Genome-wide DNA methylation profiling of 68 GBM (primary & recurrent), 4 glioma spheres and 5 non-tumor brain samples
ABSTRACT: DNA methylation analysis of 68 glioblastoma specimen of patients treated within clinical trials, 5 samples of normal brain tissue (non-tumor brain) and 4 tumor-derived glioma sphere lines. The data was used to identify changes in DNA methylation which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison Bisulphite converted genomic DNA from the 77 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip
Project description:aCGH was used to profile copy-number aberrations (CNA) in 64 glioblastoma specimen of patients treated within clinical trials. The data was used to identify changes in CNA which contribute to the aberrant of expression of HOX transcription factors. Our group had previously demonstrated that expression of HOX genes was associated with increased resistance to chemo-radiotherapy and worse outcome in GBM patients Keywords: Disease state comparison Genomic DNA from the 64 samples and synthetic normal reference DNA were labelled with Cy3 and Cy5 respectively and hybridised to HumArray3 and HumArray2 chips. The unified platform HumArray3.1 is used for annotation purposes
Project description:Autism is a common neurodevelopmental syndrome. Numerous rare genetic etiologies are reported; most cases are idiopathic. To uncover important gene dysregulation in autism, we analyzed carefully selected idiopathic autistic and control cerebellar and BA19 (occipital) brain tissues using high-resolution whole genome gene expression and DNA methylation microarrays. No changes in DNA methylation were identified in autistic brain but gene expression abnormalities in two areas of metabolism were apparent: down-regulation of genes of mitochondrial oxidative phosphorylation and of protein translation. We also found associations between specific behavioral domains of autism and specific brain gene expression modules related to myelin/myelination, inflammation/immune response and purinergic signaling. This work highlights two largely unrecognized molecular pathophysiological themes in autism and suggests differing molecular bases for autism behavioral endophenotypes. In this set of DNA methylation data, 9 cerebellar autism, 9 cerebellar control, 8 BA19 (occipital cortex) autism, and 8 BA19 control samples were used. Samples are labeled with a B followed by a unique number and letter identifying the subject and brain region, followed by an optional hyphenated number indicating the technical replicates performed on sample 1.
Project description:Melanoma is one of the most aggressive and treatment-resistant cancers. It represents the most life-threatening neoplasm of the skin, and its incidence has been increasing for the last three decades. Melanoma evolves from the local transformation of melanocytes to primary tumors, which can metastasize to multiple organs. Brain metastases represent one of the most significant causes of death in cutaneous melanoma patients. Despite aggressive multi-modality threapy, patients with melanoma brain metastasis have a median survival of less than a year, with a majority of these patients dying as a result of their intracranial disease. We aimed to find brain metastasis-specific molecular markers. To identify alterations in DNA methylation related to brain metastasis, we used Illumina 450K BeadChips to assess differentially methylated regions in melanocytes, primary melanomas, lymph node metastases, and brain metastases. Bisulphite-converted DNA from 40 specimens was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.
Project description:Alzheimer's disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. We undertook an epigenome-wide association study across three independent brain tissue cohorts (total n = 999) to identify differential DNA methylation associated with neuropathology in the superior temporal gyrus and prefrontal cortex. We present robust evidence for elevated DNA methylation associated with AD neuropathology across an extended region spanning the HOXA gene cluster on chromosome 7. Prefrontal cortex and superior temporal gyrus tissue from 147 individuals with varying levels of AD pathology. DNA modifications for these samples were quantified using the Illumina Infinium Human 450K Methylation Array.
Project description:Our main objective was to study genome-wide differential methylation in de novo glioblastoma multiforme (GBM, grade IV glioma). We evaluated CpG sites in gene promoters of 26,000+ genes using an array-based chip. We retrieved 54 GBM from biorepositories of two institutions(40 from Columbia University and 14 from Case Western Reserve University) and 24 control brain tissues from the New York Brain Bank, which collected control brain tissues from consented subjects without history of neurological diseases at autopsy. Bisulfite modified DNA was extracted from 54 GBM and 24 control brain tissue. The HumanMethylation27 Analysis Bead-Chips (Illumina) were used to interrogate 26,486 informative CpG sites in the autosomes.
Project description:The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. Genome wide DNA methylation profiling of normal and osteoarthritic samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in cartilage knee samples. Samples included 18 healthy controls and 23 OA patients. Bisulphite converted DNA from the 31 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
Project description:Genome-wide DNA methylation profiling of human ileal neobladder samples. Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Project description:Analysis of DNA methylation in the bed nucleus of the stria terminalis/preoptic area and striatum in response to perinatal testosterone exposure. The hypothesis tested was that treatment of females with testosterone on the day of birth would lead to masculinization of the methylome in adulthood. There were three experimental groups: males, females, and females treated with T on the day of birth. The methylation patterns in each group was determined using reduced representation bisulfite sequencing. Two brain regions and two time points (day 4 and day 60) were surveyed in each group. Each biological replicate is a pool of tissue from three animals.
Project description:Analysis of gene expression in the bed nucleus of the stria terminalis/preoptic area and striatum in response to perinatal testosterone exposure. The hypothesis tested was that differences in DNA methylation would be reflected in differences in gene expression. Analysis of gene expression in the bed nucleus of the stria terminalis/preoptic area and striatum in response to perinatal testosterone exposure. The hypothesis tested was that differences in DNA methylation would be reflected in differences in gene expression.
Project description:We treated melanoma cells with BRAF mutation with BRAF inhibitor and screened for BRAF inhibitor resistant cells. We extracted DNA from parental cells and resistant cell lines. We compared the DNA methylation via Illumina 450K Methylation Array Bisulphite converted DNA from the 4 specimens was hybridised to the Illumina Infinium 450k Human Methylation Beadchip