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Background <p>Inflammatory events followed by bacterial infections are related to the progression of the atherosclerosis process. The study investigated the signaling and metabolic pathways of endothelial cells (ECs), macrophages (MQs), vascular smooth muscle cells (VSMCs), and dendritic cells (DCs) after exposure to Gram-negative bacterial infections. Moreover, it aimed at cross-talking and enriching the pathways on the cellular and plaque networks.</p> Methods and Materials <p>High-throughput expression data series (<i>n</i> = 9) were selected through GEO and MAT data repositories. Upregulated differential expression genes (DEGs) were determined using R software and applied to identify the cellular signaling pathways using Enricher/Reactome tools. Then, the cell networks were visualized using the Cytoscape software and enriched by the pathways of secretory proteins identified using Gene ontology (GO).</p> Results <p>The important pathways of the Cytokines (Degree 4, <i>p</i> &lt; 6 × 10<sup>–26</sup>), and INF (Degree 4, <i>p</i> &lt; 8.6 × 10<sup>–31</sup>) in ECs, Cytokines (Degree 4, <i>p</i> &lt; 9.35 × 10<sup>–8</sup>), and GPCR (Degree 3, <i>p</i> &lt; 1.45 × 10<sup>–4</sup>) in MQs, NOTCH (Degree 6, <i>p</i> &lt; 0.027) in VSMCs, and Cytokines (Degree 4, <i>p</i> &lt; 1.45 × 10<sup>–17</sup>) in DCs were found to be activated and enriched after exposure to Gram-negative bacterial infections on the cell networks. Furthermore, the Netrin- 1 (Degree 6, <i>p</i> &lt; 0.028), and EGFR (Degree 5, <i>p</i> &lt; 0.036) pathways were activated in the intimal thick/xanthoma plaque network while the innate (Degree 9, <i>p</i> &lt; 8.9 × 10<sup>–20</sup>) and adaptive (Degree 7, <i>p</i> &lt; 4.1 × 10<sup>–12</sup>) immune systems pathways were activated in the fibrous cap atheroma plaque network.</p> Conclusion <p>The study revealed the signaling pathways after exposure to Gram-negative bacterial infections on the cell networks in the vessel microenvironment. Furthermore, the cell cross-talks exacerbated these pathways in cells and unstable plaques.</p> Clinical Trial Number <p>Not applicable.</p>

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Gram-negative bacteria activate cellular pathways in plaque microenvironment; Systems biology approach

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月24日

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  • Reza Ganjali,
  • Mohammad Elahimanesh,
  • Hamidreza Aghazadeh,
  • Mohammad Najafi

摘要

Background

Inflammatory events followed by bacterial infections are related to the progression of the atherosclerosis process. The study investigated the signaling and metabolic pathways of endothelial cells (ECs), macrophages (MQs), vascular smooth muscle cells (VSMCs), and dendritic cells (DCs) after exposure to Gram-negative bacterial infections. Moreover, it aimed at cross-talking and enriching the pathways on the cellular and plaque networks.

Methods and Materials

High-throughput expression data series (n = 9) were selected through GEO and MAT data repositories. Upregulated differential expression genes (DEGs) were determined using R software and applied to identify the cellular signaling pathways using Enricher/Reactome tools. Then, the cell networks were visualized using the Cytoscape software and enriched by the pathways of secretory proteins identified using Gene ontology (GO).

Results

The important pathways of the Cytokines (Degree 4, p < 6 × 10–26), and INF (Degree 4, p < 8.6 × 10–31) in ECs, Cytokines (Degree 4, p < 9.35 × 10–8), and GPCR (Degree 3, p < 1.45 × 10–4) in MQs, NOTCH (Degree 6, p < 0.027) in VSMCs, and Cytokines (Degree 4, p < 1.45 × 10–17) in DCs were found to be activated and enriched after exposure to Gram-negative bacterial infections on the cell networks. Furthermore, the Netrin- 1 (Degree 6, p < 0.028), and EGFR (Degree 5, p < 0.036) pathways were activated in the intimal thick/xanthoma plaque network while the innate (Degree 9, p < 8.9 × 10–20) and adaptive (Degree 7, p < 4.1 × 10–12) immune systems pathways were activated in the fibrous cap atheroma plaque network.

Conclusion

The study revealed the signaling pathways after exposure to Gram-negative bacterial infections on the cell networks in the vessel microenvironment. Furthermore, the cell cross-talks exacerbated these pathways in cells and unstable plaques.

Clinical Trial Number

Not applicable.