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CRIPTO’s multifaceted role in driving aggressive prostate cancer unveiled by in vivo, organoid, and patient data

GSE262362 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2024/12/04 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 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)
Samples
26 samples: 8 conditions, mostly in triplicateGroups 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
CRIPTO's multifaceted role in driving aggressive prostate cancer unveiled by in vivo, organoid, and patient dataOncogene · 2025
Summary (written by the submitters)
CRIPTO, (or CR-1 or TDGF1), is a protein that plays an active role in tumor initiation and progression. We have confirmed that increased expression of CRIPTO is associated with clinical and prostate-specific antigen (PSA) progression in human prostate tissues. To further study CRIPTO signaling in vivo, we developed new genetically engineered mouse models (GEMMs) in which we genetically knocked out CRIPTO to specifically investigate its role in castration-resistant Nkx3.1 expressing cells (CARNs), which are targeted for oncogenic transformation in prostate cancer (PCa).
Read the full summary ↓
The most aggressive stage was modeled using an inducible Cre driver, Pten inactivation, oncogenic Kras activation, and lineage tracing with yellow fluorescence protein (E-YFP). Our findings provide evidence that selective depletion of CRIPTO in epithelial cells in vivo reduces the invasive phenotype, particularly in more advanced tumor stages. Moreover, in vitro experiments with CRIPTO overexpression demonstrated alterations in the physical features of organoids, which correlated with increased tumorigenic activity. Transcriptomic analyses revealed a unique CRIPTO/MYC co-activation signature which was further associated with PSA progression in a human PCa cohort.
Published in
CRIPTO's multifaceted role in driving aggressive prostate cancer unveiled by in vivo, organoid, and patient data
Rodrigues Sousa E, de Brot S, Zoni E et al. · Oncogene 2025 · PMID 39592836 · doi:10.1038/s41388-024-03230-x
This dataset
Open GSE262362 in finder → Find more mouse RNA-seq datasets →
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 GSE262362_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 PRJNA1091582 and SRA study SRP497614. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39592836) ↗
Study design
8 conditions, mostly in triplicate
Prostate, Organoid, NPKC, ×4 Prostate, Tissue, Untreated, ×4 Prostate, Organoid, N, ×3 Prostate, Organoid, NPC, ×3 Prostate, Organoid, NP, ×3 Prostate, Organoid, NPK, ×3 Prostate, Organoid, NC, ×3 Prostate, Tissue, Treated, ×3

Supports a between-group comparison across 26 samples.

How we read this: 8 replicated groups read from 26 sample titles; they account for 26 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
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