GEO series
The melanocytic transcriptomic state is independently associated with poor overall survival in long term follow up of patients with metastatic melanoma
GSE325123
Homo sapiens (human)
RNA-seq (gene expression)
272 samples
Submitted 2026/03/24
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 272 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
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 272 samples: 23 conditions, mostly with about 12 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.
Summary (written by the submitters)
Introduction: Advanced cutaneous melanoma shows substantial heterogeneity in clinical outcomes, even among patients classified within the same clinical stage. Understanding the molecular drivers underlying this heterogeneity is critical for advancing treatment strategies. Previous studies have identified distinct melanoma transcriptomic states - Tirosh et al.
Read the full summary ↓
and Balderson et al. have agreed on a four-subtype model defining “Undifferentiated/AP1”, “Neural Crest/AP2”, “Transitory”, and “Melanocytic” states. However, their biological and clinical relevance remains unclear. Here we profiled in-transit melanoma (ITM) using digital spatial RNA profiling to associate melanoma transcriptomic states with overall survival (OS) and acral melanoma (AM) status. Methods: Digital spatial profiling (Nanostring GeoMx Whole Transcriptome Atlas) was performed across a tissue microarray constructed from patients with ITM diagnosed from 1990-2020. After filtering poor quality areas of interest (AOIs), we processed the data using noise correction and quantile normalization. We applied Principal Component Analysis (PCA) to define melanoma subtype signatures by ranking genes contributing to each of the first four PCs. We performed gene set enrichment analysis using GSEA with significance defined as an adjusted p-value < 0.05. Association between gene or gene-set expression and overall survival was evaluated using optimal expression cutoffs to define high and low groups, with a minimum group size of 20% to avoid overfitting. Cox proportional hazards models were then used to assess survival differences between groups. Results: We analyzed a cohort of 84 patients (116 AOIs) with ITM passing spatial transcriptomic QC. PCA of transcriptional profiles revealed distinct transcriptional states. The PC1 axis differentiated Transitory from Undifferentiated melanoma, PC2 reflected immune cell infiltration, PC3 corresponded to stromal cells and Neural crest-like melanoma, and PC4 associated with Melanocytic melanoma. We derived gene sets from the PCA results and associated the expression of each gene set with OS. Across a cohort of treatment-naïve ITM, high expression of the melanocytic state conferred a median overall survival difference of 7.59 years and independently associated with poor survival in multivariate analysis. AMs showed higher melanocytic state gene expression compared to non-acral cases. These findings were validated in external datasets, supporting that the melanocytic state predicts poor prognosis. Conclusion: The melanocytic transcriptional state was independently associated with worse overall survival in patients with metastatic melanoma and was enriched in acral melanoma, suggesting that assessment of the melanocytic state may have value for clinical risk stratification.
This dataset
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.
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 GSE325123_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1438670 and SRA study SRP684506. Searching any of these in the dataset finder brings you back here.
Study design
23 conditions, mostly with about 12 replicates each
Melanoma, A-A ×12
Melanoma, A-B ×12
Melanoma, A-C ×12
Melanoma, A-D ×12
Melanoma, A-E ×12
Melanoma, A-F ×12
Melanoma, A-G ×12
Melanoma, A-H ×12
+15 more
Supports a between-group comparison across 272 samples.
How we read this: 23 replicated groups read from 272 sample titles; they account for 272 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
- GSM9596213 Melanoma, A-A01 Melanoma, A-A
- GSM9596214 Melanoma, A-A02 Melanoma, A-A
- GSM9596215 Melanoma, A-A03 Melanoma, A-A
- GSM9596216 Melanoma, A-A04 Melanoma, A-A
- GSM9596217 Melanoma, A-A05 Melanoma, A-A
- GSM9596218 Melanoma, A-A06 Melanoma, A-A
- GSM9596219 Melanoma, A-A07 Melanoma, A-A
- GSM9596220 Melanoma, A-A08 Melanoma, A-A
- GSM9596221 Melanoma, A-A09 Melanoma, A-A
- GSM9596222 Melanoma, A-A10 Melanoma, A-A
- GSM9596223 Melanoma, A-A11 Melanoma, A-A
- GSM9596224 Melanoma, A-A12 Melanoma, A-A
- GSM9596225 Melanoma, A-B01 Melanoma, A-B
- GSM9596226 Melanoma, A-B02 Melanoma, A-B
- GSM9596227 Melanoma, A-B03 Melanoma, A-B
- GSM9596228 Melanoma, A-B04 Melanoma, A-B
- GSM9596229 Melanoma, A-B05 Melanoma, A-B
- GSM9596230 Melanoma, A-B06 Melanoma, A-B
- GSM9596231 Melanoma, A-B07 Melanoma, A-B
- GSM9596232 Melanoma, A-B08 Melanoma, A-B
- GSM9596233 Melanoma, A-B09 Melanoma, A-B
- GSM9596234 Melanoma, A-B10 Melanoma, A-B
- GSM9596235 Melanoma, A-B11 Melanoma, A-B
- GSM9596236 Melanoma, A-B12 Melanoma, A-B
- GSM9596237 Melanoma, A-C01 Melanoma, A-C
- GSM9596238 Melanoma, A-C02 Melanoma, A-C
- GSM9596239 Melanoma, A-C03 Melanoma, A-C
- GSM9596240 Melanoma, A-C04 Melanoma, A-C
- GSM9596241 Melanoma, A-C05 Melanoma, A-C
- GSM9596242 Melanoma, A-C06 Melanoma, A-C
- GSM9596243 Melanoma, A-C07 Melanoma, A-C
- GSM9596244 Melanoma, A-C08 Melanoma, A-C
- GSM9596245 Melanoma, A-C09 Melanoma, A-C
- GSM9596246 Melanoma, A-C10 Melanoma, A-C
- GSM9596247 Melanoma, A-C11 Melanoma, A-C
- GSM9596248 Melanoma, A-C12 Melanoma, A-C
- GSM9596249 Melanoma, A-D01 Melanoma, A-D
- GSM9596250 Melanoma, A-D02 Melanoma, A-D
- GSM9596251 Melanoma, A-D03 Melanoma, A-D
- GSM9596252 Melanoma, A-D04 Melanoma, A-D
+ 232 more — browse all 272 samples with per-sample file links →
More Melanoma datasets
- GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · shares metastatic, melanoma
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma, state
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares melanoma
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples same disease briefing · shares state
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares melanoma
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.