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.
How this study connects
Role on claims
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The composition difference is the durable finding; the specific gene list is not.
Immune cell composition differs in sepsis, but small-sample transcriptomics identifies hub genes unreliably. Single-cell and microarray analysis found six t-SNE clusters and seven hub genes (CD28, CD3D, CD2, CD4, IL7R, LCK, CD3E), six of them reduced in sepsis — from ten sepsis arrays, where hub-gene algorithms overfit.
Evidence for the claim as stated.
These studies subdivide critical illness with very different evidentiary weight. Macrophage activation-like syndrome is defined by a specific threshold and validated in a second cohort, while the sepsis transcriptomic clusters rest on ten arrays with algorithms the authors acknowledge overfit small public datasets.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
These studies subdivide critical illness with very different evidentiary weight. Macrophage activation-like syndrome is defined by a specific threshold and validated in a second cohort, while the sepsis transcriptomic clusters rest on ten arrays with algorithms the authors acknowledge overfit small public datasets.
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
Structured fields used in claim comparison tables when every cited study has a complete layer.
Inspect source passages
Which immune genes drop in sepsis single-cell maps?
These passages occur verbatim in the stored paper text. They support the points listed below; they do not verify every statement in the explanation.
GSE28750 included 10 sepsis and 20 normal samples.
There was a total of 10 sepsis samples and 20 normal samples in GSE28750 dataset
61 DEGs were obtained with limma.
A total of 61 differentially expressed genes (DEGs) between sepsis samples and normal samples were obtained through the ‘limma’ package
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.
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