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Characterization of leukemic stem cells in FLT3-ITD-positive acute myeloid leukemia

GSE254097 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2026/06/30 Platform GPL24676Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 26 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)
Topic
Acute myeloid leukemiaThis series is part of our curated briefing on it.
Samples
26 samples: 26 samples, each with a distinct title — no replicated groupsGroups 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)
Despite major treatment advances, FLT3-ITD mutated acute myeloid leukemia (FLT3-ITDmut AML) still remains an unmet clinical need. We previously showed that rare CD34/CD123/CD25/CD99+ FLT3-ITDmut leukemic progenitor cells (LPCs), may persist after induction treatment and be responsible for drug resistance and disease progression. We aimed at the functional characterization of FLT3-ITDmut LPCs, also using a NSG mouse model.
Read the full summary ↓
The transcriptomic profile of paired blasts and LPCs, purified from 13 FLT3-ITDmut AML using RNAseq showed significant upregulation of receptor tyrosine kinases pathway, primarily lymphocyte-specific protein tyrosine kinase (LCK), which also cooperates with STAT5. Interestingly, LCK upregulation was confirmed in 28 additional FLT3-ITDmut samples, suggesting a specific therapeutic vulnerability. Indeed, a clear anti-proliferative effect of the LCK inhibitor Dasatinib was detected on the FLT3-ITDmut MV4-11 cell line and 3 primary AML LPCs, together with inhibition of FLT3 and STAT5 signalling, further potentiated by the addition of Gilteritinib. Dasatinib also induced significant downregulation of ABC transporters, a well-known cause of LSCs multi-drug resistance. Sorted LPCs were then injected into conditioned NSG mice, demonstrating their potential to engraft and induce leukemia. Interestingly, after sequential passages in mice, the LPCs compartment expanded, indicating unveil of the ancestral leukemic precursor cells. In conclusions, we deeply characterized the FLT3-ITDmut LSCs compartment in AML, providing the first evidence that FLT3-ITDmut progenitors may engraft NSG mice, while maintaining the stem cell potential. Dasatinib/Gilteritinib combinations are able to target FLT3-ITDmut LSCs and may support eradication of residual leukemic cells harbinger of relapse.
This dataset
Open GSE254097 in finder → Find more human RNA-seq datasets → Acute myeloid leukemia landscape →
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 GSE254097_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 PRJNA1068553 and SRA study SRP485696. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
26 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 26 sample titles: 26 distinct titles with little repetition. 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
More Acute myeloid leukemia datasets

Search all human RNA-seq datasets in GEO →

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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.