Decoding Immune Dynamics in Pregnant Women: Key Gene Expression Changes Following Influenza Vaccination

Abstract

Pregnant women are at an increased risk of severe influenza complications, necessitating vaccination as a preventive measure. Despite World Health Organization (WHO) recommendations for influenza vaccination during pregnancy, vaccination rates remain suboptimal in many regions. This study aims to identify key differentially expressed genes (DEGs) and biological pathways modulated by influenza vaccination in pregnant women pre- and post-vaccination, contributing to improved vaccine strategies. Microarray data from gene expression omnibus GEO dataset GSE166545 was analyzed to identify DEGs in blood samples from pregnant women at three time points: pre-vaccination (Day 0) and post-vaccination (Days 0 and 1) (Days 1 and 7). DEGs were filtered using an adjusted p-value < 0.05 and |log2 fold change| ≥ 1. Protein/protein interaction (PPI) networks, hub gene identification, and pathway enrichment analyses were conducted using STRING, Cytoscape, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome databases. Hub gene validation was performed using the Human Protein Atlas (HPA) and GTEx Portal. The GSE166545 dataset analysis revealed 60 up-regulated and 12,854 down-regulated genes (Day 1 vs. 7), 55 up-regulated and 12,933 down-regulated genes (Day 0 vs. 1), and two up-regulated with no down-regulated genes (Day 0 vs. 7). Key pathways included interferon alpha/beta (IFN-γ\ β) signaling and toll-like receptor signaling (TLR). Hub genes such as GBP1, CXCL10, RSAD2, and IFI44 demonstrated robust up-regulation, correlating with enhanced immune responses. The initial observation of JCHAIN's notable up-regulation occurred on the seventh day following vaccination. Validation confirmed these genes' roles in antiviral defense mechanisms and vaccine responses. The findings reveal distinct immune response dynamics in pregnant women following influenza vaccination, highlighting potential biomarkers for vaccine efficacy. This study underscores the importance of tailored vaccine strategies to improve maternal and neonatal outcomes.

Keywords: hub genes; influenza; interferon pathway; pregnant women; transcriptomic analysis; vaccine.

Figure 1

Volcano plots depicting the distribution of all differentially expressed genes (DEGs) in (a) GSE166545: Day 0 versus Day 1, (b) GSE166545: Day 7 versus Day 0, and (c) GSE166545: Day 7 versus Day 1. Red, blue, and black colors represent up-regulated genes, down-regulated genes, and genes with no significant difference in expression, respectively.

Figure 2

Significant Reactome pathways at Days 0–1, Days 1–7, and Days 0–7 (a,c,e), respectively. KEGG pathways at Days 0–1, Days 01–7, and Days 0–7 (b,d,f), respectively, enriched with DEGs. *—p value for each pathway.

Figure 3

(a) Hub genes in the interferon alpha and beta KEGG pathway. (b) Hub genes in the interferon alpha and beta Reactome pathway.

Figure 4

(a) Analysis of protein/protein interactions and identification of hub genes for pre- and post-vaccination periods (Days 0–1). The STRING database was used to predict interactions among the 56 up-regulated and 12,958 down-regulated differentially expressed genes (DEGs) common to both microarray datasets. (b) Data analysis was conducted using the Network Analyzer plugin for Cytoscape. (c) Subsequently, the Cytohubba plugin was employed to analyze hub genes and determine the top-ranking genes (top 10 presented). Red = High up-regulation of gene expression, Orange = Moderate up-regulation, and Yellow = Low up-regulation or mild expression change.

Figure 5

(a) Analysis of protein/protein interactions and identification of hub genes for post-vaccination periods (Days 1–7). The STRING database was used to predict interactions among the 60 up-regulated and 13,092 down-regulated differentially expressed genes (DEGs) common to both microarray datasets. (b) Data analysis was conducted using the Network Analyzer plugin for Cytoscape. (c) Subsequently, the Cytohubba plugin was employed to analyze hub genes and determine the top-ranking genes (top 10 presented). Red = High up-regulation of gene expression, Orange = Moderate up-regulation, and Yellow = Low up-regulation or mild expression change.

Figure 6

(a) Analysis of protein/protein interactions and identification of hub genes for post-vaccination periods (Days 0–7). The STRING database was used to predict interactions among the 2 up-regulated and 13,158 down-regulated differentially expressed genes (DEGs) common to both microarray datasets. (b) Represents both the Network Analyzer plugin for Cytoscap and the Cytohubba plugin to analyze hub genes and determine the top-ranking genes (top 2 presented).

Figure 7

(A,B) GTEx dataset detected expression of all ten hub genes on Days (0–1) and (1–7) pre- and post-vaccination, respectively, and the two novel genes on Days (0–7) post-vaccination on the immune cells and their roles as antiviral and influenza vaccine pathways.

Figure 7

(A,B) GTEx dataset detected expression of all ten hub genes on Days (0–1) and (1–7) pre- and post-vaccination, respectively, and the two novel genes on Days (0–7) post-vaccination on the immune cells and their roles as antiviral and influenza vaccine pathways.

Figure 8

The Human Protein Atlas dataset detected expression of all ten hub genes on Days (0–1) and Days (1–7) pre- and post-vaccination, respectively, and the two novel genes on Days (0–7) post-vaccination on the immune cells and their roles as antiviral and influenza vaccine pathways.

Figure 9

(A,B) Transcriptional profiles and modular expression analysis following influenza vaccination. (A) Heatmap showing differentially expressed genes (adjusted p < 0.05) across study participants, highlighting immune-related gene expression patterns. (B) Modular expression analysis at Day 1 post-vaccination comparing previously vaccinated (PV) and non-previously vaccinated (NPV) individuals. Overexpression (red), underexpression (blue), and unchanged expression (white) are indicated. Data cited from GSE166545.