KEGG pathway enrichment of differential proteins was most significantly enriched in metabolic pathways
Firstly, we performed differential proteomic analysis of 10 samples of submitted tissues (5 samples of colon cancer tissues and 5 samples of adjacent tissues). Figure 1.A shows the results of differential analysis.A total of 1536 differential proteins were obtained, of which 977 were significantly up-regulated and 559 were significantly down-regulated. Figure 1. The results of cluster analysis can distinguish cancer tissues and adjacent tissues well. A total of 1209 differentially expressed proteins were identified (p < 0.05,log2(FC) > 1or<-1) after excluding proteins that were not detected in cancer tissues or adjacent tissues.
GO and KEGG enrichment analysis were performed on the 1209 differentially expressed proteins screened out in the DAVID database. Figure 1.b shows the enrichment results. In GO_BP enrichment analysis, 1209 differentially expressed proteins were mainly enriched in innate immune response, rRNA processing, RNA splicing, mRNA processing, and mRNA splicing. via spliceosome, defense response to bacterium, DNA replication, complement activation, classical pathway, translation, phagocytosis, recognition and other biological processes; GO_CC enrichment results suggested that the differential proteins were mainly located in cytosol, nucleus, nucleoplasm, extracellular exosome, membrane and extracellular region, extracellular space, nucleolus and endoplasmic reticulum; GO_MF enrichment results showed that the differential proteins were mainly enriched in protein binding, RNA binding, identical protein binding, antigen binding, nucleic acid binding and ATPase activity, mRNA binding, structural constituent of ribosome, immunoglobulin receptor binding, extracellular matrix structural constituent and other molecular functions. The 1209 differentially expressed proteins were mainly enriched in Metabolic pathways, Coronavirus disease-COVID-19, Ribosome biogenesis in KEGG enrichment analysis eukaryotes, Ribosome, Spliceosome, DNA replication, Nucleocytoplasmic transport, Drug metabolism-Cytochrome P450, Metabolism xenobiotics by cytochrome P450, Complement and coagulation cascades. Interestingly, we found that these 1209 differential proteins were significantly enriched (FDR < 0.05) in metabolic pathways, with the most enriched differential proteins (144). Therefore, these 144 differential proteins were selected for further analysis.
PPI network analysis identified the top 10 most important proteins in protein-protein interactions
To further explore the interaction between these 144 differentially expressed proteins enriched in metabolic pathways, we performed protein-protein interaction network analysis by Cytoscape software (Fig. 2.a), counted the number of connections between nodes by CytoHubba plug-in, and selected the top 10 proteins with the most connections: ADH1A, ADH1B, ADH1C, ADH5, ALDH18A1, ALDH3A1, GSTA1, GSTA2, HPGDS, GSR. Figure 2.a shows the interactions among these 10 proteins. In order to further explore the correlation between these 10 proteins that play key roles in metabolic pathways, we conducted correlation analysis (Spearman correlation analysis) through the Timer database and found that there were obvious correlations between some proteins (either positive or negative correlation). Figure 2.b specifically shows the results of their correlation analysis.
Colon cancer patients with high expression of GSR have a higher overall survival rate
Survival analysis using the GEPIA2 database showed that only GSR significantly affected the overall survival of patients with colon cancer, and the expression of GSR was significantly positively correlated with the overall survival of patients with colon cancer (p = 0.0017, HR = 0.45). It has been reported that GSR plays a key role in tumor metabolism (26). Through the previous correlation analysis, it was found that ADH5 had the strongest correlation with GSR (Cor = 0.32, P < 0.05). Although the effect of ADH5 on overall survival was not statistically significant, it seemed to have the same trend as GSR from the KM curve. In addition, it has been reported that ADH5 plays an important role in tumorigenesis and development (27).
GSR has a significant impact on the immune microenvironment and molecular subtypes of colon cancer
We wanted to further investigate whether GSR, while affecting colon cancer metabolism, could affect immune effects in the tumor microenvironment. Using Timer database, we analyzed the correlation between GSR and immune cell infiltration. In colon cancer, the expression of GSR was correlated with dendritic cells (Cor = 0.277, P < 0.05), central granulocytes (Cor = 0.266, P < 0.05), CD8 + cells (Cor = 0.282, P < 0.05), and the expression of GSR was correlated with immune cell infiltration. P < 0.05) and B cell infiltration (Cor = 0.177, P < 0.05). Through the analysis of different somatic copy number changes of GSR gene and immune cell infiltration levels, it was found that in colon cancer, arm deletion and arm amplification of GSR gene mutations can significantly reduce the level of B cell infiltration, and deep deletion, arm deletion and high amplification can significantly reduce the level of CD8 + T cell infiltration. Deep deletion and arm deletion significantly reduced the infiltration level of neutrophils, while deep deletion, arm deletion and arm amplification significantly reduced the infiltration level of dendritic cells.
We used the TISIDB database for further analysis. In terms of the correlation between tumor infiltrating lymphocytes (TILs) and GSR gene expression in colon cancer, there was a significant positive correlation between GSR and iDC, Act_DC, Th2 and Monocyte infiltration. There was a significant positive correlation between GSR and CD244 expression (Cor = 0.246, P < 0.05). For the correlation between immune stimulator and GSR gene expression in colon cancer, GSR was associated with TNFSF13 (Cor = 0.26, P < 0.05), TNFSF9 (Cor = 0.323, P < 0.05), RAET1E (Cor = 0.208, P < 0.05), and TNFSF9 (cor = 0.323, P < 0.05). P < 0.05) and KLRC1 (Cor = 0.256, P < 0.05). There was a significant positive correlation between the expression of GSR and B2M (Cor = 0.266, P < 0.05). There was a significant positive correlation between GSR and CXCL3 (Cor = 0.202, P < 0.05) and CXCL8 (Cor = 0.211, P < 0.05).
Correlation of GSR gene expression with clinical information in colon cancer patients
Using the UALCAN database, we analyzed the correlation between the expression of GSR and clinical information of colon cancer patients. Firstly, we found that the expression of GSR was significantly decreased in colon cancer tissues compared with normal tissues (p < 0.05). Previously, we found that colon cancer patients with high expression of GSR had better prognosis, suggesting that GSR may play a tumor suppressor role in colon cancer. The expression of GSR was the highest in Stage1 colon cancer. With the decrease of GSR expression, the stage of colon cancer was worse, and the expression of GSR was the lowest in Stage4 colon cancer. For N stage, we found that the expression of GSR in N0 was significantly higher than that in N1 and N2 (p < 0.05), indicating that colon cancer with low expression of GSR was more likely to have lymph node metastasis, leading to a later pathological overall stage. Finally, we found that GSR expression was significantly down-regulated in TP53-mutated colon cancers compared with TP53-unmutated colon cancers (p < 0.05). It is well known that TP53 gene acts as the "guardian" of malignant transformation, and its mutation predicts poor tumor staging and prognosis (28) (29) (30) (31). GSR and TP53 may play a synergistic role or have an upstream and downstream regulatory relationship in the development of colon cancer. In conclusion, our results suggest that GSR expression predicts better N stage, overall stage, and lower mutation rate of TP53 in colon cancer.
Immunohistochemical analysis of GSR in colon cancer
Finally, the results of immunohistochemical analysis of the HPA database showed that the degree of immunohistochemical staining of GSR in colon cancer suggested high staining, and the degree of intensity suggested strong intensity. GSR was mainly expressed in the cytoplasm and nuclear membrane of colon cancer cells.