Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons

<p>Abstract</p> <p>Background</p> <p>A central goal in Huntington's disease (HD) research is to identify and prioritize candidate targets for neuroprotective intervention, which requires genome-scale information on the modifiers of early-stage neuron injury in HD.</p> <p>Results</p> <p>Here, we performed a large-scale RNA interference screen in <it>C. elegans </it>strains that express N-terminal huntingtin (htt) in touch receptor neurons. These neurons control the response to light touch. Their function is strongly impaired by expanded polyglutamines (128Q) as shown by the nearly complete loss of touch response in adult animals, providing an <it>in vivo </it>model in which to manipulate the early phases of expanded-polyQ neurotoxicity. In total, 6034 genes were examined, revealing 662 gene inactivations that either reduce or aggravate defective touch response in 128Q animals. Several genes were previously implicated in HD or neurodegenerative disease, suggesting that this screen has effectively identified candidate targets for HD. Network-based analysis emphasized a subset of high-confidence modifier genes in pathways of interest in HD including metabolic, neurodevelopmental and pro-survival pathways. Finally, 49 modifiers of 128Q-neuron dysfunction that are dysregulated in the striatum of either R/2 or CHL2 HD mice, or both, were identified.</p> <p>Conclusions</p> <p>Collectively, these results highlight the relevance to HD pathogenesis, providing novel information on the potential therapeutic targets for neuroprotection in HD.</p

Etude IRM individuelle et multimodale dans la maladie d'Alzheimer

La maladie d Alzheimer (MA) est un problème majeur de Santé Publique et nécessite un diagnostic précoce. Les mesures IRM pourraient servir comme marqueurs précoces pour la MA. Dans cette thèse nous proposons une méthode automatique, rapide et robuste de catégorisation des patients MA et des sujets âgés sains à partir de données IRM. Nous évaluons aussi l utilité diagnostique de différents marqueurs IRM. Les marqueurs les plus discriminants sont sélectionnés et utilisés dans un SVM pour catégoriser les sujets. La méthode est d abord appliquée aux images anatomiques et validée avec des jeux de données indépendants. Ensuite, le pouvoir discriminant des mesures de diffusion est évalué. Enfin, différentes approches sont étudiées pour combiner les paramètres anatomiques et de diffusion afin d améliorer les performances de classification. Les résultats obtenus montrent que les marqueurs IRM permettent une bonne catégorisation des sujets et constituent un outil diagnostique potentiel.PARIS-BIUSJ-Mathématiques rech (751052111) / SudocSudocFranceF

Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA

International audienceCirculating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients

Support vector machine-based classification of Alzheimer's disease from whole-brain anatomical MRI

International audiencePURPOSE: We present and evaluate a new automated method based on support vector machine (SVM) classification of whole-brain anatomical magnetic resonance imaging to discriminate between patients with Alzheimer's disease (AD) and elderly control subjects. MATERIALS AND METHODS: We studied 16 patients with AD [mean age +/- standard deviation (SD) = 74.1 +/- 5.2 years, mini-mental score examination (MMSE) = 23.1 +/- 2.9] and 22 elderly controls (72.3 +/- 5.0 years, MMSE = 28.5 +/- 1.3). Three-dimensional T1-weighted MR images of each subject were automatically parcellated into regions of interest (ROIs). Based upon the characteristics of gray matter extracted from each ROI, we used an SVM algorithm to classify the subjects and statistical procedures based on bootstrap resampling to ensure the robustness of the results. RESULTS: We obtained 94.5% mean correct classification for AD and control subjects (mean specificity, 96.6%; mean sensitivity, 91.5%). CONCLUSIONS: Our method has the potential in distinguishing patients with AD from elderly controls and therefore may help in the early diagnosis of AD

Nonlethal CHRNA1-Related Congenital Myasthenic Syndrome with a Homozygous Null Mutation

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fondation Maladies RaresFrance Genomique National infrastructureUniv Sao Paulo, Dept Neurol, Fac Med, Ave Dr Eneas de Carvalho Aguiar 255, 5 Andar, BR-05403900 Sao Paulo, Brazil|Inst Genom, Ctr Natl Genotypage, Evry, FranceUniv Fed Sao Paulo, Dept Neurol, Setor Doencas Neuromusculares, Sao Paulo, BrazilNouvel Hop Civil, Fac Med, Lab Diagnost Genet, Strasbourg, FranceUniv Strasbourg, Coll France, Dept Translat Med & Neurogenet, IGBMC,INSERM U964,CNRS UMR7104, Illkirch Graffenstaden, FranceSetor de Doenças Neuromusculares, Departamento de Neurologia, Universidade Federal de São Paulo São Paulo, BrazilCAPES: 1286/51-2France Genomique National infrastructure: ANR-10-INBS-09Web of Scienc

Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples

<div><p>Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell^™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.</p></div

Percentage of duplicated reads for FF and FFPE samples.

<p>A: FF and FFPE samples. B: FFPE samples grouped by extraction method.</p

Difference in number of variants between FF and FFPE samples for all matched FF/FFPE pairs.

<p>A: SNVs. B: INDELs.</p