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Profiling of histone modifications reveal tumor microenvironment-acquired super-enhancer regulates progression of esophageal squamous cell carcinoma

GSE304098 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 11 samples Submitted 2026/07/31 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Topic
Esophageal cancerThis series is part of our curated briefing on it.
Samples
11 samples: 4 × ESCC Tumor tissue vs 4 × ESCC cancer associated fibroblast vs 3 × ESCC cell lineGroups 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)
Genomic and proteomic studies have advanced our understanding of esophageal squamous cell carcinoma (ESCC) biology and pathogenesisGenomic and proteomic studies of esophageal squamous cell carcinoma (ESCC) have advanced our understanding of the biology and pathogenesis of the disease. However, the histone modification landscape inprofile of ESCC remains poorly characterized, especially from human clinical samplesunderstood.
Read the full summary ↓
Here, we performed comprehensive histone modification profiling of paired samples from 122 ESCC patients, identifying numerous aberrantly expressed histone modification sitesand identified a number of modification sites that are aberrantly expressed in ESCC. Most of these alterations correlate with patient survivalMost of these differentially expressed histone modification sites are associated with survival in ESCC patients. In particular, H3K27ac is aberrantly expressed in tumor tissue and stroma and its high expression is significantly correlated with poor prognosis of ESCC patients. We analyzed the H3K27ac ChIP-seq data for primary ESCC tumor tissues and ESCC cell lines and identified hundreds of altered putative super-enhancers (SEs) in ESCC tissues respectively relative to ESCC cell lines. Moreover, these differential SEs contribute to the transcriptomic aberrations in ESCC tissues. Genes regulated by ESCC tissue- gained SEs are highly expressed in ESCC tissues compared to ESCCthan in cell lines and are mostly enriched in microenvironment-related pathways. We definerefer to these SEs as tumor microenvironment-acquired super-enhancers (TMEA-SEs). Through integrative analysis of ChIP-seq, RNA-seq, scRNA-seq and ATAC-seq data, we identified a TMEA-SE activated in cancer-associated fibroblasts (CAFs) and found that IL1R1 is directly regulated by this TMEA-SE. We demonstrated that IL1R1 activation can affect CAFs to promotes ESCC cells migration and invasion via CAFs. Collectively, our findings these observations reveal that a critical oncogenic mechanism in ESCC whereby TMEA-SE drive malignancy by activating IL1R1 in CAFs.
This dataset
Open GSE304098 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Esophageal cancer 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 GSE304098_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1298907 and SRA study SRP604679. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × ESCC Tumor tissue vs 4 × ESCC cancer associated fibroblast vs 3 × ESCC cell line

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 11 sample titles; they account for 11 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 Esophageal cancer datasets

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