Diagnostic and Predictive Value of Immune-Related Genes in Crohn's Disease

Abstract

Abnormal immune cell infiltration is associated with the pathogenesis of Crohn's disease (CD). This study aimed to determine the diagnostic and predictive value of immune-related genes in CD. Seven Gene Expression Omnibus datasets that analyzed the gene expression in CD tissues were downloaded. Single-sample gene set enrichment analysis (ssGSEA) was used to estimate the infiltration of the immune cells in CD tissues. Immune-related genes were screened by overlapping the immune-related genes with differentially expressed genes (DEGs). The protein-protein interaction (PPI) network was used to identify key immune-related DEGs. Diagnostic value of CD and predictive value of anti-TNFα therapy were analyzed. Immunohistochemical (IHC) assay was used to verify gene expression in CD tissues. There were significant differences among CD tissues, paired CD tissues, and normal intestinal tissues regarding the infiltration of immune cells. AQP9, CD27, and HVCN1 were identified as the key genes of the three sub-clusters in the PPI network. AQP9, CD27, and HVCN1 had mild to moderate diagnostic value in CD, and the diagnostic value of AQP9 was better than that of CD27 and HVCN1. AQP9 expression was decreased in CD after patients underwent anti-TNFα therapy, but no obvious changes were observed in non-responders. AQP9 had a moderate predictive value in patients who had undergone treatment. IHC assay confirmed that the expression of AQP9, CD27, and HVCN1 in CD tissues was higher than that in normal intestinal tissues, and AQP9, CD27 was correlated with the activity of CD. Immune-related genes, AQP9, CD27, and HVCN1 may act as auxiliary diagnostic indicators for CD, and AQP9 could serve as a promising predictive indicator in patients who underwent anti-TNF therapy.

Keywords: Crohn’s disease; differentially expressed genes; gene set enrichment analysis; immune-related genes; protein-protein interaction.

Figure 1

Heatmap of the landscape of 28 immune cell subpopulations infiltration in CD (n=60 tissues).

Figure 2

The protein-protein interaction (PPI) network for the DEGs. (A) PPI network for 166 immune-related DEGs, each round node represent a gene; (B–D) Sub-clusters of PPI network, the green diamond shape of node indicated the key gene of sub-cluster.

Figure 3

Diagnostic values of AQP9, CD27 and HVCN1 in CD. (A) Diagnostic value of AQP9, CD27, HVCN1 in CD using non-inflammatory tissues as controls (GSE95095 dataset); (B) Diagnostic value of AQP9, CD27, HVCN1 in CD using normal intestinal tissues as controls (GSE95095 dataset); (C) Diagnostic value of AQP9, CD27, HVCN1 in CD (GSE36807 dataset); (D) Diagnostic value of AQP9, CD27, HVCN1 in CD (GSE102133 dataset); (E) Diagnostic value of AQP9, CD27, HVCN1 in CD (GSE16879 dataset); (F) Diagnostic value of AQP9, CD27, HVCN1 in CD (GSE10616 dataset).

Figure 4

Expression of AQP9, CD27 and HVCN1 in CD tissues that underwent anti-TNFα therapy (A) Expression of AQP9, CD27 and HVCN1 in GSE98820 (this dataset do not has CD27 gene); (B) Expression of AQP9, CD27 and HVCN1 in GSE112366; (C) Expression of AQP9, CD27 and HVCN1 in GSE16879 (only selected responders); (D) Expression of AQP9, CD27 and HVCN1 in GSE16879 (only selected non-responders).

Figure 5

Predictive values of AQP9, CD27 and HVCN1 in the treatment of CD. (A) Predictive value of AQP9 and HVCN1 in the treatment of CD (GSE98820); (B) Predictive value of AQP9, CD27 and HVCN1 in the treatment of CD (GSE16879); (C) Predictive value of AQP9, CD27 and HVCN1 in the treatment of CD (GSE112366).

Figure 6

(A) Typical endoscopic images of CD: left, ileum in remission; middle, ileocecal valve; right, colon with ulcer; (B) Expression of AQP9, CD27 and HVCN1 in adjacent normal intestinal tissues, fewer immunostaining can be seen in the mucosa (Magnification ×200); (C) Expression of AQP9, CD27 and HVCN1 in CD tissues, more immunostaining can be seen in the mucosa (Magnification ×200).

Figure 7

(A) Comparison of IHC intensity score between adjacent normal intestinal tissues and CD tissues regarding the AQP9, CD27 and HVCN1; (B) Correlation analysis between the CDAI scores and the expression of AQP9, CD27 and HVCN1 in CD tissues. IHC, Immunohistochemical; CDAI, Crohn’s Disease Activity Index, *indicated p-value < 0.05.