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The essential clathrin adaptor protein complex-2 is tumor suppressive specifically in vivo

GSE233173 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2024/12/12 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 48 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)
Samples
48 samples: 12 conditions, mostly with about 5 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.
Paper
The essential clathrin adapter protein complex-2 is tumor suppressive specifically in vivoNature communications · 2025
Summary (written by the submitters)
The microenvironment is a rich source of new cancer targets. While whole-genome CRISPR/Cas9 screens have identified vulnerabilities in cultured cells, it is a challenge to use this approach in tumors to interrogate the microenvironment. To this end, we screened a panel of pancreatic cancer lines grown in culture versus as tumors with a phosphatidylinositol metabolism CRISPR/Cas9 library.
Read the full summary ↓
This revealed the Adaptor Protein complex-2 (AP2) of clathrin-mediated endocytosis behaves as common essential in culture but tumor suppressive in vivo. These polar-opposite phenotypes were attributed to different microenvironments. In culture, AP2 loss reduces endocytosis of transferrin and iron import. In tumors, alternative iron transport pathways allow pro-tumor signaling to manifest. In the most sensitive case, AP2 loss reprograms the plasma membrane proteome, retaining integrins on the surface leading to downregulation of the tumor-suppressor PTEN. Analysis of human tumors suggests a similar tumor suppressive activity. AP2 may foreshadow other proteins unique to the tumor-microenvironment.
Published in
The essential clathrin adapter protein complex-2 is tumor suppressive specifically in vivo
Zimmerman SP, DeGraw LB, Counter CM · Nature communications 2025 · PMID 40050266 · doi:10.1038/s41467-025-57521-2
This dataset
Open GSE233173 in finder → Find more human 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 GSE233173_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 PRJNA975168 and SRA study SRP438983. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40050266) ↗
Study design
12 conditions, mostly with about 5 replicates each
XenoBXPC3MinusDox ×5 XenoBXPC3PlusDox ×5 XenoPancMinusDox ×5 XenoPancPlusDox ×5 XenoCFPACMinusDox ×5 XenoCFPACPlusDox ×5 CellsBXPC3MinusDox ×3 CellsBXPC3PlusDox ×3 +4 more

Supports a between-group comparison across 48 samples.

How we read this: 12 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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