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The Peptide Genomic Therapy Increases Antibacterial Immunity and Survival in Sepsis by Reprograming the Gene Orthologs of Human Immunodeficiencies in the Spleen and Lungs

GSE308045 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2025/10/31 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 samples: 3 × Sham + Saline, biol vs 3 × CM + Saline, biol vs 3 × CM + NTCI, biol vs 2 × CM + Mero, biolGroups 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
The peptide genomic therapy increases antibacterial immunity and survival in sepsis by reprograming the gene orthologs of human immunodeficiencies in the spleen and lungsFrontiers in immunology · 2025
Summary (written by the submitters)
Sepsis is a life-threatening complication of infections afflicting 49 million patients worldwide with 11 million sepsis-related deaths. In the USA, this growing public health problem concerns 1.7 million adult and pediatric patients. An estimated 1 million patients with asplenia or hyposplenia are particularly vulnerable to sepsis. As the spleen is a major blood-filtering immune organ, we show that its anti-bacterial immunity was increased 9 times by the Peptide Genomic Therapy with the cell-penetrating Nuclear Transport Checkpoint Inhibitor (NTCI) in the preclinical model.
Read the full summary ↓
Likewise, the antibacterial immunity was increased in the lungs, the frequent site of bacterial infections in spleen-compromised hosts. We also show that the survival increased from 44% to 80%, when the NTCI was added to the antibiotic therapy. Strikingly, the NTCI reprogrammed the expression of the gene orthologs responsible for human immunodeficiencies, aka the Inborn Errors of Immunity (IEI). Among them, the 227 IEI genes were reprogrammed in the spleen and 215 in the lungs, while the mediators of inflammation in blood (IL-6, IL-10, TNFα, Interferon γ, and MCP1) were normalized. Thus, the antibacterial immunity in the spleen and lungs was dramatically increased by the Peptide Genomic Therapy with the NTCI that almost doubled survival in sepsis when added to the antibiotic.
Published in
The peptide genomic therapy increases antibacterial immunity and survival in sepsis by reprograming the gene orthologs of human immunodeficiencies in the spleen and lungs
Qiao H, Zienkiewicz J, Liu Y et al. · Frontiers in immunology 2025 · PMID 41229427 · doi:10.3389/fimmu.2025.1635081
This dataset
Open GSE308045 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 GSE308045_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 PRJNA1328647 and SRA study SRP620435. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41229427) ↗
Study design
3 × Sham + Saline, biol vs 3 × CM + Saline, biol vs 3 × CM + NTCI, biol vs 2 × CM + Mero, biol

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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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