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Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination
Lavida R K Rogers1,2, Gustavo de Los Campos2,3,4, George I Mias2,5
1Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.
Frontiers in Immunology
|December 3, 2019
Summary
This study analyzed gene expression differences between influenza infection and vaccination. It identified key genes and pathways involved in immune response, with potential for improving influenza vaccines across different ages and sexes.
Area of Science:
- Immunology
- Genetics
- Bioinformatics
Background:
- Influenza is a widespread communicable disease with higher risks for vulnerable populations.
- Understanding gene expression in response to influenza infection and vaccination is crucial for public health.
- Previous studies have not comprehensively analyzed gene expression variability due to age and sex in influenza.
Purpose of the Study:
- To identify differentially expressed genes in influenza disease compared to influenza vaccination.
- To investigate the influence of age and sex on gene expression related to influenza.
- To uncover key gene signatures and pathways for influenza infection and vaccination.
Main Methods:
- Conducted a meta-analysis of 18 publicly available microarray datasets (3,481 samples).
- Pre-processed data using R packages and applied Box-Cox transformation.
- Utilized linear mixed effects models and likelihood ratio tests (LRT) for differential gene expression analysis, with Bonferroni correction and quantile filtering.
Main Results:
- Identified 4,889 statistically significant genes related to influenza disease.
- Gene enrichment analysis revealed involvement of innate immune response, viral processes, and NF-kappa B signaling.
- Discovered 978 genes associated with influenza infection and vaccination, respectively, and identified significant disease-age (907 genes) and disease-sex (48 genes) interactions.
Conclusions:
- The meta-analysis successfully identified key gene signatures and pathways for influenza infection and vaccination.
- Specific genes influenced by age and sex in relation to influenza were pinpointed.
- Findings offer potential for enhancing current influenza vaccines and developing universal vaccination strategies.
