Identification of Immune Infiltration in Odontogenic Keratocyst by Integrated Bioinformatics Analysis

Abstract

Background: Odontogenic keratocyst (OKC) is a relatively common odontogenic lesion characterized by local invasion in the maxillary and mandibular bones. In the pathological tissue slices of OKC, immune cell infiltrations are frequently observed. However, the immune cell profile and the molecular mechanism for immune cell infiltration of OKC are still unclear. We aimed to explore the immune cell profile of OKC and to explore the potential pathogenesis for immune cell infiltration in OKC.

Methods: The microarray dataset GSE38494 including OKC and oral mucosa (OM) samples were obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in OKC were analyzed by R software. The hub genes of OKC were performed by protein-protein interaction (PPI) network. The differential immune cell infiltration and the potential relationship between immune cell infiltration and the hub genes were performed by single-sample gene set enrichment analysis (ssGSEA). The expression of COL1A1 and COL1A3 were confirmed by immunofluorescence and immunohistochemistry in 17 OKC and 8 OM samples.

Results: We detected a total of 402 differentially expressed genes (DEGs), of which 247 were upregulated and 155 were downregulated. DEGs were mainly involved in collagen-containing extracellular matrix pathways, external encapsulating structure organization, and extracellular structure organization. We identified ten hub genes, namely FN1, COL1A1, COL3A1, COL1A2, BGN, POSTN, SPARC, FBN1, COL5A1, and COL5A2. A significant difference was observed in the abundances of eight types of infiltrating immune cells between the OM and OKC groups. Both COL1A1 and COL3A1 exhibited a significant positive correlation with natural killer T cells and memory B cells. Simultaneously, they demonstrated a significant negative correlation with CD56dim natural killer cells, neutrophils, immature dendritic cells, and activated dendritic cells. Immunohistochemistry analysis showed that COL1A1 (P = 0.0131) and COL1A3 (P < 0.001) were significantly elevated in OKC compared with OM.

Conclusions: Our findings provide insights into the pathogenesis of OKC and illuminate the immune microenvironment within these lesions. The key genes, including COL1A1 and COL1A3, may significantly impact the biological processes associated with OKC.

Keywords: Bioinformatics; Hub gene; Immune cell infiltration; Odontogenic keratocyst.

Fig. 1

The flowchart of present study

Fig. 2

Validation of the dataset GSE38494 by Pearson’s correlation analysis (A) and PCA (B)

Fig. 3

Identification of DEGs between oral mucosa (OM) samples and odontogenic keratocyst (OKC) samples. Volcano plot (A) and heatmap (B) showed the differentially expressed genes of GSE38494.

Fig. 4

Biofunctional enrichment analysis of differentially expressed genes (DEGs) between oral mucosa (OM) samples and odontogenic keratocyst (OKC) samples. (A) Gene Ontology (GO) enrichment analysis of the DEGs. (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs.

Fig. 5

Interaction network and analysis of the hub genes. PPI network was constructed with the DEGs. The red points represent the upregulation of the expression of genes. The green points represent downregulated genes. The most significant module was obtained from PPI network with 10 nodes

Fig. 6

Immune cell infiltration patterns in oral mucosa (OM) samples and odontogenic keratocyst (OKC) samples. (A) Relative distribution of 28 immune cells in all samples. (B) Boxplot showing the differentially infiltrated immune cell types between OM group (green) and OKC group (red). ns, not significant, *P < 0.05, **P < 0.01. (C) Correlation heatmap of immune cell types in all samples. Red squares indicate positive correlation and blue squares indicate negative correlation, with deeper colored squares indicating stronger correlations

Fig. 7

The Pearson’s correlation between hub genes COL1A1 (A) and COL3A1 (B) obtained above and the 8 different immune cell types was calculated. The size of the dots represents the strength of the correlation between genes and immune cells, and the color of the dots represents the P-value

Fig. 8

Validation of the hub genes in odontogenic keratocyst (OKC) samples and oral mucosa (OM) tissues. (A) Immunofluorescence assay showed the expression of COL1A1 and COL3A1 in OKC tissue. (B) Immunohistochemistry assay detected the expression of COL1A1 in OM and OKC tissues, and the differential analysis of COL1A1 in OM and OKC tissues. **P < 0.01. (C) Immunohistochemistry assay detected the expression of COL3A1 in OM and OKC tissues, and differential analysis of COL3A1 in OM and OKC tissues. *P < 0.05