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Co-targeting CDK7/CDK9 and CKIα exerts efficacious anticancer effects against TERT gene-rearranged neuroblastoma

GSE262443 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/04/08 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × A51_control vs 3 × A51_A51 vs 3 × A51_Ceritinib vs 3 × A51_A51CeriGroups 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.
Summary (written by the submitters)
TERT gene rearrangement with transcriptional super-enhancers leads to substantial TERT over-expression and neuroblastoma. No targeted therapy is available for clinical trials in patients. Here we show that the transcriptional kinases CDK7/CDK9 and the casein kinase CKIα were required for TERT gene over-expression and p53 protein degradation respectively in TERT-rearranged neuroblastoma cells.
Read the full summary ↓
Co-knockdown of CDK7/CDK9 and CKIα or treatment with the CDK7/CDK9 and CKIα co-inhibitor A51 reduced TERT gene transcriptional initiation, elongation and expression, activated p53 protein expression, co-operatively induced apoptosis and suppressed tumor progression in mouse models. Screening of an approved oncology drug library identified Ceritinib as the agent exerting the best synergistic anticancer effects with A51. A51 and Ceritinib synergistically down-regulated mitochondrial complex I gene expression and induced oxidative stress and TERT-rearranged neuroblastoma cell apoptosis. In mice xenografted with TERT-rearranged patient-derived xenograft neuroblastoma cells, A51 and Ceritinib synergistically induced tumor cell apoptosis, suppressed tumor progression and improved mouse survival. A51 and Ceritinib combination therapy is therefore a good candidate for translation into the first clinical trial of a targeted therapy against TERT-rearranged neuroblastoma.
This dataset
Open GSE262443 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 GSE262443_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 PRJNA1091879 and SRA study SRP497834. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × A51_control vs 3 × A51_A51 vs 3 × A51_Ceritinib vs 3 × A51_A51Ceri

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 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
More Neuroblastoma datasets

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.