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Caffeine in the context of sorafenib chemotherapy: Insights from experimental hepatocarcinogenesis

GSE322844 Mus musculus (mouse) RNA-seq (gene expression) 25 samples Submitted 2026/07/22 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 25 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
Mus musculus (mouse)
Samples
25 samples: 5 conditions, mostly with about 5 replicates eachGroups 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
Caffeine in the Context of Sorafenib Chemotherapy: Insights From Experimental HepatocarcinogenesisJournal of biochemical and molecular toxicology · 2026
Summary (written by the submitters)
Background: Hepatocellular carcinoma (HCC) features a high mortality burden worldwide, highlighting the need for improved therapeutic strategies. Caffeine (CAF), a widely consumed bioactive compound, has been reported to exert chemopreventive effects in HCC, but its interaction with standard therapies remains poorly explored. Purpose: We investigated whether CAF promotes the antitumoral effects of sorafenib (SOR) chemotherapy in HCC preclinical platforms.
Read the full summary ↓
Study design: C3H/HeJ mice were submitted to diethylnitrosamine (DEN)-induced hepatocarcinogenesis and treated with CAF (50 mg/kg), SOR (30 mg/kg) or their combination for three weeks. C3A/LX2 spheroids and transwell co-cultures were also exposed to CAF, SOR or their combination at 1/5 or 1/10 of half maximal effective concentration. Results: The combination of CAF and SOR produced a synergistic reduction in tumor spheroid viability and inhibited HCC cell colony formation. Nonetheless, treatments exerted comparable effects on reducing liver tumor volume and Afp expression in vivo. Although only CAF+SOR reduced serum ALT levels and uniquely downregulated HCC-related Ccl3, treatments showed differential and subtle transcriptomic impacts during hepatocarcinogenesis - not showing promoting or additive effects when combined. Conclusion: In summary, while CAF potentiated SOR antitumoral activity in vitro, their combination did not lead to major effects in vivo, eliciting the need for further investigation.
Published in
Caffeine in the Context of Sorafenib Chemotherapy: Insights From Experimental Hepatocarcinogenesis
Valente LC, Silva JSD, Riechelmann-Casarin L et al. · Journal of biochemical and molecular toxicology 2026 · PMID 42455914 · doi:10.1002/jbt.71017
This dataset
Open GSE322844 in finder → Find more mouse 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 GSE322844_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 PRJNA1431947 and SRA study SRP680886. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42455914) ↗
Study design
5 conditions, mostly with about 5 replicates each
DEN-initiated mouse ×6 Untreated mouse ×5 DEN-initiated CAF-treated mouse ×5 DEN-initiated SOR- and CAF-treated mouse ×5 DEN-initiated SOR-treated mouse ×4

Supports a between-group comparison across 25 samples.

How we read this: 5 replicated groups read from 25 sample titles; they account for 25 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
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