GEO series

SLC29A3 supports phagosomal antibacterial signaling, and promotes autophagy by activating TRPML1 in mouse dendritic cells

GSE294902 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/12/17 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 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: The lysosomal carrier SLC29A3 supports antibacterial signaling, and promotes autophagy by activating TRPML1 in murine dendritic cellsProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

Solute carrier (SLC)29A3 exports nucleosides from lysosomes into the cytosol, maintaining solute homeostasis and providing metabolic intermediates for cellular processes. Loss-of-function mutations in SLC29A3 cause H syndrome, characterized by histiocytosis, hyperinflammation and immunodeficiency. While dysfunctions in several cell types contribute to H syndrome and to SLC29A3 deficiency in mice, the mechanisms driving hyperinflammation and immunodeficiency are incompletely understood.

Read the full summary ↓

Notably, the possible role played by dendritic cells (DCs), the most efficient antigen presenting cells and the main link between innate and adaptive immune responses, remains unknown. We show that, in murine DCs, SLC29A3 is recruited to phagosomes after bacterial capture, maintains phagosomal pH homeostasis, and ensures optimal phagosomal signaling to the production of IL-6, IL-12, and CCL-22. In addition, SLC29A3 promotes Ag presentation on MHC-II molecules to initiate adaptive immune responses. Notably, SLC29A3 supports the activity of the lysosomal calcium channel TRPML1, promoting transcription factor TFEB nuclear translocation and inducing autophagy, a major anti-inflammatory mechanism. Overexpression of human SLC29A3, but not the transport mutant G437R, in SLC29A3-deficient murine DCs restores cytokine production in response to bacteria phagocytosis, suggesting that SLC29A3 transport activity is required to drive anti-bacterial phagosomal signaling. Our data suggest that SLC29A3 plays a dual role in supporting immune function by promoting effective anti-microbial signaling and Ag presentation in DCs and inducing autophagy to control inflammation. Our findings also uncover a novel TRPML1-dependent mechanism by which SLC29A3 activates TFEB and suggest that defects in phagosomal signaling, TFEB activation and autophagy may contribute to immunodeficiency and hyperinflammation in SLC29A3 disorders.

Published in

The lysosomal carrier SLC29A3 supports antibacterial signaling, and promotes autophagy by activating TRPML1 in murine dendritic cells

Netting DJ, López-Haber C, Hutchins Z et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 41284877 · doi:10.1073/pnas.2511539122

This dataset

Open GSE294902 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 GSE294902_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 PRJNA1252020 and SRA study SRP579408. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41284877) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

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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.