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Mixed-lineage leukemia cells undergo unique adaptations in the CNS niche

GSE303671 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/03/05 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
36 samples: 9 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Mixed-lineage leukemia cells undergo unique adaptations in the CNS nicheExperimental hematology · 2026
Summary (written by the submitters)
KMT2A-rearranged (KMT2A-r) infant leukaemia can present as a lymphoid, myeloid or mixed lineage leukaemia and frequently involves the central nervous system (CNS), yet the impact of this lineage diversity and plasticity on CNS involvement remains poorly understood. Using a fully murine model of KMT2A-AFF1+ mixed lineage infant leukaemia, we investigated how the CNS niche influences the phenotype and function of leukaemia propagating cells (LPC).
Read the full summary ↓
Previously defined bone marrow (BM)-derived LPCs were transplanted and shown to engraft the CNS, although not equally; LK/CLP cells were consistently underrepresented in the niche. Transplants of CNS-derived LPCs, modelling relapse, demonstrated reduced systemic repopulation capacity, with many recipients exhibiting stable long-term engraftment without developing overt leukaemia, a phenomenon not observed in BM-derived transplants. Transcriptomic profiling of matched CNS- and BM-derived LPCs revealed enrichment of pathways involved in hypoxia, lipid and cholesterol homeostasis, and inflammatory signalling. Notably, LPC subsets that successfully adapted to the CNS niche upregulated lipid and fatty acid metabolic programmes. CNS-derived LPCs showed increased expression of genes involved in T cell immune modulation, suggesting a skew to a more immunosuppressive environment. These findings indicate that the CNS niche imposes lasting metabolic, functional, and immunological constraints on leukemic cells, impairing their ability to reestablish systemic disease. We show that the CNS niche imposes selective pressures and causes functional reprogramming of mixed lineage LPCs, affecting their systemic repopulation capacity and, we hypothesise, immune cell interactions. We further believe this study has relevance to primary mixed lineage infant leukaemia and, increasingly important, lineage-switched infant leukaemia.
Published in
Mixed-lineage leukemia cells undergo unique adaptations in the CNS niche
Duguid A, Malouf C, Nitsche L et al. · Experimental hematology 2026 · PMID 41371538 · doi:10.1016/j.exphem.2025.105347
This dataset
Open GSE303671 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 GSE303671_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 PRJNA1297052 and SRA study SRP603653. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41371538) ↗
Study design
9 conditions, mostly with about 4 replicates each
mixed_leukaemia_BM_HSC ×4 mixed_leukaemia_CNS_HSC ×4 mixed_leukaemia_BM_LMPP ×4 mixed_leukaemia_CNS_LMPP ×4 mixed_leukaemia_BM_LK ×4 mixed_leukaemia_CNS_LK ×4 control_BM_HSC ×4 control_BM_LMPP ×4 +1 more

Supports a between-group comparison across 36 samples.

How we read this: 9 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
Datasets on a similar topic

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