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Gene expression profiling in human primary hepatocytes and human induced pluripotent stem cell-derived hepatocytes before and after IL-1β Treatment

GSE254235 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/09/22 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)
Samples
12 samples: 12 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
IL1β signaling mediates the interaction between hepatitis B and C virusesHepatology (Baltimore, Md.) · 2026
Summary (written by the submitters)
The shared transmission routes of hepatitis B virus (HBV) and hepatitis C virus (HCV) result in coinfections that accelerate and exacerbate liver disease. The clinical burden is further exacerbated in the era of direct-acting antivirals (DAAs) against HCV, where reports of HBV reactivation post-DAA treatment in coinfected patients have emerged.
Read the full summary ↓
Beyond an HCV-induced canonical interferon (IFN) response, the mechanisms through which HCV suppresses HBV remain poorly understood. Here, we employ a multicellular liver culture system, co-culturing human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes, hepatic stellate cells and macrophages, that supports productive HCV and HBV infection and replicates clinical coinfection dynamics. We demonstrate that IL1β from macrophages activated by HCV modulates host factors involved in HBV infection independent of IFN signaling. By combining bioinformatic predictions with reporter assay validation, we identified the transcriptional mediators of these changes. Hepatocytes downregulate expression of HBV receptor SLC10A1 due to induction of a truncated C/EBPβ isoform, which negatively regulates the full-length variant’s activity. Simultaneously, IL1β induces the expression of ISG20, a known anti-HBV factor, through USF1 phosphorylation. Finally, we show that a modified treatment protocol combining DAA with an HBV entry inhibitor effectively prevents HBV reactivation. Our findings position this liver culture platform as a tool not only for detailed mechanistic dissection of the complex multicellular responses in HBV-HCV coinfection, but also for nominating and testing future therapeutic avenues for coinfected patients.
Published in
IL1β signaling mediates the interaction between hepatitis B and C viruses
Zhang F, Zhao Y, Bian L et al. · Hepatology (Baltimore, Md.) 2026 · PMID 40938198 · doi:10.1097/HEP.0000000000001525
This dataset
Open GSE254235 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 GSE254235_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 PRJNA1069056 and SRA study SRP485964. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40938198) ↗
Study design
12 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 4 samples read as cases, 2 as controls.

How we read this: Read from 12 sample titles: 12 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
Datasets on a similar topic

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