GEO series

An EGFR Co-amplified Long Noncoding RNA HELDR Promotes Glioblastoma Malignancy through KAT7-driven gene programs [HELDR]

GSE286318 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/02/07 Platform GPL34281

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)
Samples: 12 samples: 6 conditions, mostly in duplicateGroups 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: An EGFR co-amplified lncRNA HELDR promotes glioblastoma malignancy through KAT7-driven gene programsNature cell biology · 2026

Summary (written by the submitters)

EGFR amplification at extrachromosome DNAs (ecDNAs) is a major driving mutation in glioblastoma (GBM). However, targeting EGFR for GBM treatments remain unsatisfied. Here we identify a de novo long non-coding RNA (lncRNA) that is co-amplified with EGFR which we named hidden EGFR long non-coding downstream RNA (HELDR). HELDR is a GBM-specific lncRNA that promotes tumorigenicity independent of EGFR expression and signaling.

Read the full summary ↓

HELDR globally binds genomic DNA and recruits a transcription co-activator p300 to the promoter of KAT7. p300-induced H3K27ac at KAT7 promoter enlists other co-transcription factors, activating KAT7 transcription. KAT7 induces H3K14ac H4K12ac that activate the transcription of KAT7-targeting gene programs critical for GBM malignancy. Targeting KAT7 synergistically enhances therapeutic effects of targeting EGFR for GBM treatment. These results not only reveal the role of HELDR in EGFR-driven GBM malignancy, but also provide strong rationale to characterize the roles of lncRNAs co-amplified with driver oncogenes at ecDNAs in human cancers.

Published in

An EGFR co-amplified lncRNA HELDR promotes glioblastoma malignancy through KAT7-driven gene programs

Yu X, Song X, Schäfer RA et al. · Nature cell biology 2026 · PMID 41896311 · doi:10.1038/s41556-026-01924-w

This dataset

Open GSE286318 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 GSE286318_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 PRJNA1208665 and SRA study SRP556392. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41896311) ↗

Study design

6 conditions, mostly in duplicate

sh2CTRL_HELDR ×2 sh2_HELDR ×2 sh1CTRL_HELDR ×2 sh1_HELDR ×2 ASO_CTRL ×2 ASO_HELDR ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 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

GSM8723581 sh2CTRL_HELDR_REP1 sh2CTRL_HELDR
GSM8723582 sh2CTRL_HELDR_REP2 sh2CTRL_HELDR
GSM8723583 sh2_HELDR_REP1 sh2_HELDR
GSM8723584 sh2_HELDR_REP2 sh2_HELDR
GSM9283711 sh1CTRL_HELDR_REP1 sh1CTRL_HELDR
GSM9283712 sh1CTRL_HELDR_REP2 sh1CTRL_HELDR
GSM9283713 sh1_HELDR_REP1 sh1_HELDR
GSM9283714 sh1_HELDR_REP2 sh1_HELDR
GSM9283715 ASO_CTRL_REP1 ASO_CTRL
GSM9283716 ASO_CTRL_REP2 ASO_CTRL
GSM9283717 ASO_HELDR_REP1 ASO_HELDR
GSM9283718 ASO_HELDR_REP2 ASO_HELDR

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