Identification of key genes and evaluation of immune cell infiltration in vitiligo

Xiangyue Zhang; Wen Hu; Zixian Lei; Hongjuan Wang; Xiaojing Kang; Xiangyue Zhang; Wen Hu; Zixian Lei; Hongjuan Wang; Xiaojing Kang

doi:10.3934/mbe.2021057

Mathematical Biosciences and Engineering

2021, Volume 18, Issue 2: 1051-1062. doi: 10.3934/mbe.2021057

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Research article Special Issues

Identification of key genes and evaluation of immune cell infiltration in vitiligo

1.
Graduate School of Xinjiang Medical University, Urumqi 830000, China
2.
Department of Dermatology, Xinjiang Uygur Autonomous Region People's Hospital, Urumqi 830001, China

Received: 13 October 2020 Accepted: 20 December 2020 Published: 08 January 2021

Background
To improve the understanding of the molecular mechanism of vitiligo is necessary to predict and formulate new targeted gene therapy strategies.
Methods
GSE65127, GSE75819, GSE53146 and GSE90880 were collected, and obtained four groups of differentially expressed genes (DEGs) by limma R package. Through weighted gene co-expression network analysis (WGCNA), the co-expression of genes with large variance in GSE65127 and GSE75819 was identified. Enrichment analysis of intersection gene between module genes and DEGs with the same up-regulated or down-regulated in GSE65127 and GSE75819 was performed. In addition, ssGSEA was used to identify the immune infiltration of vitiligo in four datasets.
Results
A total of 3083 DEGs and 16 modules were identified from GSE65127, and 5014 DEGs and 6 modules were screened from GSE75819. Finally, 77 important DEGs were identified. Enrichment analysis showed that 77 DEGs were mainly involved in spliceosome etc. The results of GSVA showed that melanogenesis, Fc gamma R-mediated phagocytosis, leishmaniasis, Wnt pathway and glycolipid metabolism were important KEGG pathways. The genes involved in these pathways were identified as key genes (MARCKSL1, MC1R, PNPLA2 and PRICKLE2). The AUC values of MC1R were the highest. Furthermore, different immune cells had different infiltration in vitiligo. There was a high correlation between immune cells and key genes.
Conclusions
MC1R was found as a key gene in vitiligo and involved in the melanogenesis. The immune cells were different infiltration in vitiligo. These results suggested that key genes may be used as markers of vitiligo, and were associated with immune cell, especially MC1R.
- vitiligo,
- WGCNA,
- MC1R,
- melanogenesis,
- immunity
Citation: Xiangyue Zhang, Wen Hu, Zixian Lei, Hongjuan Wang, Xiaojing Kang. Identification of key genes and evaluation of immune cell infiltration in vitiligo[J]. Mathematical Biosciences and Engineering, 2021, 18(2): 1051-1062. doi: 10.3934/mbe.2021057

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Abstract

Background

To improve the understanding of the molecular mechanism of vitiligo is necessary to predict and formulate new targeted gene therapy strategies.

Methods

GSE65127, GSE75819, GSE53146 and GSE90880 were collected, and obtained four groups of differentially expressed genes (DEGs) by limma R package. Through weighted gene co-expression network analysis (WGCNA), the co-expression of genes with large variance in GSE65127 and GSE75819 was identified. Enrichment analysis of intersection gene between module genes and DEGs with the same up-regulated or down-regulated in GSE65127 and GSE75819 was performed. In addition, ssGSEA was used to identify the immune infiltration of vitiligo in four datasets.

Results

A total of 3083 DEGs and 16 modules were identified from GSE65127, and 5014 DEGs and 6 modules were screened from GSE75819. Finally, 77 important DEGs were identified. Enrichment analysis showed that 77 DEGs were mainly involved in spliceosome etc. The results of GSVA showed that melanogenesis, Fc gamma R-mediated phagocytosis, leishmaniasis, Wnt pathway and glycolipid metabolism were important KEGG pathways. The genes involved in these pathways were identified as key genes (MARCKSL1, MC1R, PNPLA2 and PRICKLE2). The AUC values of MC1R were the highest. Furthermore, different immune cells had different infiltration in vitiligo. There was a high correlation between immune cells and key genes.

Conclusions

MC1R was found as a key gene in vitiligo and involved in the melanogenesis. The immune cells were different infiltration in vitiligo. These results suggested that key genes may be used as markers of vitiligo, and were associated with immune cell, especially MC1R.

References

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Supplementary-Table S1.pdf
Supplementary-Table S2.pdf

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