Which immune genes drop in sepsis single-cell maps?

Open paper intelligence

In GSE28750 (10 sepsis vs 20 controls), 61 DEGs and single-cell t-SNE (T/NK/monocyte/megakaryocyte/DC/B cells) pointed to seven T-cell hub genes; six of them were lower in sepsis, with animal assays as follow-up.

Source

Single-cell transcriptomics reveals immune infiltrate in sepsis

Tu X, Huang H, Xu S, et al. · Frontiers in pharmacology · 2023

doi.org/10.3389/fphar.2023.1133145 Read the full paper ↗21 citationscc by

Study at a glance

Design: Computational / modelling — GEO GSE28750 bulk microarray (10 sepsis vs 20 controls) plus single-cell clustering, hub-gene network algorithms, and follow-up animal immunoassays
N: N=30 · GSE28750: 10 sepsis and 20 normal samples; 61 DEGs; 7 hub genes; plus in vivo animal validation assays
Population: Public human GEO sepsis vs control transcriptomes (GSE28750) with single-cell maps and animal immune-factor assays
Outcome: Differentially expressed and hub immune genes (CD28, CD3D, CD2, CD4, IL7R, LCK, CD3E) and immune-cell cluster shifts in sepsis

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What they did

Downloaded GEO data, called DEGs with limma on GSE28750, clustered single-cell profiles with Seurat t-SNE into six immune lineages, intersected immune genes, and ranked hubs with MCC/MNC/DMNC, then ran Western blot, flow, ELISA, and qPCR in animals.

What they found

61 DEGs; after stricter microarray filters, 599 genes up and 599 down. Six t-SNE clusters. Seven hubs (CD28, CD3D, CD2, CD4, IL7R, LCK, CD3E); six (all but CD2 in the lower-expression list) were reduced in sepsis, with immune-cell composition differing from controls.

The limits

What it doesn't show

n=10 sepsis arrays cannot define treatment targets; hub-gene algorithms overfit small GEO sets, and animal assays do not prove the same network in human ICU sepsis.

Key terms

Sepsis: Life-threatening dysregulated response to infection with high morbidity and mortality.
GSE28750: GEO Affymetrix dataset with 10 sepsis and 20 normal samples.
t-SNE/Seurat: Single-cell embedding used to show six immune-cell clusters.
Hub genes: CD28, CD3D, CD2, CD4, IL7R, LCK, CD3E ranked by MCC/MNC/DMNC.
limma: R package used to call differentially expressed genes.
DEG: Differentially expressed gene; 61 between sepsis and normal in the abstract analysis.

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GSE28750 samples were:

Common questions

GEO sample sizes?

10 sepsis and 20 normal samples in GSE28750.

How many abstract DEGs?

61 between sepsis and normal.

Hub genes?

CD28, CD3D, CD2, CD4, IL7R, LCK, and CD3E.

Were hubs up in sepsis?

Six of them were lower in sepsis samples.