GEO series

Single-cell profiling of the human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia

GSE309534 Homo sapiens (human) Single-cell RNA-seq 10 samples Submitted 2025/09/29 Platform GPL30173

At a glance

Single-cell RNA-seq · human · 10 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 10 samples: 10 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.
Paper: Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasiaNature communications · 2025

Summary (written by the submitters)

Somatic mutations in hematopoietic stem/progenitor cells (HSPCs) can lead to clonal hematopoiesis of indeterminate potential (CHIP) and progression to myelodysplastic syndromes (MDS). Using single-cell and anatomical profiling of a large cohort of human bone marrow (BM), we show that the HSPC BM niche in CHIP and MDS is undergoing inflammatory remodeling.

Read the full summary ↓

This includes loss of CXCL12⁺ adipogenic stromal cells and the emergence of a distinct population of inflammatory mesenchymal stromal cells (iMSCs), which arise in CHIP and become more prevalent in MDS. Functional studies in primary BM HSPC-MSC co-cultures reveals that healthy aged and CHIP HSPCs activate stromal support, while MDS HSPCs fail to do so. In contrast, MDS blasts further suppress HSPC support and trigger inflammation, indicating disease-stage-specific stromal disruption. In parallel, we show that iMSCs retain partial support and angiogenic potential in MDS, coinciding with expanded BM vasculature. Additionally, we identify IFN-responsive T cells that preferentially interact with iMSCs, potentially reinforcing local inflammation. These findings position iMSCs as central mediators of early BM niche dysfunction and potential therapeutic targets for intercepting pre-malignant hematopoiesis.

Published in

Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia

Prummel KD, Woods K, Kholmatov M et al. · Nature communications 2025 · PMID 41253811 · doi:10.1038/s41467-025-65803-y

This dataset

Open GSE309534 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 GSE309534_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1336221 and SRA study SRP629699. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41253811) ↗

Study design

10 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 10 sample titles: 10 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

GSM9268801 Stroma Control3+CHIP1 multiplexed
GSM9268802 T cells + HSPC CHIP2+MDS4 multiplexed
GSM9268803 Stroma Control1+MDS1 multiplexed
GSM9268804 T cells + HSPC Control1+MDS1 multiplexed
GSM9268805 T cells + HSPC Control3+CHIP1 multiplexed
GSM9268806 Stroma CHIP2+MDS4 multiplexed
GSM9268807 Stroma Control2+CHIP1+MDS3 multiplexed
GSM9268808 T cells + HSPC Control2+CHIP1+MDS3 multiplexed
GSM9268809 Stroma CHIP2+MDS2+MDS4 multiplexed
GSM9268810 T cells + HSPC CHIP2+MDS2+MDS4 multiplexed

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