GEO series

The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages

GSE243269 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/09/30 Platform GPL21103

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: 3 × Fl/Fl BMDM, 0h LPS, vs 3 × Fl/Fl BMDM, 5h LPS, vs 3 × KO BMDM, 0h LPS, vs 3 × KO BMDM, 5h LPS,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: Myeloid-specific HNRNPA2B1 deficiency disrupts macrophage function and in vivo responsesJournal of immunology (Baltimore, Md. : 1950) · 2025

Summary (written by the submitters)

Heterogeneous nuclear ribonucleoprotein A2B1 (HNRNPA2B1) is a well known RNA binding protein but the mechanisms by which it contributes to innate immune gene regulation is poorly understood. Here we report that HNRNPA2B1 functions in macrophages to regulate IFNG signaling through alternative splicing of the IFNG receptor. Specific deletion of HNRNPA2B1 in macrophages using our newly developed conditional mice crossed to LysMCre resulted in altered cytokine responses in both an endotoxic shock model and following Salmonella infection.

Read the full summary ↓

Interestingly, while HNRNPA2B1 can function as a viability gene, we observed increased macrophage and neutrophil numbers in the KO mice following LPS induced endotoxic shock. HNRNPA2B1 KO mice were more susceptible to Salmonella and Mycobacterium Tuberculosis infections and failed to effectively clear the pathogens. Mechanistically, loss of HNRNPA2B1 resulted in an increase in No-GO transcripts of the IFNG receptor (Ifngr) leading to lower expression of the receptor at the cell surface impacting the downstream IFNG signaling cascade. Collectively, our data highlights an important role for HNRNPA2B1 in regulating IFNG signaling in macrophages.

Published in

Myeloid-specific HNRNPA2B1 deficiency disrupts macrophage function and in vivo responses

Salih MM, Weindel CG, Malekos E et al. · Journal of immunology (Baltimore, Md. : 1950) 2025 · PMID 40414614 · doi:10.1093/jimmun/vkaf073

This dataset

Open GSE243269 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 GSE243269_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 PRJNA1017506 and SRA study SRP460596. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40414614) ↗

Study design

3 × Fl/Fl BMDM, 0h LPS, vs 3 × Fl/Fl BMDM, 5h LPS, vs 3 × KO BMDM, 0h LPS, vs 3 × KO BMDM, 5h LPS,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM7782538 Fl/Fl BMDM, 0h LPS, rep1 Fl/Fl BMDM, 0h LPS,
GSM7782539 Fl/Fl BMDM, 0h LPS, rep2 Fl/Fl BMDM, 0h LPS,
GSM7782540 Fl/Fl BMDM, 0h LPS, rep3 Fl/Fl BMDM, 0h LPS,
GSM7782541 Fl/Fl BMDM, 5h LPS, rep1 Fl/Fl BMDM, 5h LPS,
GSM7782542 Fl/Fl BMDM, 5h LPS, rep2 Fl/Fl BMDM, 5h LPS,
GSM7782543 Fl/Fl BMDM, 5h LPS, rep3 Fl/Fl BMDM, 5h LPS,
GSM7782544 KO BMDM, 0h LPS, rep1 KO BMDM, 0h LPS,
GSM7782545 KO BMDM, 0h LPS, rep2 KO BMDM, 0h LPS,
GSM7782546 KO BMDM, 0h LPS, rep3 KO BMDM, 0h LPS,
GSM7782547 KO BMDM, 5h LPS, rep1 KO BMDM, 5h LPS,
GSM7782548 KO BMDM, 5h LPS, rep2 KO BMDM, 5h LPS,
GSM7782549 KO BMDM, 5h LPS, rep3 KO BMDM, 5h LPS,

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