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Neurodevelopmental origins of structural and psychomotor defects in CXCR4-linked primary immunodeficiency

GSE266671 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2025/06/06 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 2 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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
2 samples
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
Neurodevelopmental origins of structural and psychomotor defects in CXCR4-linked primary immunodeficiencyNeuron · 2025
Summary (written by the submitters)
Primary immunodeficiency diseases (PIDDs) encompass a range of congenital disorders that adversely influence both innate and adaptive immune systems. While individuals diagnosed with PIDDs often exhibit elevated levels of emotional distress and neuropsychological challenges - such as depression and anxiety - the neurobiological underpinnings linking genetic alterations in PIDDs to their neurological manifestations have not been so far explored.
Read the full summary ↓
Here, by mapping the expression of PIDD genes in transcriptional datasets sampling the human brain across multiple areas and ages, we identified a notable regional enrichment in the cerebellum, which encompasses neuronal and glial subtypes, extending beyond the immune cells. Aiming at elucidating the impact of PIDD genetic alterations on brain development, we focus on WHIM syndrome, caused by CXCR4 mutations. Consistently with clinical reports on WHIM patients, magnetic resonance imaging and histological analysis performed on WHIM mouse model showed distinct cerebellar foliation deficits associated with mild motor impairment and anxiety-like behavior from early development. Despite the restricted expression of CXCR4 in rhombic lip-derived progenitors, single-cell profiling uncovered a pervasive transcriptional alteration across various cerebellar cell types, well beyond the cell-autonomous effects of the mutation on the granule lineage. Significant downregulation of genes involved in dendrite branching and axonal elongation molecularly defined the reduced arborization observed in WHIM Purkinje cells, which is associated with altered lobule-specific frequency patterns by high-density multielectrode array recordings. In utero intraventricular administration of CXCR4 antagonist AMD3100 - currently in clinical trials in patients - successfully rescued both morphological and behavioral defects. This unravels a direct effect of the WHIM-associated Cxcr4-Cxcl12 axis on compromised cerebellar assembly of motor and anxiety-associated circuits. Our findings underscore the contribution of the cerebellum to emotional distress while emphasizing the importance of considering neurological implications in the management of PIDDs.
Published in
Neurodevelopmental origins of structural and psychomotor defects in CXCR4-linked primary immunodeficiency
Demenego G, Mancinelli S, Borreca A et al. · Neuron 2025 · PMID 40482638 · doi:10.1016/j.neuron.2025.05.016
This dataset
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.

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 GSE266671_RAW.tar (it can run to tens of gigabytes).

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.

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 PRJNA1108246 and SRA study SRP505922. Searching any of these in the dataset finder brings you back here.

Samples in this study

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