← BioTransfer GEO Dataset Finder
GEO series

Leukaemia cell intrinsic and extrinsic factors cooperate to facilitate the survival and proliferation of KMT2A-rearranged B-ALL in the CNS niche.

GSE280505 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2026/04/12 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × BM LSK vs 4 × CNS LSK vs 4 × BM LK/CLP vs 4 × CNS LK/CLPGroups 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
miR-93-mediated PTEN suppression and CNS-specific T cell exhaustion shape the leukemia niche in infant KMT2A::AFF1+ B-ALLCell reports · 2026
Summary (written by the submitters)
Infant B-cell acute lymphoblastic leukaemia (B-ALL) is a rare, aggressive entity characterised by KMT2A-rearrangements and poor outcomes. One of the unique features of KMT2A-rearranged infant ALL contributes to these poor outcomes is a particularly high rate of central nervous system (CNS) involvement. In this study we used an immune competent KMT2A-AFF1+ infant B-ALL murine model (https://doi.org/10.1182/blood.2020006610) to explore the cell-intrinsic and cell-extrinsic mechanisms that underpin this clinically significant complication.
Read the full summary ↓
We show novel functional impacts on leukaemia propagating cells (LPCs) following exposure to the CNS niche which results in unique leukaemia repopulation dynamics. Transcriptomic and immune cell profiling comparisons by niche showed differences in the immune microenvironment between the CNS and bone marrow (BM) niches. We observe the CNS niche demonstrates supressed T cell and macrophage activity which may be part of a wider CNS niche-specific immune escape mechanism. Our transcriptomic comparisons by niche also led us to explore the role of PI3K pathway activation in the propagation of leukaemia cells within the CNS niche. We identify miR-93 as a possible master regulator of this process. The importance of miR-93 is emphasised as it is shown to be upregulated in CNS leukaemia cells across multiple murine KMT2A-AFF1 B-ALL model systems and in primary KMT2A-AFF1 B-ALL patient samples. We conclude by showing impaired CNS engraftment of leukaemia cells upon miR-93 knockdown, cementing its importance in CNS leukaemia biology.
Published in
miR-93-mediated PTEN suppression and CNS-specific T cell exhaustion shape the leukemia niche in infant KMT2A::AFF1+ B-ALL
Duguid A, Malouf C, Leah T et al. · Cell reports 2026 · PMID 42139054 · doi:10.1016/j.celrep.2026.117353
This dataset
Open GSE280505 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 GSE280505_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 PRJNA1178723 and SRA study SRP541655. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42139054) ↗
Study design
4 × BM LSK vs 4 × CNS LSK vs 4 × BM LK/CLP vs 4 × CNS LK/CLP

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.