Critical care
Which immune genes drop in sepsis single-cell maps?
Open access · cc by · source: Europe PMC
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.
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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Key findings
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.
Methodology
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.
Limitations
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.
How this study connects
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