Transcriptomics

Dataset Information

4

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


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 (7dup). 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 differentiated a representative subset of patient-derived iPSC lines into three disease-relevant lineages: dorsal telencephalic progenitors (Neural Progenitor Cells, NPC), Neural Crest Stem Cells (NCSC) and Mesenchymal Stem Cells (MSC). We profiled NCSC and NPC through microarray (current dataset), and MSC through RNA-seq.

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  Giuseppe Testa  Elisa Biamino  Ronald McKay  Massimo Carella  Sina Atashpaz  Emilio Donti  Veronica Albertin  Giancarlo Pruneri  Bartolomeo Augello  Giuseppe Merla  Christian Unger  Matteo Zanella  Brad Hamilton 

PROVIDER: E-GEOD-63040 | ArrayExpress | 2014-12-15

SECONDARY ACCESSION(S): GSE63040PRJNA266523

REPOSITORIES: GEO, ArrayExpress

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