Identification of potential genes associated with immune cell infiltration in atherosclerosis

Xiaodong Xia; Manman Wang; Jiao Li; Qiang Chen; Heng Jin; Xue Liang; Lijun Wang; Xiaodong Xia; Manman Wang; Jiao Li; Qiang Chen; Heng Jin; Xue Liang; Lijun Wang

doi:10.3934/mbe.2021112

Mathematical Biosciences and Engineering

2021, Volume 18, Issue 3: 2230-2242. doi: 10.3934/mbe.2021112

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Research article Special Issues

Identification of potential genes associated with immune cell infiltration in atherosclerosis

1.
Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin City, 300052, China
2.
Department of Cardiology, Affiliated Hospital of Jining Medical University, Jining City, 272000, Shandong, China
3.
Department of Cardiology, Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin City, 300121, China
4.
Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular disease, Department of Cardiology, Tianjin Institute of Cardiology, the Second Hospital of Tianjin Medical University, Tianjin City, 300211, China
^† These two authors contributed equally

Received: 06 November 2020 Accepted: 17 February 2021 Published: 05 March 2021

Background
This study aimed to analyze the potential genes associated with immune cell infiltration in atherosclerosis (AS).
Methods
Gene expression profile data (GSE57691) of human arterial tissue samples were downloaded, and differentially expressed RNAs (DERNAs; long-noncoding RNA [lncRNAs], microRNAs [miRNAs], and messenger RNAs [mRNAs]) in AS vs. control groups were selected. Based on genome-wide expression levels, the proportion of infiltrating immune cells in each sample was assessed. Genes associated with immune infiltration were selected, and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, a competing endogenous RNA (ceRNA) network was constructed, and the genes in the network were subjected to functional analyses.
Results
A total of 1749 DERNAs meeting the thresholds were screened, including 1673 DEmRNAs, 63 DElncRNAs, and 13 DEmiRNAs. The proportions of B cells, CD4+ T cells, and CD8+ T cells were significantly different between the two groups. In total, 341 immune-associated genes such as HBB, FCN1, IL1B, CXCL8, RPS27A, CCN3, CTSZ, and SERPINA3 were obtained that were enriched in 70 significantly related GO biological processes (such as immune response) and 15 KEGG pathways (such as chemokine signaling pathway). A ceRNA network, including 33 lncRNAs, 11 miRNAs, and 216 mRNAs, was established.
Conclusion
Genes such as FCN1, IL1B, and SERPINA3 may be involved in immune cell infiltration and may play important roles in AS progression via ceRNA regulation.
- atherosclerosis,
- immune cell infiltration,
- mRNA,
- lncRNA,
- ceRNA
Citation: Xiaodong Xia, Manman Wang, Jiao Li, Qiang Chen, Heng Jin, Xue Liang, Lijun Wang. Identification of potential genes associated with immune cell infiltration in atherosclerosis[J]. Mathematical Biosciences and Engineering, 2021, 18(3): 2230-2242. doi: 10.3934/mbe.2021112

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Abstract

Background

This study aimed to analyze the potential genes associated with immune cell infiltration in atherosclerosis (AS).

Methods

Gene expression profile data (GSE57691) of human arterial tissue samples were downloaded, and differentially expressed RNAs (DERNAs; long-noncoding RNA [lncRNAs], microRNAs [miRNAs], and messenger RNAs [mRNAs]) in AS vs. control groups were selected. Based on genome-wide expression levels, the proportion of infiltrating immune cells in each sample was assessed. Genes associated with immune infiltration were selected, and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, a competing endogenous RNA (ceRNA) network was constructed, and the genes in the network were subjected to functional analyses.

Results

A total of 1749 DERNAs meeting the thresholds were screened, including 1673 DEmRNAs, 63 DElncRNAs, and 13 DEmiRNAs. The proportions of B cells, CD4+ T cells, and CD8+ T cells were significantly different between the two groups. In total, 341 immune-associated genes such as HBB, FCN1, IL1B, CXCL8, RPS27A, CCN3, CTSZ, and SERPINA3 were obtained that were enriched in 70 significantly related GO biological processes (such as immune response) and 15 KEGG pathways (such as chemokine signaling pathway). A ceRNA network, including 33 lncRNAs, 11 miRNAs, and 216 mRNAs, was established.

Conclusion

Genes such as FCN1, IL1B, and SERPINA3 may be involved in immune cell infiltration and may play important roles in AS progression via ceRNA regulation.

References

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