Symmetrical dose-dependent DNA methylation profiles in children with deletion or duplication of chromosome 7q11.23
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Lucy Osborne
PROVIDER: E-GEOD-66552 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Genome wide DNA methylation in blood derived DNA from individuals with deletion or duplication of 7q11.23
2015-07-09 | GSE66552 | GEO
Project description:We apply the cellular reprogramming experimental paradigm to two disorders caused by symmetrical copy number variations (CNV) of 7q11.23 and displaying a striking combination of shared as well as symmetrically opposite phenotypes: Williams Beuren syndrome (WBS) and 7q microduplication syndrome (7dupASD). Through a uniquely large and informative cohort of transgene-free patient-derived induced pluripotent stem cells (iPSC), along with their differentiated derivatives, we find that 7q11.23 CNV disrupt transcriptional circuits in disease-relevant pathways already at the pluripotent state. These alterations are then selectively amplified upon differentiation into disease-relevant lineages, thereby establishing the value of large iPSC cohorts in the elucidation of disease-relevant developmental pathways. In addition, we functionally define the quota of transcriptional dysregulation specifically caused by dosage imbalances in GTF2I (also known as TFII-I), a transcription factor in 7q11.23 thought to play a critical role in the two conditions, which we found associated to key repressive chromatin modifiers. Finally, we created an open-access web-based platform (accessible at http://bio.ieo.eu/wbs/ ) to make accessible our multi-layered datasets and integrate contributions by the entire community working on the molecular dissection of the 7q11.23 syndromes. We reprogrammed skin fibroblasts from patients harbouring a 7q11.23 hemi-deletion (WBS, 4 patients; +1 atypical deletion, AtWBS) or microduplication (7dupASD; 2 patients), as well as from one unaffected relative and two unrelated controls, using integration-free mRNA-reprogramming, leading to the establishment of a total of 27 characterized iPSC clones. We profiled by aCGH each established iPSC clone as well as the original fibroblasts (for all patients and the unaffected relative).
2014-12-15 | E-GEOD-63028 | biostudies-arrayexpress
Project description:We apply the cellular reprogramming experimental paradigm to two disorders caused by symmetrical copy number variations (CNV) of 7q11.23 and displaying a striking combination of shared as well as symmetrically opposite phenotypes: Williams Beuren syndrome (WBS) and 7q microduplication syndrome (7dupASD). Through a uniquely large and informative cohort of transgene-free patient-derived induced pluripotent stem cells (iPSC), along with their differentiated derivatives, we find that 7q11.23 CNV disrupt transcriptional circuits in disease-relevant pathways already at the pluripotent state. These alterations are then selectively amplified upon differentiation into disease-relevant lineages, thereby establishing the value of large iPSC cohorts in the elucidation of disease-relevant developmental pathways. In addition, we functionally define the quota of transcriptional dysregulation specifically caused by dosage imbalances in GTF2I (also known as TFII-I), a transcription factor in 7q11.23 thought to play a critical role in the two conditions, which we found associated to key repressive chromatin modifiers. Finally, we created an open-access web-based platform (accessible at http://bio.ieo.eu/wbs/ ) to make accessible our multi-layered datasets and integrate contributions by the entire community working on the molecular dissection of the 7q11.23 syndromes. We tested three antibodies against GTF2I for ChIP-seq application, and selected the one showing the best enrichment to profile GTF2I bindings across a panel of 12 iPSC lines established from patients harbouring a 7q11.23 hemi-deletion (WBS; 5 patients) or microduplication (7dupASD; 2 patients), as well as from two independent controls individuals.
2014-12-15 | E-GEOD-63057 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of peripheral blood samples obtained from normal controls and children born SGA. Illumina's HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450.000 CpGs. Bisulphite converted DNA from the 110 samples were hybridised to the Illumina HumanMethylation450 Beadchip.
