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Dual Role of IL-6 in Maintaining the resistance of Gastrointestinal stromal tumor and tumor angiogenesis

GSE289088 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/02/12 Platform GPL23227
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)
Topic
Gastrointestinal stromal tumourThis series is part of our curated briefing on it.
Samples
12 samples: 6 conditions, mostly in duplicateGroups 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)
Resistance is a major obstacle to the effective treatment of many tumor types, including Gastrointestinal stromal tumor (GIST). Although Imatinib (IM) is considered the gold standard for targeted therapy in GIST, resistance to IM ultimately occurs in many patients, leading to disease progression. The precise mechanisms underlying this resistance remain poorly understood.
Read the full summary ↓
Our study reveals that high expression of Interleukin-6 (IL-6) is closely associated with poor survival outcomes in patients with GIST. Elevated levels of IL-6 not only sustain the viability of GIST cells but also promote tumoral angiogenesis within the tumor microenvironment (TME) via paracrine mechanisms. Notably, the combination of the IL-6 receptor inhibitor Tocilizumab (TCZ) with IM significantly inhibited tumor growth in a GIST xenograft mouse model. Mechanistic investigations indicate that IL-6, through its interaction with IL-6R, reactivates the PI3K/Akt/mTOR signaling pathway, which is suppressed by IM. Additionally, as a secreted protein, IL-6 regulates the secretion of vascular endothelial growth factors controlled by the JAK2/STAT3 signaling pathway in endothelial cells via paracrine action. Thus, IL-6 may serve as a critical biomarker for predicting the prognosis of GIST, and the combined treatment strategy of IM with TCZ shows promising potential in overcoming resistance in GIST.
This dataset
Open GSE289088 in finder → Find more human RNA-seq datasets → Gastrointestinal stromal tumour 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 GSE289088_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 PRJNA1221287 and SRA study SRP562388. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in duplicate
Homo sapiens, 882R Cells, control blank, biol ×2 Homo sapiens, 882R Cells, sh1 IL-6 knock down… ×2 Homo sapiens, 882R Cells, sh2 IL-6 knock down… ×2 Homo sapiens, T1R Cells, control blank, biol ×2 Homo sapiens, T1R Cells, sh1 IL-6 knock down,… ×2 Homo sapiens, T1R Cells, sh2 IL-6 knock down,… ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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 Gastrointestinal stromal tumour datasets

Search all human RNA-seq datasets in GEO →

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