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Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in acute myeloid leukaemia [human RNA-seq]

GSE295647 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/06/16 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 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.
Summary (written by the submitters)
Understanding the molecular pathogenesis of MLL fusion oncoproteins (MLL-FP) has spawned epigenetic therapies that have improved clinical outcomes in this and other molecular subtypes of acute myeloid leukaemia (AML). Using genetic and pharmacological approaches, we define the individual and combined contribution of KAT6A, KAT6B and KAT7, in range of AML models.
Read the full summary ↓
Whilst inhibition of KAT6A/B is efficacious in some pre-clinical models, simultaneous targeting of KAT7, with the novel inhibitor PF-9363, increases the therapeutic efficacy. KAT7 interacts with Menin and the MLL complex and is co-localised at chromatin to co-regulate the oncogenic transcriptional program. Focussing on MLL-FP AML, we show that inhibition of KAT6/KAT7 provides an orthogonal route to targeting Menin to disable the transcriptional activity of the MLL-FP. Consequently, combined inhibition rapidly evicts the MLL-FP from chromatin, potently represses oncogenic transcription and overcomes primary resistance to Menin inhibitors. Moreover, PF-9363 or genetic depletion reveals that KAT7 remains an important targetable dependency in acquired genetic/non-genetic resistance to Menin inhibition. These data provide the molecular rationale for rapid clinical translation of combination therapy, particularly in MLL-FP AML.
This dataset
Open GSE295647 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 GSE295647_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 PRJNA1255519 and SRA study SRP581364. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
MV411_MEN1-M327I_DMSO ×3 MV411_MEN1-M327I_PF9363_2.5uM_48h ×3 MV411_MEN1-M327I_SNDX5613_100nM_48h ×3 MV411_MEN1-WT_DMSO ×3 MV411_MEN1-WT_PF9363_2.5uM_48h ×3 MV411_MEN1-WT_SNDX5613_100nM_48h ×3 OCI-AML2_resistant_DMSO ×3 OCI-AML2_resistant_PF9363_2.5uM_48h ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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