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RBM39 promotes hepatocarcinogenesis by regulating RFX1's alternative splicing and subsequent activation of integrin signaling pathway

GSE275347 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/03/03 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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)
Topic
Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples
16 samples: 5 × T vs 5 × NT vs 3 × Huh7 cells,shControl vs 3 × Huh7 cells,shRBM39Groups 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)
There is increasing evidence that alternative splicing (AS) is crucial for tumor cells because it can produce various protein isoforms that may play different or even opposing roles in tumor growth and metastasis. Despite its significance, the role of AS and related splicing factors, particularly splicing-related messenger ribonucleoproteins (mRNPs), in hepatocarcinogenesis is poorly understood.
Read the full summary ↓
High-throughput transcriptome sequencing of HCC patients revealed that the spliceosome pathway may play an important role in HCC development. Through the combined analysis of the three gene clusters consisting of differentially expressed genes (DEGs), genes encoding RNA-binding proteins (RBPs) and genes related to splicing-related mRNPs, the splicing factor RBM39 was identified, which was highly expressed in HCC tumor tissues with prognostic value. Functional studies showed that RBM39 silencing inhibited cell proliferation, migration and invasion via the integrin pathway. By performing RNA immunoprecipitation sequencing (RIP-seq), we found that RBM39 combined with RFX1 pre-mRNA and regulated alternative splicing of its exon 2. Mechanistically, the skipping of exon 2 in RFX1, influenced by high RBM39 expression in HCC cells, led to production of an N-terminal truncated RFX1, which lost the ability to transcriptionally repress oncogenic collagen genes. This process further activated the downstream FAK/PI3K/AKT signaling pathway. Furthermore, we further validated these findings in the hydrodynamic tail vein injection (HTVI) mouse model and human HCC tissues. Therefore, we hypothesized that high RBM39 expression enhances the malignant capabilities of HCC cells by regulating the alternative splicing of RFX1 and subsequently activating the FAK/PI3K/AKT signaling pathway.
This dataset
Open GSE275347 in finder → Find more human RNA-seq datasets → Hepatocellular carcinoma 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 GSE275347_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 PRJNA1150507 and SRA study SRP527738. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × T vs 5 × NT vs 3 × Huh7 cells,shControl vs 3 × Huh7 cells,shRBM39

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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 Hepatocellular carcinoma datasets

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