GEO series

SOX10 regulates melanoma metastasis through the IRF1-ITGA3/EphA2-FAK pathway.

GSE298445 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/12/03 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Topic: MelanomaThis series is part of our curated briefing on it.
Samples: 12 samples: 3 × A2058 vs 3 × siCNTL vs 3 × siSOX10_1 vs 3 × siSOX10_2Groups 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: SOX10 Regulates Melanoma Metastasis Through the IRF1-ITGA3/EphA2-FAK PathwayCancer science · 2025

Summary (written by the submitters)

Melanoma heterogeneity is associated with an enhanced metastatic potential. Although an invasive state with MITFlow/AXLhigh in the melanoma subpopulation has been identified using a single-cell RNA-seq analysis, the mechanisms by which these cells acquire their invasiveness remains unclear. In the present study, we identified the gene set related to cell migration as one of the enriched gene ontologies after the knockdown of SOX10 in melanoma.

Read the full summary ↓

We demonstrated that the knockdown of SOX10 induced melanoma migration independent of MITF reduction or AXL induction. An in silico analysis and in vitro analysis revealed that ITGA3 and EphA2 were downstream molecules for SOX10-mediated migration, and were required for adhesive and random motile abilities, respectively. In addition, the oncogenic activation of MAPK was required for increased random motility through EphA2 phosphorylation at the Ser 897 residue. We also demonstrated the significance of IRF1 in the induction of both ITGA3 and EphA2 after the knockdown of SOX10. The FAK inhibitor, defactinib, suppressed metastasis in vivo. In summary, the present study showed that the reduced expression of SOX10 induced melanoma metastasis through the IRF1-ITGA3/EphA2-FAK pathway and also suggests the potential of FAK inhibitors as candidate drugs for the treatment of melanoma metastasis.

Published in

SOX10 Regulates Melanoma Metastasis Through the IRF1-ITGA3/EphA2-FAK Pathway

Kaminaka R, Takahashi N, Nishizawa M et al. · Cancer science 2025 · PMID 40808260 · doi:10.1111/cas.70173

This dataset

Open GSE298445 in finder → Find more human RNA-seq datasets → 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 GSE298445_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 PRJNA1269479 and SRA study SRP588527. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40808260) ↗

Study design

3 × A2058 vs 3 × siCNTL vs 3 × siSOX10_1 vs 3 × siSOX10_2

Supports a between-group comparison across 12 samples.

How we read this: 4 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

GSM9014471 A2058_1 A2058
GSM9014472 A2058_2 A2058
GSM9014473 A2058_3 A2058
GSM9014474 siCNTL_1 siCNTL
GSM9014475 siCNTL_2 siCNTL
GSM9014476 siCNTL_3 siCNTL
GSM9014477 siSOX10_1_1 siSOX10_1
GSM9014478 siSOX10_1_2 siSOX10_1
GSM9014479 siSOX10_1_3 siSOX10_1
GSM9014480 siSOX10_2_1 siSOX10_2
GSM9014481 siSOX10_2_2 siSOX10_2
GSM9014482 siSOX10_2_3 siSOX10_2

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