Project description:Down syndrome is characterized by a wide spectrum of clinical signs, which include cognitive and endocrine disorders and haematological abnormalities. Although it is well established that the causative defect of Down syndrome is the trisomy of chromosome 21, the molecular bases of Down syndrome phenotype are still largely unknown. We used the Infinium HumanMethylation450 BeadChip to investigate DNA methylation patterns in whole blood from 29 subjects affected by Down syndrome (DS), using their healthy relatives as controls (mothers and unaffected siblings). This family-based model allowed us to monitor possible confounding effects on DNA methylation patterns deriving from genetic and environmental (lifestyle) factors. The identified epigenetic signature of Down syndrome includes differentially methylated regions that, although enriched on chromosome 21, interest most of the other chromosomes and can be functionally linked to the developmental and haematological defects characteristic of the disease. DNA was extracted from whole peripheral blood using the QIAamp 96 DNA Blood Kit (QIAGEN) and quantified by Quant-iT™ PicoGreen (Invitrogen). Sodium bisulphite conversion of 500 ng of each sample was performed using the EZDNA Methylation-Gold Kit according to the manufacturer's recommendation for Illumina Infinium Assay. 4 ul of bisulfite converted DNA were hybridized on Infinium HumanMethylation 450 BeadChip, following manufacturer’s instructions. Arrays were scanned by HiScan SQ scanner (Illumina) and the intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation levels of each CpG is reported as beta value.
Project description:DNA methylation is an epigenetic event whose pattern is altered frequently in a wide variety of human diseases. Smoking affects DNA methylation possibly leading to abnormal expression of a broad spectrum of genes which in turn may result to the various side effects and diseases associated with smoking. The long term effects of smoking have been widely studied but the mechanism(s) by which those effects may be reversible by smoking cessation are not clearly understood. Here, we conducted an epigenome-wide association study in peripheral-blood DNA in 464 individuals who were current, former and never-smokers. We identified 15 distinct loci (10 of which were novel) where DNA methylation was reduced in smokers and was reversed (but did not reach non-smoking levels) upon smoking cessation within 12 weeks. Although the functional impact of this reversal of DNA methylation is still not understood, this study illustrates the potential of epigenomics to provide insights into mechanisms of environmental and lifestyle exposures, and to suggest new avenues for clinical intervention Bisulfite converted DNA from the 464 samples were hybridized to the Illumina Infinium HumanMethylation450 BeadChip
Project description:We assayed leukocyte global gene expression for a prospective discovery cohort of 106 adult patients admitted to UK intensive care units with sepsis due to community acquired pneumonia or faecal peritonitis. We assigned all samples to sepsis response signature groups after performing unsupervised analysis of the transcriptomic data.
Project description:We assayed leukocyte global gene expression for a prospective validation cohort of 106 adult patients admitted to UK intensive care units with severe sepsis due to community acquired pneumonia.
Project description:Fetal health is dependent upon the epigenetic-based regulation of gene expression in placenta. Genomic imprinting is an epigenetic phenomenon common to placenta and refers to the monoallelic expression of a gene in a parental-specific manner. We aimed to detect novel imprinted genes in human placenta by applying whole transcriptome RNA-sequencing and genotyping of coding variants. Ten family trios with healthy spontaneous single term pregnancy were recruited. Parental and child DNA genotypes were analysed using exome SNP genotyping microarrays, revealing the inheritance of parental alleles. Total RNA was extracted from placental tissue for whole transcriptome analysis. The imprinted genes showed consistent expression from either parental allele as demonstrated by the SNP content of sequenced transcripts. We found seven novel imprinted genes (ABP1, BCLAF1, IFI30, LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed five known imprinted genes (AIM1, PEG10, RHOBTB3, ZFAT and ZFAT-AS1). The main functions of the proteins encoded by the imprinted genes can be grouped as being involved in: i) cellular apoptosis and tissue development; ii) regulating inflammation and modulating the immune system; iii) facilitating metabolic processes and iv) regulating the cell cycle. Ten family trios (mother, father, child) were analysed using SNP genotyping. Raw data contains additional two samples that were not used.
Project description:Metabolic Syndrome (MetS) is a strong predictor for diabetes and cardiovascular disease and is defined by a constellation of phenotypes including increased and adverse body fat distribution, insulin resistance, abnormalities in lipids and lipoproteins, malfunctional cardiovascular performance, and abnormal levels of adipokines and cytokines. We assayed in a subset of our family cohort phentoyped for MetS phentoypes, the genome-wde transcript levels using the Illumina Human WG-6 v3 expression arrays. Genome-wide gene expression was assayed in members of families that originally contribute to linkage signals in a previous genome-wide linkage scans for multiple MetS phenotypes.
Project description:Metabolic Syndrome (MetS) is a strong predictor for diabetes and cardiovascular disease and is defined by a constellation of phenotypes including increased and adverse body fat distribution, insulin resistance, abnormalities in lipids and lipoproteins, malfunctional cardiovascular performance, and abnormal levels of adipokines and cytokines. We assayed in a subset of our family cohort phentoyped for MetS phentoypes, the genome-wde transcript levels using the Illumina Human WG-6 v2 expression arrays. Genome-wide gene expression was assayed in members of families that originally contribute to linkage signals in a previous genome-wide linkage scans for multiple MetS phenotypes.
Project description:The abscence of TBR2 gene in human leads to microcephaly. This condition is mimicked by the specific ablation of the murine gene in developing cerebral cortex. Herein we compared gene expression in control and Tbr2 cKO in E14.5 cerebral cortices. This approach represents a useful tool to identify the molecular mechanisms at the basis of the phenotype. 6 samples, 3x Tbr2 +/+;Foxg1::Cre (control) and 3x Tbr2 fl/fl;Foxg1::Cre