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. 2023 Jan 19:14:1086898.
doi: 10.3389/fimmu.2023.1086898. eCollection 2023.

Identification of gene signatures associated with ulcerative colitis and the association with immune infiltrates in colon cancer

Zhaoji Pan  1 , Hao Lin  2 , Yanyan Fu  3 , Fanpeng Zeng  1 , Feng Gu  1 , Guoping Niu  1 , Jian Fang  4 , Bing Gu  5
Affiliations

Identification of gene signatures associated with ulcerative colitis and the association with immune infiltrates in colon cancer

Zhaoji Pan et al. Front Immunol. .

Abstract

Background: Inflammatory bowel diseases, including ulcerative colitis (UC) and Crohn's disease, are some of the most common inflammatory disorders of the gastrointestinal tract. The dysfunction of the immune system in the intestines is suggested to be the underlying cause of the pathogenesis of UC. However, the mechanisms regulating these dysfunctional immune cells and inflammatory phenotypes are still unclear.

Methods: The differential expression analysis on microarray datasets were performed including GSE24287, GSE87466, GSE102133, and GSE107499, including 376 samples. "Gene Ontology" and "Kyoto Encyclopedia of Genes and Genomes" pathway enrichment analyses were conducted to identify the common differentially expressed genes (DEGs) in these datasets and explore their underlying biological mechanisms. Further algorithms like "Cell-type Identification by Estimating Relative Subsets of RNA Transcripts" were used to determine the infiltration status of immune cells in patients with UC. "Cytoscape" and "Gene Set Enrichment Analysis" were used to screen for hub genes and to investigate their biological mechanisms. The Tumor Immune Estimation Resource database was used to study the correlation between hub genes and infiltrating immune cells in patients with UC. A total of three hub genes, CCL3, MMP3, and TIMP1, were identified using Cytoscape.

Results: A positive correlation was observed between these hub genes and patients with active UC. These genes served as a biomarker for active UC. Moreover, a decrease in CCL3, MMP3, and TIMP1 expression was observed in the mucosa of the intestine of patients with active UC who responded to Golimumab therapy. In addition, results show a significant positive correlation between CCL3, MMP3, and TIMP1 expression and different immune cell types including dendritic cells, macrophages, CD8+ T cells, and neutrophils in patients with colon cancer. Moreover, CCL3, MMP3, and TIMP1 expression were strongly correlated with different immune cell markers.

Conclusion: Study results show the involvement of hub genes like CCL3, MMP3, and TIMP1 in the pathogenesis of UC. These genes could serve as a novel pharmacological regulator of UC. These could be used as a therapeutic target for treating patients with UC and may serve as biomarkers for immune cell infiltration in colon cancer.

Keywords: GEO dataset; UC; biomarkers; colon cancer; immune.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Identification and functional annotation of DEGs and hub gene selection. (A) Venn diagram shows overlapping genes from four gene sets. (B) GO and KEGG pathway enrichment analysis of DEGs. (C) Identification of three hub genes.
Figure 2
Figure 2
CIBERSORT was used to determine immune cell infiltration status in samples from the GSE87466 and GSE107499 datasets. GSEA was performed on CCL3, MMP3, and TIMP1 to identify biological processes. (A) Stacked bar plots and box plots show the relative levels of 22 immune cells in the GSE87466 dataset. (B) Stacked bar plots and boxplots show the relative levels of 22 immune cells in the GSE107499 dataset. (C, D) GSEA shows the biological processes related to CCL3, MMP3, and TIMP1 in GSE87466 and GSE107499. "*" corresponds to a significant level of 5%, that is, p<0.05. p<0.05 indicates that the difference is 95% certain and has statistical significance. "**" corresponds to a significant level of 1%, that is, p<0.01, which indicates that the difference is 99% certain, and the difference is significant, with statistical significance. "***" corresponds to a significant level of 0.1%, that is, p<0.001. p<0.001 indicates that the difference is 99.9%, which is very significant and statistically significant.
Figure 3
Figure 3
Verification of hub genes. (A, B) The expression of CCL3, MMP3, and TIMP1 in GSE87466 and GSE107499. (C, D) ROC analysis of CCL3, MMP3, and TIMP1 in the GSE87466 and GSE107499 datasets. "****" corresponds to 0.01% significant level, that is, p<0.0001, p<0.0001, which indicates that the difference is 99.99% certain, and the difference is very significant, with statistical significance.
Figure 4
Figure 4
CCL3, MMP3, and TIMP1 expression levels in patients with active UC. (A) The expression of CCL3, MMP3, and TIMP1 in the GSE53306 dataset. (B) The expression of CCL3, MMP3, and TIMP1 in the GSE59071 dataset. "*" corresponds to a significant level of 5%, that is, p<0.05. p<0.05 indicates that the difference is 95% certain and has statistical significance. "**" corresponds to a significant level of 1%, that is, p<0.01, which indicates that the difference is 99% certain, and the difference is significant, with statistical significance. "***" corresponds to a significant level of 0.1%, that is, p<0.001. p<0.001 indicates that the difference is 99.9%, which is very significant and statistically significant. ns means no statistical significance.
Figure 5
Figure 5
Expression of CCL3, MMP3, and TIMP1 in UC patients and induced enteritis cells. (A) The expression of CCL3. (B) The expression of MMP3. (C) The expression of TIMP1. (D) The protein expression levels of CCL3, MMP3 and TIMP1 in UC patients and healthy controls. (E) The inflammatory factors IL-8 and IL-1β secretion level after 1 ug LPS stimulated NCM460 cells for 0h, 12h and 24h. (F) The protein expression levels of CCL3, MMP3 and TIMP1 in NCM460 cells stimulated with LPS for 0h, 12h and 24h.
Figure 6
Figure 6
CCL3, MMP3, and TIMP1 expression in DSS-induced colitis mouse model. (A) HE staining of tissues of DSS-induced colitis mice and the control group. (B) The expression of CCL3 in DSS-induced colitis mouse model. (C) The expression of MMP3 in DSS-induced colitis mouse model.
Figure 7
Figure 7
Expression of CCL3, MMP3, and TIMP1 on GLM in patients with UC. (A) Expression of CCL3, MMP3, and TIMP1 in the intestinal mucosa of patients with active UC in the non-response and response groups before GLM treatment. (B) Expression of CCL3, MMP3, and TIMP1 in the intestinal mucosa of patients with active UC after 6 weeks of GLM treatment in the response and non-response groups.
Figure 8
Figure 8
Relationship between CCL3, MMP3, and TIMP1 expression and level of immune cell infiltration in colon cancer. (A) CCL3. (B) MMP3. (C) TIMP1.
See this image and copyright information in PMC

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