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Updated: Feb 3, 2026
RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
Published on: February 13, 2013
RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ
Marta Pulido-Salgado1,2, Jose M Vidal-Taboada3,4,5, Gerardo Garcia-Diaz Barriga6,2
1Department of Biomedical Sciences, Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain.
Abstract:
Microglia, the main resident immune cells in the CNS, are thought to participate in the pathogenesis of various neurological disorders. LPS and LPS + IFNγ are stimuli that are widely used to activate microglia. However, the transcriptomic profiles of microglia treated with LPS and LPS + IFNγ have not been properly compared. Here, we treated murine primary microglial cultures with LPS or LPS + IFNγ for 6 hours and then performed RNA-Sequencing. Gene expression patterns induced by the treatments were obtained by WGCNA and 11 different expression profiles were found, showing differential responses to LPS and LPS + IFNγ in many genes. Interestingly, a subset of genes involved in Parkinson's, Alzheimer's and Huntington's disease were downregulated by both treatments. By DESeq analysis we found differentially upregulated and downregulated genes that confirmed LPS and LPS + IFNγ as inducers of microglial pro-inflammatory responses, but also highlighted their involvement in specific cell functions. In response to LPS, microglia tended to be more proliferative, pro-inflammatory and phagocytic; whereas LPS + IFNγ inhibited genes were involved in pain, cell division and, unexpectedly, production of some inflammatory mediators. In summary, this study provides a detailed description of the transcriptome of LPS- and LPS + IFNγ treated primary microglial cultures. It may be useful to determine whether these in vitro phenotypes resemble microglia in in vivo pathological conditions.
Insights
This study compares the effects of lipopolysaccharide (LPS) and LPS plus interferon-gamma (IFNγ) on microglia. Results reveal distinct transcriptomic profiles, impacting inflammatory and cellular functions, offering insights into neurological disease mechanisms.
Area of Science:
- Neuroscience
- Immunology
- Genomics
Background:
- Microglia are key immune cells in the central nervous system (CNS) implicated in neurological disorders.
- Lipopolysaccharide (LPS) and LPS plus interferon-gamma (IFNγ) are common stimuli for activating microglia in vitro.
- Comparative transcriptomic analysis of microglia treated with LPS versus LPS + IFNγ is lacking.
Purpose of the Study:
- To comprehensively compare the transcriptomic profiles of primary microglial cultures stimulated with LPS and LPS + IFNγ.
- To identify differential gene expression patterns and cellular functions affected by these two activation stimuli.
- To investigate the potential relevance of observed transcriptomic changes to neurodegenerative diseases.
Main Methods:
- Primary murine microglial cultures were treated with LPS or LPS + IFNγ for 6 hours.
- RNA-Sequencing was performed to analyze gene expression.
- Weighted Gene Co-expression Network Analysis (WGCNA) and DESeq analysis were employed to identify gene expression patterns and differentially expressed genes.
Main Results:
- Eleven distinct gene expression profiles were identified, highlighting differential responses to LPS and LPS + IFNγ.
- Both treatments upregulated genes associated with microglial pro-inflammatory responses.
- LPS treatment promoted proliferation, inflammation, and phagocytosis, while LPS + IFNγ inhibited genes related to pain, cell division, and some inflammatory mediators. Notably, genes linked to Parkinson's, Alzheimer's, and Huntington's diseases were downregulated by both stimuli.
Conclusions:
- This study provides a detailed transcriptomic comparison of LPS- and LPS + IFNγ-activated primary microglia.
- The findings reveal distinct functional responses to different activation stimuli, impacting inflammatory and cellular processes.
- The results offer a valuable resource for understanding microglial roles in neurological conditions and validating in vitro findings with in vivo pathological states.
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