GEO series

The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapy

GSE293137 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2025/04/04 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 14 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: 14 samples: 5 × EC, Cesium TBI, vs 4 × EC, non-treated, vs 3 × EC, IgG non-targeted radioimmunotherapy, vs 2 × EC, CD45-targeted radioimmunotherapy,Groups 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: The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapyBlood advances · 2026

Summary (written by the submitters)

Radioimmunotherapy (RIT) is used to treat patients with hematological malignancies known to infiltrate the bone marrow (BM) microenvironment. RIT uses target-specific monoclonal antibodies stably conjugated to radionuclides to deliver cytotoxic radiation to cells of interest. While RIT is effective at delivering radiation to cancer cells, normal tissue is also exposed to radiation upon RIT, the consequences of which are largely unknown.

Read the full summary ↓

Here, we studied the cellular and molecular effects of CD45-targeted astatine-211 (211At) RIT, IgG non-targeted 211At RIT, and Cesium-137 total-body irradiation (TBI) on hematopoietic cells and their BM niche in wild-type immunocompetent mice. Relative to non-targeted RIT or TBI, CD45-targeted RIT significantly delayed hematopoietic regeneration overall in the peripheral blood and BM and reduced hematopoietic stem/progenitor cell recovery and colony-forming ability. While BM endothelial cells (ECs) do not express the CD45 antigen, CD45-targeted RIT significantly depleted BM ECs compared to non-targeted RIT or TBI. RNA sequence analysis revealed significantly different transcriptomic profiles of BM ECs from CD45-RIT-treated mice compared to non-targeted RIT or TBI. ECs from CD45-RIT-treated mice, but not TBI or IgG-RIT-treated mice, were transcriptionally enriched for TGFβ, NOTCH, and IFNα signaling pathways compared to untreated mice. Collectively, our study indicates that CD45-targeted RIT severely impacts hematopoietic and EC niche recovery compared to non-targeted approaches. Future studies are required to determine the long-term consequences of such RIT-driven effects on BM niche physiology and how BM niche reprogramming by RIT affects cancer cells.

Published in

The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapy

Hagen MW, Setiawan NJ, Dexter S et al. · Blood advances 2026 · PMID 41671449 · doi:10.1182/bloodadvances.2025017065

This dataset

Open GSE293137 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 GSE293137_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 PRJNA1242868 and SRA study SRP573670. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41671449) ↗

Study design

5 × EC, Cesium TBI, vs 4 × EC, non-treated, vs 3 × EC, IgG non-targeted radioimmunotherapy, vs 2 × EC, CD45-targeted radioimmunotherapy,

Supports a case/control comparison: 4 samples read as cases, 3 as controls.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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

GSM8877230 EC, Cesium TBI, rep 1 EC, Cesium TBI,
GSM8877231 EC, non-treated, rep 1 EC, non-treated,
GSM8877232 EC, non-treated, rep 2 EC, non-treated,
GSM8877233 EC, Cesium TBI, rep 3 EC, Cesium TBI,
GSM8877234 EC, non-treated, rep 3 EC, non-treated,
GSM8877235 EC, non-treated, rep 4 EC, non-treated,
GSM8877236 EC, Cesium TBI, rep 4 EC, Cesium TBI,
GSM8877237 EC, Cesium TBI, rep 5 EC, Cesium TBI,
GSM8877238 EC, Cesium TBI, rep 6 EC, Cesium TBI,
GSM8877239 EC, IgG non-targeted radioimmunotherapy, rep 1 EC, IgG non-targeted ra…
GSM8877240 EC, IgG non-targeted radioimmunotherapy, rep 2 EC, IgG non-targeted ra…
GSM8877241 EC, IgG non-targeted radioimmunotherapy, rep 3 EC, IgG non-targeted ra…
GSM8877242 EC, CD45-targeted radioimmunotherapy, rep 1 EC, CD45-targeted radio…
GSM8877243 EC, CD45-targeted radioimmunotherapy, rep 2 EC, CD45-targeted radio…

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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.