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Biobank of genetically defined murine prostate cancer tumoroids uncovers oncogenic pathways and drug vulnerabilities driven by PTEN-loss

GSE291912 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/03/21 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 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
Biobank of genetically defined murine prostate cancer tumoroids uncovers oncogenic pathways and drug vulnerabilities driven by PTEN-lossCell reports methods · 2026
Summary (written by the submitters)
Prostate cancer (PCa) is the second most common cancer in men and shows high inter- and intra-patient heterogeneity. Thus, treatment options are limited and there is a lack of representative preclinical models. Here we establish a biobank of murine organoids and tumoroids that reflect common patient mutations. The deletion of Pten alone, or in combination with Stat3, or Tp53, led to an upregulation of cancer-related pathways in organoids and in tissue-derived tumoroids.
Read the full summary ↓
By performing a medium-throughput drug screen we identify two compounds, the PDPK1/AKT/FLT dual pathway inhibitor and tenovin-6, that effectively inhibited tumoroid growth. Additionally, these compounds inhibited the growth of several human PCa cell lines and could be used in combination with Enzalutamide. Overall, we provide evidence that murine tumoroids are versatile preclinical models for studying PCa tumorigenesis and drug sensitivities to develop novel therapeutic options for PCa patients.
Published in
Biobank of genetically defined murine prostate cancer tumoroids uncovers oncogenic pathways and drug vulnerabilities driven by PTEN-loss
Kalla J, Dillinger T, Pavlovicova Z et al. · Cell reports methods 2026 · PMID 41916299 · doi:10.1016/j.crmeth.2026.101370
This dataset
Open GSE291912 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 GSE291912_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 PRJNA1235768 and SRA study SRP570308. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41916299) ↗
Study design
8 conditions, mostly in triplicate
WT in vivo organoid, biol ×3 Pten KO in vivo tumoroid, biol ×3 Pten_Stat3 KO in vivo tumoroid, biol ×3 Pten_P53 KO in vivo tumoroid, biol ×3 WT in vitro organoid, biol ×3 Pten KO in vitro tumoroid, biol ×3 Pten_Stat3 KO in vitro tumoroid, biol ×3 Pten_P53 KO in vitro tumoroid, biol ×3

Supports a case/control comparison: 18 samples read as cases, 6 as controls.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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