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Human iPSC-Derived Mononuclear Phagocytes Improve Cognition and Neural Health across Multiple Mouse Models of Aging and Alzheimer's Disease

GSE220548 Mus musculus (mouse) Single-nucleus RNA-seq 15 samples Submitted 2025/09/10 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 15 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
15 samples: 5 × Mouse hippocampus from young animals treated with vehicle, vs 5 × Mouse hippocampus from aging animals treated with vehicle, vs 5 × Mouse hippocampus from aging animals treated with iMPs,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
Human iPSC-Derived Mononuclear Phagocytes Improve Cognition and Neural Health across Multiple Mouse Models of Aging and Alzheimer's DiseaseAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
Summary (written by the submitters)
Young blood or plasma and young bone marrow improves cognitive function in aged animals, though the cell type responsible for these regenerative effects remains unknown. The current study used induced pluripotent stem cells (iPSCs) to assess the potential of mononuclear phagocytes as a therapeutic for age-associated cognitive decline, as iPSCs provide a source of autologous blood cells without the risk of immune rejection or graft vs.
Read the full summary ↓
host disease. Human iPSCs differentiated into mononuclear phagocytes (iMPs) were administered to aging, genetically immunocompromised NOD scid gamma mice via tail vein injection. Aging mice receiving iMP treatment showed significant improvements in behavioral tasks relying on spatial working memory and on hippocampus-dependent short-term memory. iMP treatment also had significant effects on several key neural health markers. Expression of the synaptic transporter, VGLUT1, was decreased in untreated aging mice, and levels were restored in aging mice treated with iMPs. Aging mice also had increased numbers of astrocytes and microglia, as well as decreased microglial branching, which were all reversed by iMP treatment. Profiling of the plasma via proteomics and the hippocampus via single nuclei RNA sequencing identified several pathways that may mediate the effects of iMPs. snRNA-seq analysis also revealed that iMP treatment increased a subpopulation of hippocampal mossy cells in aging mice. iPSCs offer an autologous therapy and based on a range of benefits, iPSC-derived mononuclear phagocytes are a promising new therapeutic strategy for age-associated declines in cognition and neural health.
Published in
Human iPSC-Derived Mononuclear Phagocytes Improve Cognition and Neural Health across Multiple Mouse Models of Aging and Alzheimer's Disease
Moser VA, Dimas-Harms LJ, Lipman RM et al. · Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 · PMID 40850934 · doi:10.1002/advs.202417848
This dataset
Open GSE220548 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 GSE220548_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 PRJNA910182 and SRA study SRP412042. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40850934) ↗
Study design
5 × Mouse hippocampus from young animals treated with vehicle, vs 5 × Mouse hippocampus from aging animals treated with vehicle, vs 5 × Mouse hippocampus from aging animals treated with iMPs,

Supports a between-group comparison across 15 samples.

How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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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