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SRX23958574: GSM8148854: Ngn2 iNeurons REST WBS isoWBS REST inhibitor X5050 3; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 30.8M spots, 3.1G bases, 978.3Mb downloads

External Id: GSM8148854_r1
Submitted by: Neurogenomics, Fondazione Human Technopole
Study: 7q11.23 CNV alters ribosomal biogenesis, mTOR and neuronal intrinsic excitability [RNA-seq]
show Abstracthide Abstract
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. Overall design: We differentiated isogenic and patient-derived lines to induced Neurons (iNeurons) using Ngn2 overexpression, and profiled their transcriptome. In addition, we tested the effect of REST inhibition in WBS isogenic lines.
Sample: Ngn2 iNeurons REST WBS isoWBS REST inhibitor X5050 3
SAMN40469270 • SRS20758587 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM8148854
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was isolated using the RNeasy mini Kit (QIAGEN) and genomic DNA was removed using the RNase-Free DNase Set (QIAGEN). Retrotranscribed cDNA was obtained from 1 μg of total RNA using the SuperScript VILO Retrotranscription kit from Life Technologies according to the manufacturer's instructions. Library preparation for RNA-seq was done with the Ribo-Zero Total RNA sample preparation kit (Illumina), starting from 250 ng to 1 g of total RNA. The quality of cDNA libraries was assessed by Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit.
Runs: 1 run, 30.8M spots, 3.1G bases, 978.3Mb
Run# of Spots# of BasesSizePublished
SRR2835324230,767,4113.1G978.3Mb2024-03-20

ID:
32264154

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