Recherche et Qualité : Avancées a l'Université de Franche-Comté

International audienceAu sein de l'Université de Franche-Comté, plusieurs laboratoires ont mis en place, depuis plus ou moins longtemps, des démarches qualité : l'Institut Carnot FEMTO-Innovation regroupe des laboratoires de recherche structurés en six départements; et s'est engagé à mener des projets de recherche partenariale avec un niveau de qualité conforme aux meilleurs standards internationaux. Une comptabilité des activités partenariales a été élaborée, des procédures administratives et managériales homogènes ont été mises en place, et la gestion de la propriété intellectuelle et de la confidentialité a été prise en compte. L'université regroupe également depuis plusieurs décennies des laboratoires accrédités par le COFRAC selon le référentiel ISO17025. Ainsi, le Laboratoire Temps-Fréquence de Besançon est reconnu officiellement de part son association au LNE et ses accréditations, tout comme le Service d'Analyse et de Caractérisation

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

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GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Mineralocorticoid receptor antagonists and kidney diseases: pathophysiological basis

International audienceChronic kidney disease (CKD) represents a global health concern, and its prevalence is increasing. The ultimate therapeutic option for CKD is kidney transplantation. However, the use of drugs that target specific pathways to delay or halt CKD progression, such as angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and sodium-glucose co-transporter-2 (SGLT-2) inhibitors is limited in clinical practice. Mineralocorticoid receptor activation in nonclassical tissues, such as the endothelium, smooth muscle cells, inflammatory cells, podocytes, and fibroblasts may have deleterious effects on kidney structure and function. Several preclinical studies have shown that mineralocorticoid receptor antagonists (MRAs) ameliorate or cure kidney injury and dysfunction in different models of kidney disease. In this review, we present the preclinical evidence showing a benefit of MRAs in acute kidney injury, the transition from acute kidney injury to CKD, hypertensive and diabetic nephropathy, glomerulonephritis, and kidney toxicity induced by calcineurin inhibitors. We also discuss the molecular mechanisms responsible for renoprotection related to MRAs that lead to reduced oxidative stress, inflammation, fibrosis, and hemodynamic alterations. The available clinical data support a benefit of MRA in reducing proteinuria in diabetic kidney disease and improving cardiovascular outcomes in CKD patients. Moreover, a benefit of MRAs in kidney transplantation has also been observed. The past and present clinical trials describing the effect of MRAs on kidney injury are presented, and the risk of hyperkalemia and use of other options, such as potassium binding agents or nonsteroidal MRAs, are also addressed. Altogether, the available preclinical and clinical data support a benefit of using MRAs in CKD, an approach that should be further explored in future clinical trials.Copyright © 2019 International Society of Nephrology. Published by Elsevier Inc. All rights reserved

Cardiovascular Comorbidities Are the Main Predictors of Cardiac Reverse Remodeling following Kidney Transplantation

International audienceBackground: End-stage renal disease is associated with cardiac remodeling, which is partly reversible after kidney transplantation (KT). We aimed to determine the association of cardiovascular comorbidities or kidney-related factors with cardiac reverse remodeling after KT.Methods: We performed echocardiography in 56 patients (aged 48 ± 15 years, mean ± SD) before and 24 months after undergoing their first KT. Echocardiograms were reviewed using a standardized process with blinding for the patient characteristics and evaluation timing. Multivariable linear regression analysis was used to evaluate the association between comorbidities and changes in cardiac structure and systolic/diastolic function.Results: Left ventricular mass index (LVMI) and diastolic parameters did not change significantly, while left ventricular ejection fraction (LVEF) increased from 63.9 to 69.6% (p = 0.046). Multivariable analysis revealed associations of histories of valvular heart disease with a smaller reduction in LVMI (β = -27.3, p = 0.04), of coronary artery disease or heart failure with a smaller increase in LVEF (β = 7.17, p = 0.02), and of diabetes mellitus with less improvement in E wave (β = -0.19, p = 0.05), e' (β = 4.15, p = 0.046), and E/e' (β = -5.00, p < 0.01).Conclusion: Cardiovascular comorbidities were -associated with less improvement in cardiac structure and function following KT. Our findings suggest that patients with CV comorbidities may experience limited "favorable" reverse cardiac remodeling following KT

Nonepithelial mineralocorticoid receptor activation as a determinant of kidney disease

International audienceChronic kidney disease is a major global health challenge, and mineralocorticoid receptor (MR) signaling is thought to play a role in disease progression. The classic role of the MR is the regulation of fluid and electrolyte homeostasis via differential gene expression, and recently its role in modulating inflammation and fibrosis has been identified. In addition to expression of the MR in renal epithelial cells, it is also found in nonepithelial cells, such as endothelial cells, vascular smooth muscle cells, podocytes, and fibroblasts. Targeting the MR in these cells may play a role in offering protection against inflammation and fibrosis in the kidneys and the cardiovascular system. Herein, data from preclinical cell-specific MR knockout mouse models and in vitro studies that help uncover the role of the MR in nonepithelial cells are presented. This review also discusses several potential targets that offer opportunities for the targeting of MR signaling in nonepithelial cells