GEO series

PDE4B deficiency aids macrophage Trojan horses to transfer Cryptococcus neoformans into the brain

GSE287392 Mus musculus (mouse) Single-cell RNA-seq 1 samples Submitted 2025/11/06 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 1 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: 1 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: PDE4B deficiency aids macrophage differentiation and contributes to Cryptococcus neoformans brain infectionPLoS pathogens · 2026

Summary (written by the submitters)

Cryptococcal meningitis (CM) is a fatal compliation. Macrophages work as Trojan horses transferring Cryptococcus neoformans (C. neoformans) into the brain. Mechanisms for C. neoformans Trojan horses are largely elusive. In this study, we performed scRNA-Seq on immune cells infiltrated into the brain in a murine model of CM. Bioinformatics analysis reveals that phosphodiesterase 4B (PDE4B) ranks top in regulating macrophage Trojan horses.

Read the full summary ↓

Melanin, a virulence factor for Cn, decreased PDE4B in macrophages. PDE4B inhibitor promoted the Cn Trojan horse across the blood-brain-barrier (BBB) in vitro and in vivo. As similar, PDE4B knockout increased fungi burden in the brain, which is, at least partially, rescued by macrophages depletion. In contrast, PDE4B activation diminished C. neoformans brain infection. Mechanistically, PDE4B inhibition increased CXCR4 and CCR7 on C. neoformans macrophage Trojan horses, a process regulated by the cAMP/PKA signaling pathway. Dexamethasone, commonly used to treat Pneumocystis infections in AIDS patients, significantly decreased PDE4B expression in macrophages. Overall, this study reveals that PDE4B plays a crucial role in C. neoformans macrophage Trojan horses and serves as a potential therapeutic target for CM.

Published in

PDE4B deficiency aids macrophage differentiation and contributes to Cryptococcus neoformans brain infection

Gong Y, Wang T, Chen X et al. · PLoS pathogens 2026 · PMID 41805786 · doi:10.1371/journal.ppat.1014040

This dataset

Open GSE287392 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 GSE287392_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 PRJNA1212550 and SRA study SRP558271. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41805786) ↗

Samples in this study

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+ 1 more — browse all 1 samples with per-sample file links →

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