GEO series

POGZ loss increases TGFβ signaling and potentiates TNBC metastasis

GSE247628 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/07/31 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 6 × POGZ_KO vs 6 × POGZ_VCGroups 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 Neurodevelopmental Protein POGZ Suppresses Metastasis in Triple-Negative Breast Cancer by Attenuating TGFβ SignalingCancer research · 2024

Summary (written by the submitters)

The pogo transposable element derived zinc finger protein, POGZ, is notably associated with autism-like or intellectual disabilities through its role in gene transcription. Indeed, many proteins involved in neurological development are often dysregulated in cancer. We provide the first experimental evidence that POGZ influences the growth and metastatic spread of triple negative breast cancers (TNBC).

Read the full summary ↓

Utilizing a well-characterized immunocompetent model of TNBC, we show that POGZ exerts a dual role, both as a tumor promoter and metastasis suppressor. Mechanistically, we show that POGZ loss potentiates TGFβ pathway activation in TNBC, to exert cytostatic effects while simultaneously increasing the mesenchymal and migratory properties of breast tumors. Finally, we demonstrate that whereas POGZ levels are elevated in human breast cancers, the most aggressive TNBC tumors, including those with increased mesenchymal and metastatic properties, dampen POGZ levels, associated with inferior clinical outcomes. Combined these data suggest that POGZ is a critical regulator of the early stages of metastatic cascade

Published in

The Neurodevelopmental Protein POGZ Suppresses Metastasis in Triple-Negative Breast Cancer by Attenuating TGFβ Signaling

Heath J, Mirabelli C, Annis MG et al. · Cancer research 2024 · PMID 39137399 · doi:10.1158/0008-5472.CAN-23-3887

This dataset

Open GSE247628 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 GSE247628_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 PRJNA1039840 and SRA study SRP471597. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39137399) ↗

Study design

6 × POGZ_KO vs 6 × POGZ_VC

Supports a between-group comparison across 12 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 12 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

GSM7898145 POGZ_KO_1 POGZ_KO
GSM7898146 POGZ_KO_2 POGZ_KO
GSM7898147 POGZ_KO_3 POGZ_KO
GSM7898148 POGZ_KO_8454 POGZ_KO
GSM7898149 POGZ_KO_8455 POGZ_KO
GSM7898150 POGZ_KO_8459 POGZ_KO
GSM7898151 POGZ_VC_1 POGZ_VC
GSM7898152 POGZ_VC_2 POGZ_VC
GSM7898153 POGZ_VC_3 POGZ_VC
GSM7898154 POGZ_VC_8447 POGZ_VC
GSM7898155 POGZ_VC_8448 POGZ_VC
GSM7898156 POGZ_VC_8451 POGZ_VC

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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.