the WT. The time constants of fast recovery from inactivation and of fast and slow deactivation analyzed between –120 and +20 mV were not changed. The voltage-dependent distribution of the current amplitudes among fast-, slow- and non-deactivating fractions was unaltered. A 6.6 % increase in APD90 from 323.5 ms to 345 ms was observed using the human cardiac ventricular myocyte model.Conclusions: Such a decrease in hERG current as evidenced here when co-expressing the hERG/R148W variant with the WT may have predisposed to the observed long QT syndrome and associated TdP. Therefore, the heterozygous carriers of hERG/R148W may be at risk of cardiac sudden death

A Novel PITX2c Gain-Of-Function Mutation, p.Met207Val, in Patients With Familial Atrial Fibrillation

International audienceGenome-wide studies have associated several genetic variants upstream of PITX2 on chromosome 4q25 with atrial fibrillation (AF), suggesting a potential role of PITX2 in AF. Our study aimed at identifying rare coding variants in PITX2 predisposing to AF. The Polymerase chain reaction sequencing of PITX2c was performed in 60 unrelated patients with idiopathic AF. The p.Met207Val variant was identified in 1 of 60 French patients with early onset AF and in none of 389 French referents. This variant, located in the inhibitory domain 1 distal to the homeodomain, was evaluated by the software MutationTaster as a disease-causing mutation with a probability of 0.999. Reporter gene assays demonstrated that p.Met207Val caused a 3.1-fold increase in transactivation activity of PITX2c in HeLa cells in comparison with its wild-type counterpart. When the variant was coexpressed with wild-type PITX2c in the HL-1 immortalized mouse atrial cell line, this gain-of-function caused an increase in the mRNA level of KCNH2 (2.6-fold), SCN1B (1.9-fold), GJA5 (3.1-fold), GJA1 (2.1-fold), and KCNQ1 in the homozygous form (1.8-fold). These genes encode for the IKr channel α subunit, the β-1 Na+ channel subunit, connexin 40, connexin 43 and the IKs channel α subunit, respectively. These conditions may contribute to the propensity to AF found in patients carrying the p.Met207Val variant. In conclusion, the present report is the first to associate a gain-of-function mutation of PITX2c with increased vulnerability to AF, therefore, restoration of normal PITX2c function may be a potential therapeutic target in AF patients