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CRISPR/Cas9-MEDIATED PHOX2B FUNCTIONAL KNOCK-OUT IN IMR32 NEUROBLASTOMA CELLS IMPAIRS NEURONAL EXCITABILITY THROUGH DYSREGULATION OF ION CHANNELS GENES

GSE330047 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2026/07/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 13 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)
Topic
NeuroblastomaThis series is part of our curated briefing on it.
Samples
13 samples: 3 × IMR32_CTRL vs 3 × IMR32_KO vs 3 × IMR32_KO_rescue1 vs 3 × IMR32_KO_rescue2Groups 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
CRISPR/Cas9-mediated PHOX2B functional knock-out in IMR32 neuroblastoma cells impairs neuronal excitability through dysregulation of ion channels genesFrontiers in physiology · 2026
Summary (written by the submitters)
Introduction: PHOX2B is a master transcriptional regulator of autonomic nervous system development whose mutations cause neurocristopathies including neuroblastoma and congenital central hypoventilation syndrome (CCHS). However, the identification and functional relevance of PHOX2B target genes remain incompletely defined, partly due to the lack of robust cellular models.
Read the full summary ↓
Methods: Through CRISPR/Cas9-engineering we established a PHOX2B knockout IMR32 neuroblastoma model, and combined transcriptomic, chromatin-binding, electrophysiological, and live-cell imaging analysis to investigate PHOX2B-dependent pathways. We then assessed the developmental relevance of the obtained results in iPSC‑derived sympathetic neurons from CCHS patients carrying different PHOX2B mutations. Results: PHOX2B-knockout (PHOX2B-KO) cells exhibited morphological and molecular features indicative of enhanced neuronal maturation. RNA-seq and ChIP-seq analyses highlighted an unexpected direct role for PHOX2B in regulating the expression of ion channels, including KCNQ5, SCN3A and RYR2, primarily through transcriptional repression. Functionally, PHOX2B KO cells displayed significant alterations in intrinsic electrical properties, including depolarized resting membrane potential, reduced action potential amplitude, attenuated Ca2+ responses and profoundly altered K+ efflux dynamics. Functional rescue experiments confirmed that PHOX2B re-expression restores both transcriptional and electrophysiological phenotypes, thereby establishing a causal relationship between PHOX2B expression and the maintenance of intrinsic excitability homeostasis. Extending these findings to development, sympathetic neurons differentiated from CCHS patient-derived iPSCs displayed dysregulated maturation, transcriptional network rewiring, and altered expression of the same ion channel genes, supporting their relevance to disease. Discussion: Together, our data establish the PHOX2B knockout neuroblastoma model as a valuable platform for functional genomics, enabling systematic analysis of PHOX2B targets and highlightening its critical role in coordinating transcriptional programs that shape neuronal excitability and maturation.
Published in
CRISPR/Cas9-mediated PHOX2B functional knock-out in IMR32 neuroblastoma cells impairs neuronal excitability through dysregulation of ion channels genes
Cardani S, Bertocchi M, Donà E et al. · Frontiers in physiology 2026 · PMID 42422362 · doi:10.3389/fphys.2026.1844142
This dataset
Open GSE330047 in finder → Find more human RNA-seq datasets → Neuroblastoma landscape →
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 GSE330047_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 PRJNA1462635 and SRA study SRP697903. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42422362) ↗
Study design
3 × IMR32_CTRL vs 3 × IMR32_KO vs 3 × IMR32_KO_rescue1 vs 3 × IMR32_KO_rescue2

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 12 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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