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7q11.23 CNV alters ribosomal biogenesis, mTOR and neuronal intrinsic excitability [RNA-seq]

GSE261691 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/03/20 Platform GPL16791Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
24 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Multiscale modeling uncovers 7q11.23 copy number variation-dependent changes in ribosomal biogenesis and neuronal maturation and excitabilityThe Journal of clinical investigation · 2024
Summary (written by the submitters)
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.
Read the full summary ↓
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.
Published in
Multiscale modeling uncovers 7q11.23 copy number variation-dependent changes in ribosomal biogenesis and neuronal maturation and excitability
Mihailovich M, Germain PL, Shyti R et al. · The Journal of clinical investigation 2024 · PMID 39007270 · doi:10.1172/JCI168982
This dataset
Open GSE261691 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261691_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1088436 and SRA study SRP495430. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39007270) ↗
Study design
6 conditions, mostly in triplicate
Ngn2 iNeurons isogenic CTL isoCTL ×3 Ngn2 iNeurons isogenic WBS isoWBS ×3 Ngn2 iNeurons isogenic 7Dup isoDup (242K) ×3 Ngn2 iNeurons REST WBS isoWBS REST inhibitor … ×3 Ngn2 iNeurons REST WBS isoWBS DMSO ×3 Ngn2 iNeurons patientDerived CTL 809 ×2 Ngn2 iNeurons patientDerived 7Dup 242K ×1 Ngn2 iNeurons patientDerived WBS 306O ×1 +5 more

Supports a case/control comparison: 5 samples read as cases, 6 as controls.

How we read this: 6 replicated groups read from 24 sample titles; they account for 17 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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