GEO series

HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype [RNA-seq]

GSE239860 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/05/29 Platform GPL24676Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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: HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotypeJournal of experimental & clinical cancer research : CR · 2025

Summary (written by the submitters)

Background and Aims: Complex host-virus interactions account for HBV-specific T and B cells dysfunction and the persistence of the viral cccDNA mini-chromosome, key features of HBV chronicity and challenges for HBV cure. The extent of HBV impact on liver transcriptome remains controversial. Transcriptional activation in eukaryotic cells has been tightly linked with disruption of nucleosome organization at accessible genomic sites of remodeled chromatin.

Read the full summary ↓

We used ATAC-seq (Assay for Transposase Accessible Chromatin followed by high throughput sequencing) to detect early changes in chromatin accessibility in HBV-infected Primary Human Hepatocytes (PHHs). Results. ATAC-seq analysis revealed that after HBV infection an increasing number of genomic sites change their chromatin accessibility over time with a prevalent global reduction of accessibility (that is) partially prevented by inhibiting HBV transcription and replication. Motif Enrichment Analysis identified several TF involved in liver cell identity, glucose and lipid metabolism as potential regulators of differentially accessible genes 72h post-infection, when cccDNA transcription and viral replication are established. ATAC-seq and RNA-seq integration confirmed HBV infection impact on liver metabolism, the early establishment of a premalignant phenotype and identified a 39-genes liver iron signature modulated by chromatin accessibility changes. The upregulation of iron uptake genes translates in a significant increase of iron content in HBV-infected PHHs whereas iron chelation results in a drastic inhibition of cccDNA transcription and viral replication. Conclusions. Altogether our results show that HBV infection impacts on host cell chromatin landscape and specific transcriptional programs and that HBV modulates intracellular available iron to boost its replication.

Published in

HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype

Alfano V, Pascucci GR, Corleone G et al. · Journal of experimental & clinical cancer research : CR 2025 · PMID 40380227 · doi:10.1186/s13046-025-03414-7

This dataset

Open GSE239860 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 GSE239860_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 PRJNA1001287 and SRA study SRP452927. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40380227) ↗

Study design

18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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

GSM7675681 Donor 1 (s1), HBV, 2h
GSM7675682 Donor 2 (s2), HBV, 2h
GSM7675683 Donor 3 (s3), HBV, 2h
GSM7675684 Donor 1 (s1), Mock, 2h
GSM7675685 Donor 2 (s2), Mock, 2h
GSM7675686 Donor 3 (s3), Mock, 2h
GSM7675687 Donor 1 (s1), HBV, 72h
GSM7675688 Donor 2 (s2), HBV, 72h
GSM7675689 Donor 3 (s3), HBV, 72h
GSM7675690 Donor 1 (s1), Mock, 72h
GSM7675691 Donor 2 (s2), Mock, 72h
GSM7675692 Donor 3 (s3), Mock, 72h
GSM8707281 Donor 4 replicate 1 Mock-IFN
GSM8707282 Donor 4 replicate 2 Mock-IFN
GSM8707283 Donor 4 replicate 3 Mock-IFN
GSM8707284 Donor 4 replicate 1 Mock
GSM8707285 Donor 4 replicate 2 Mock
GSM8707286 Donor 4 replicate 3 Mock

Datasets on a similar topic

GSE240183 HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype [ATAC-seq] 22 samples shares accessibility, preneoplastic, homeostasis, hbv-driven, chromatin, phenotype, changes, promote
GSE290342 Caloric restriction mimetic 2-deoxyglucose alters metabolic and transcriptomic phenotype in association with changes in chromatin accessibility in human astrocytes [ATAC-Seq] 12 samples shares accessibility, chromatin, phenotype, changes
GSE178494 Chromatin accessibility and transcriptomic changes underlying progression from islet autoantibody positivity to type 1 diabetes 89 samples shares accessibility, chromatin, changes
GSE243558 PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression 29 samples shares accessibility, chromatin, promote
GSE329420 Endothelial exosomes remodel chromatin accessibility and superenhancer in cancer cells to promote liver metastatic colonization 26 samples shares accessibility, chromatin, promote
GSE291262 Anthracyclines induce global changes in chromatin accessibility in cardiomyocytes that overlap with cardiovascular disease loci [CUT&Tag] 25 samples shares accessibility, chromatin, changes
GSE309354 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice [multiome] 24 samples shares accessibility, chromatin, changes
GSE309352 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice [ChIP-Seq] 14 samples shares accessibility, chromatin, changes

Search all human RNA-seq datasets in GEO →

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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.