Transcriptomics

Dataset Information

296

7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages (RNAseq)


ABSTRACT: 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 these by RNAseq (either polyA or ribo-zero). To isolate the contribution of GTF2I to the transcriptional dysregulation, we created stable lines expressing a short hairpin against GTF2I from a representative subset of these iPSC clones, and profiled by RNAseq 7 such lines along with their respective scramble controls. Finally, we also profiled by RNAseq mesenchymal stem cells (MSC) derived from a representative subset of the lines.

ORGANISM(S): Homo sapiens  

SUBMITTER: Pierre-Luc Germain   Angelo Selicorni  Giuseppe D'Agostino  Antonio Adamo  Orazio Palumbo  Josh Chenoweth  Lucia Micale  Paolo Prontera  Carmela Fusco  Massimo Carella  Sina Atashpaz  Giuseppe Testa  Elisa Biamino  Ronald McKay  Emilio Donti  Veronica Albertin  Giancarlo Pruneri  Bartolomeo Augello  Giuseppe Merla  Christian Unger  Matteo Zanella  Brad Hamilton 

PROVIDER: E-GEOD-63055 | ArrayExpress | 2014-12-15

SECONDARY ACCESSION(S): SRP049593GSE63055PRJNA266526

REPOSITORIES: GEO, ArrayExpress, ENA

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