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The pioneer transcription factor PBX as a downstream target of MNX1 [ACT]

GSE269910 Mus musculus (mouse) Other 55 samples Submitted 2025/04/24 Platform GPL21626
At a glance

mouse · 55 samples

Organism
Mus musculus (mouse)
Samples
55 samples: 13 conditions, mostly with about 4 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.
Paper
Role of MNX1-mediated histone modifications and PBX gene family in MNX1-induced leukemogenesisScientific reports · 2026
Summary (written by the submitters)
Recently we have identified the upregulation of the homebox domain protein MNX1 associated with the paediatric t(7;12) AML as the initiating event for Leukaemia in mice. We demonstrated that MNX1 triggers abnormal histone modifications, specifically H3K4me3 and H3K27me3, by interacting with SAM-dependent methyltransferases. In the current study our aim was investigate downstream targets of MNX1 and the relationship with histone modification.
Read the full summary ↓
Employing TMT Mass spectrometry and RNA-Seq integrative analysis identified the pioneer transcription factor PBX1 as a downstream target of MNX1. We observe that MNX1 binds to the promoter region of PBX1, leading to increased expression of PBX1. This binding of MNX1 to the PBX1 promoter was associated with enhanced H3K4me3 and decreased H3K27me3 in the same promoter region. Interestingly, this binding of MNX1, but not the histone modification on the PBX1 promoter was transient and diminishes as MNX1-FL cells progress to leukaemia in mice. To gain further insight, we conducted a comparative analysis of H3K4me3 using ACT-Seq and RNA-Seq data between MNX preleukemia FL cells and leukaemia MNX1 BM blasts. Our results indicate that this phenomenon is not limited to PBX1 but is rather widespread throughout the genome, identifying several downstream targets for MNX1 mediated H3K4me3 modification. Investigating the PBX1 and 4 motifs identified from Chip-Seq, revealed a significant enrichment in MNX1 H3K4me3 and ATAC-seq peaks. This suggest that PBX family might play an important role in the function of MNX1, which was further confirmed by showing MNX1 induced PBX1 expression to be downregulated using the sinefungin inhibitor, which we have previously reported to inhibit leukemia induction by MNX1.
Published in
Role of MNX1-mediated histone modifications and PBX gene family in MNX1-induced leukemogenesis
Malmhäll-Bah E, Östlund A, Nilsson T et al. · Scientific reports 2026 · PMID 41554854 · doi:10.1038/s41598-026-36367-8
This dataset
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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE269910_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1124110. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41554854) ↗
Study design
13 conditions, mostly with about 4 replicates each
FLC_emptyvectorcontrol_H3K4me1 ×5 FLC_MNX1_H3K4me1 ×5 FLC_emptyvectorcontrol_H3K4me3 ×5 FLC_MNX1_H3K4me3 ×5 FLC_emptyvectorcontrol_IgG ×5 BM_MNX1_H3K4me1 ×4 FLCcontrol_emptyvectorcontrol_H3K4me3 ×4 BM_MNX1_H3K4me3 ×4 +5 more

Supports a between-group comparison across 55 samples.

How we read this: 13 replicated groups read from 55 sample titles; they account for 55 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

+ 15 more — browse all 55 samples with per-sample file links →

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