GEO series

Acute myeloid leukemia with mixed phenotype is characterized by stemness features with limited lineage plasticity

GSE275859 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2024/08/28 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 20 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: 20 samples: 17 distinct titles, 1 of them repeatedGroups 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)

Mixed phenotype (MP) in acute leukemias poses unique classification and management dilemmas and can be seen in entities other than de novo mixed phenotype acute leukemia (MPAL). Although WHO classification empirically recommends excluding AML with myelodysplasia related changes (AML-MRC) and therapy related AML (t-AML) with mixed phenotype (referred to as “AML-MP”) from MPAL, there is lack of studies investigating the clinical, genetic, and biologic features of AML-MP.

Read the full summary ↓

We report the first cohort of AML-MP integrating their clinical, immunophenotypic, genomic and transcriptomic features with comparison to MPAL and AML without MP. Patients with AML-MP share similar clinical and genetic features to its AML counterpart but differs from MPAL. AML-MP harbors more frequent RUNX1 mutations than AML without MP and MPAL. RUNX1 mutations or complex karyotypes did not impact the survival of MPAL patients. Unsupervised hierarchal clustering based on immunophenotype identified biologically distinct clusters with phenotype/genotype correlation and outcome differences. Furthermore, transcriptomic analysis showed an enrichment for stemness signature in AML-MP and AML without MP as compared to MPAL. Lastly, MPAL but not AML-MP often switched to lymphoid only immunophenotype after treatment. Expression of transcription factors critical for lymphoid differentiation were upregulated only in MPAL, but not in AML-MP. Our study for the first time demonstrates that AML-MP clinically and biologically resembles its AML counterpart without MP and differs from MPAL, supporting the recommendation to exclude these patients from the diagnosis of MPAL. Future studies are needed to elucidate the molecular mechanism of mixed phenotype in AML.

This dataset

Open GSE275859 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 GSE275859_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 PRJNA1153378 and SRA study SRP529155. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

17 distinct titles, 1 of them repeated

AML ×4

How we read this: Read from 20 sample titles: 17 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

GSM8486683 MPAL 1, myeloid subset
GSM8486684 MPAL 1, T subset
GSM8486685 MPAL 2, myeloid subset
GSM8486686 MPAL 2, T subset
GSM8486687 MPAL 3, myeloid subset
GSM8486688 MPAL 3, T subset
GSM8486689 MPAL 4, myeloid subset
GSM8486690 MPAL 4, T subset
GSM8486691 AML-MP 1, myeloid subset
GSM8486692 AML-MP 1, T subset
GSM8486693 AML-MP 2, myeloid subset
GSM8486694 AML-MP 2, T subset
GSM8486695 AML-MP 3, myeloid subset
GSM8486696 AML-MP 3, T subset
GSM8486697 AML-MP 4, myeloid subset
GSM8486698 AML-MP 4, T subset
GSM8486699 AML 1
GSM8486700 AML 2
GSM8486701 AML 3
GSM8486702 AML 4

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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.