2016-07-03 | E-GEOD-47880 | biostudies-arrayexpress
Project description:Copy number variations (CNVs) at 7q11.23 cause Williams-Beuren (WBS) and 7q microduplication syndromes (7Dup), two neurodevelopmental disorders with shared and opposite cognitive-behavioral phenotypes. Using patient-derived and isogenic neurons, we integrated transcriptomics, translatomics and proteomics to elucidate the molecular underpinnings of this dosage effect. We found that 7q11.23 CNVs cause opposite alterations in neuronal differentiation and neuronal excitability. Here, the 7q11.23 CNV altered proteome in iPSC differentiating neurons was measured by a fast SWATH-MS method.
2024-10-17 | PXD038156 | Pride
Project description:In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Bisulphite converted DNA from the 7 samples were hybridized to the Illumina HumanMethylation450 BeadChip.
2015-06-16 | E-GEOD-67477 | biostudies-arrayexpress
Project description:In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Bisulphite converted DNA from the 4 samples were hybridized to the Illumina HumanMethylation450 BeadChip (Sample L and SI were examined twice).
2015-06-16 | E-GEOD-67484 | biostudies-arrayexpress
Project description:Copy number variations (CNVs) at 7q11.23 cause Williams-Beuren (WBS) and 7q microduplication syndromes (7Dup), two neurodevelopmental disorders with both shared and symmetrically opposite cognitive-behavioral phenotypes. Here, we profiled the proteomes of isogenic Ngn2-driven neurons that recapitulate the three dosages of 7q11.23 (hemiduplicated, control and hemideleted).
2024-10-17 | PXD035276 | Pride
Project description:Copy number variations (CNVs) at 7q11.23 cause Williams-Beuren (WBS) and 7q microduplication syndromes (7Dup). Both neurodevelopmental disorders (NDDs) feature mild to moderate intellectual disability, accompanied by symmetrically opposite neurocognitive and behavioral features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.23-related pathophysiologies, the interplay between different layers of gene expression and the propagation of opposite symmetry arising from CNV remains elusive. Here, we uncovered 7q11.23 dosage-dependent symmetrically opposite dynamics in neuronal differentiation and intrinsic excitability. By integrating transcriptomics, translatomics and proteomics of patient-derived and isogenic induced neurons, we found that genes related to neuronal transmission follow 7q11.23 dosage and are transcriptionally controlled, while translational factors and ribosomal genes are post-transcriptionally buffered. Consistently, we found a deregulated mTOR pathway, with phospho-S6 (pS6) being downregulated in WBS and upregulated in 7Dup. Surprisingly phospho-4E-BP (p4E-BP) was going in the opposite direction, reflecting the total 4E-BP levels, thus highlighting the different roles of pS6 and p4E-BP during neurogenesis. Therefore, our work emphasizes the importance of multilayer research when investigating complex NDDs, highlighting ribosomal biogenesis and paving the way for novel treatments by uncoupling the role of pS6 and p4E-BPs in NDDs.
2024-03-20 | GSE261691 | GEO
Project description:Copy number variations (CNVs) at 7q11.23 cause Williams-Beuren (WBS) and 7q microduplication syndromes (7Dup). Both neurodevelopmental disorders (NDDs) feature mild to moderate intellectual disability, accompanied by symmetrically opposite neurocognitive and behavioral features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.23-related pathophysiologies, the interplay between different layers of gene expression and the propagation of opposite symmetry arising from CNV remains elusive. Here, we uncovered 7q11.23 dosage-dependent symmetrically opposite dynamics in neuronal differentiation and intrinsic excitability. By integrating transcriptomics, translatomics and proteomics of patient-derived and isogenic induced neurons, we found that genes related to neuronal transmission follow 7q11.23 dosage and are transcriptionally controlled, while translational factors and ribosomal genes are post-transcriptionally buffered. Consistently, we found a deregulated mTOR pathway, with phospho-S6 (pS6) being downregulated in WBS and upregulated in 7Dup. Surprisingly phospho-4E-BP (p4E-BP) was going in the opposite direction, reflecting the total 4E-BP levels, thus highlighting the different roles of pS6 and p4E-BP during neurogenesis. Therefore, our work emphasizes the importance of multilayer research when investigating complex NDDs, highlighting ribosomal biogenesis and paving the way for novel treatments by uncoupling the role of pS6 and p4E-BPs in NDDs.
2024-03-20 | GSE261690 | GEO