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Loss of DUSP1 expression creates a cold tumor microenvironment in cutaneous squamous cell carcinoma

GSE260920 Mus musculus (mouse) RNA-seq (gene expression) 17 samples Submitted 2024/09/30 Platform GPL24676Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 17 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
Mus musculus (mouse)
Topic
Cutaneous squamous cell carcinomaThis series is part of our curated briefing on it.
Samples
17 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)
Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent cancer. In most of the cases, surgical removal of the tumor is a curative treatment but 3-5% of the tumors will progress or produce metastasis having a poor prognosis. Here we demonstrated the tumor suppressive role of DUSP1, a dual phosphatase that negatively regulates ERK activity.
Read the full summary ↓
We demonstrated that DUSP1 constrains ERK signaling during inflammation and wound healing to sustain homeostasis by transiently decreasing its levels, but its permanent downregulation promotes progression to squamous cell carcinoma. Using mouse and human models we demonstrated that DUSP1 loss enhances ERK signaling, and tumor growth. RNAseq analysis revealed that DUSP1 null tumors are enriched in cancer stem cell gene signatures, but surprisingly, are also depleted from CD4, CD8, macrophages and DC cells, and DUSP1 null cancer cells express lower levels of chemo and cytokines, been immune excluded. Our data suggest that DUSP1 acts restricting cancer cell proliferation and promoting immune recruitment, presenting promising diagnostic and therapeutic potential.
This dataset
Open GSE260920 in finder → Find more RNA-seq datasets → Cutaneous squamous cell 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 GSE260920_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 PRJNA1084005 and SRA study SRP493459. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Samples in this study

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+ 17 more — browse all 17 samples with per-sample file links →

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