GEO series

GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases [scRNA-seq]

GSE317349 Homo sapiens (human) Single-cell RNA-seq 2 samples Submitted 2026/01/22 Platform GPL18573

At a glance

Single-cell RNA-seq · human · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: Uveal melanomaThis series is part of our curated briefing on it.
Samples: 2 samples
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)

Uveal melanoma (UM) results in fatal liver metastasis, yet little is known about the interactions between UM and host cells in the tumor microenvironment that promote this distinctive proclivity. We used single cell (sc)-RNA-Seq analysis of UM-hepatic stellate cell (HSC) co-cultures to demonstrate that HSCs enriched for UM cell states that expressed genes implicated in cell survival, metabolic reprogramming and angiogenesis.

Read the full summary ↓

A lead candidate driver of HSC reprogramming was the TGF-b family member GDF15, which was associated with a metastatic UM phenotype. Silencing of BAP1 in UM cells led to increased GDF15 expression and accumulation of H3K27ac marks at the GDF15 promoter. Treatment of HSCs with GDF15 led to increased expression extracellular matrix proteins, inflammatory cytokines and angiogenic factors, including IL-8. Both exogenous GDF15, IL-8 and conditioned media from UM-HSC co-cultures increased endothelial cell network formation in vitro, an effect that was blocked by anti-GDF15 antibodies. In multiple models of metastatic UM, silencing of GDF15 inhibited the outgrowth of metastatic lesions, associated with reduced deposition of extracellular matrix and recruitment of endothelial cells. UM liver metastasis development is dependent upon GDF15-mediated remodeling of the liver microenvironment leading to an angiogenic response and matrix deposition that supports tumor growth.

This dataset

Open GSE317349 in finder → Find more human RNA-seq datasets → Uveal melanoma 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 GSE317349_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1406774 and SRA study SRP665675. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

More Uveal melanoma datasets

GSE317347 GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastases [bulk RNA-seq] 6 samples same disease briefing · shares gdf15, microenvironment, reprograms, metastases, melanoma, drive, uveal
GSE233458 LKB1-SIK2 loss drives uveal melanoma proliferation and hypersensitivity to SLC8A1 and ROS inhibition 6 samples same disease briefing · shares melanoma, drive, uveal
GSE259383 Tebentafusp elicits on-target cutaneous immune responses driven by cytotoxic T cells in uveal melanoma patients 6 samples same disease briefing · shares melanoma, drive, uveal
GSE294950 Epigenetic library screen reveals novel targets for uveal melanoma 24 samples same disease briefing · shares melanoma, uveal
GSE317536 Matched sampling reveals uncoupled phenotypic plasticity during metastasis formation in uveal melanoma 23 samples same disease briefing · shares melanoma, uveal
GSE196624 The role of EHMT2 in Uveal melanoma progression [EHMT2_Inhibitors] 18 samples same disease briefing · shares melanoma, uveal
GSE231395 PRAME induces genomic instability in uveal melanoma [RNA-seq] 15 samples same disease briefing · shares melanoma, uveal
GSE287090 Exploration of tumor associated macrophages in patients with metastatic uveal melanoma by single cell RNAseq 12 samples same disease briefing · shares melanoma, uveal

Search all human RNA-seq datasets in GEO →

Share this dataset

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.