Identification and verification of three key genes associated with survival and prognosis of COAD patients via integrated bioinformatics analysis

BACKGROUND

Colorectal cancer (CRC) is the third most lethal malignancy in the world, wherein colon adenocarcinoma (COAD) is the most prevalent type of CRC. Exploring biomarkers is important for the diagnosis, treatment, and prevention of COAD.

METHODS

We used GEO2R and Venn online software for differential gene screening analysis. Hub genes were screened via Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape, following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Finally, survival analysis and RNA expression validation were performed via UALCAN online software and real-time PCR. Immunohistochemistry (IHC) was performed to verify the protein expression level of hub genes from tissues of COAD patients.

RESULTS

In the present study, we screened 323 common differentially expressed genes (DEGs) from four GSE datasets. Furthermore, four hub genes were selected for survival correlation analysis and expression level verification, three of which were shown to be statistically significant.

CONCLUSION

Our study suggests that Serpin Family E Member 1 (SERPINE1), secreted phosphoprotein 1 (SPP1) and tissue inhibitor of metalloproteinase 1 (TIMP1) may be biomarkers closely related to the prognosis of CRC patients.

Prognostic meaning of tissue inhibitors of matrix metalloproteinases TIMP-1 and TIMP-2 in patients with colorectal cancer

The aim of this study was to analyze TIMP-1 and TIMP-2 serum levels in patients with colorectal cancer (CRC) and to correlate the results with the pathological stage of the disease and outcome in order to evaluate the role of TIMP-1 and TIMP-2 serum levels as prognostic markers. The investigation has been made on 82 patients with operable CRC without distant metastases, who had undergone blood tests in order to determine the TIMP-1 and TIMP-2 serum levels in the following points of time: preoperatively, as well as 3, 6, 9 and 12 months postoperatively. Significant differences were found between serum levels of TIMP-1 and TIMP-2 obtained preoperatively and postoperatively, as well as significant association of serum TIMP-1 levels obtained preoperatively in CRC patients in stage I and III, in the 3th and in the 6th month (p<0.001) postoperatively as defined points of time with the outcome of CRC patients. Serum TIMP-2 levels obtained preoperatively was significantly associated with the outcome of the CRC patients. Analysis of the obtained TIMP-1 and TIMP-2 serum levels in CRC patients showed statistically significant differences with: disease progression, occurrence of liver metastasis, prior to and post chemotherapy treatment. The results derived a conclusion that the serum levels of TIMP-1 and TIMP-2 could be indicators for occurrence and progression of CRC, as well as valuable and useful markers for following the effects of chemotherapy treatment. Keywords: colorectal cancer, TIMP-1, TIMP-2, prognosis

HTR1D, TIMP1, SERPINE1, MMP3 and CNR2 affect the survival of patients with colon adenocarcinoma

Colorectal cancer (CRC) is a tumor that derives from the rectum or colon, and colon adenocarcinoma (COAD) is the most common type of CRC. The present study was performed to identify genes that serve critical roles in the survival of patients with COAD. RNA-sequencing data of COAD was extracted from The Cancer Genome Atlas database, which included 480 tumor samples and 41 normal samples. Using the limma package, differential expression analysis was performed to identify the differentially expressed genes (DEGs). In addition, the potential functions and pathways for the identified DEGs were analyzed using the clusterProfiler package. After the samples were divided into high and low expression groups, survival analysis for the two groups was performed using the Kaplan-Meier model. Using Cytoscape software, a protein-protein interaction network was generated for the survival-associated genes. A total of 1,519 DEGs, including 568 upregulated genes and 951 downregulated genes, were identified in the COAD samples. Enrichment analysis suggested that the DEGs were implicated in numerous functional terms and pathways. Furthermore, 109 DEGs were identified to be survival-associated genes in COAD. According to the degrees of the network nodes, 5-hydroxytryptamine receptor 1D (HTR1D), TIMP metallopeptidase inhibitor 1 (TIMP1), serpin family E member 1 (SERPINE1), matrix metallopeptidase 3 (MMP3) and cannabinoid receptor 2 (CNR2) were key nodes, and the expression levels of these genes were analyzed in clinical samples of CRC. Therefore, the results of the present study suggest HTR1D, TIMP1, SERPINE1, MMP3 and CNR2 may affect the prognosis of patients with COAD.

TIMP-1 is a novel serum biomarker for the diagnosis of colorectal cancer: A meta-analysis

Purpose

Tissue inhibitor of metalloproteinase-1 (TIMP-1) is a glycoprotein involved in cell survival and tumorigenesis. There have been some promising results regarding the diagnostic value of TIMP-1 for patients with colorectal cancer (CRC). The aim of the present study was to assess the diagnostic accuracy and clinical utility of serum TIMP-1 in CRC patients through meta-analysis.

Methods

A systematic search of online databases was performed to collect eligible studies. The pooled sensitivity, specificity, diagnostic odds ratio (DOR), and summary receiver operator characteristic (SROC) curve were generated from accuracy data using the random-effects model. Fagan’s nomogram and the likelihood matrix were applied to estimate the clinical utility of TIMP-1.

Results

A total of 9 eligible studies with 1886 patients were included. Among the patients, 819 were pathologically diagnosed with CRC, whereas 1067 did not have adenomas or other cancers. The overall sensitivity, specificity, and DOR of TIMP-1 for the diagnosis of CRC were 0.65 (95% confidence interval (CI): 0.57–0.72), 0.87 (95% CI: 0.76–0.94), and 12.73 (95% CI 5.71–28.38), respectively. The area under the SROC was 0.77 (95% CI, 0.73–0.81), suggesting the potential diagnostic value of TIMP-1 in CRC patients. Among patients with a pretest CRC probability of 20%, posttest probabilities were 56% and 9% for positive and negative TIMP-1 results, respectively.

Conclusions

TIMP-1 expression exhibits an upper moderate diagnostic value in CRC, and TIMP-1 assessment may be useful as a noninvasive screening tool for CRC in clinical practice.

Serum MMP-8 and TIMP-1 predict prognosis in colorectal cancer

BACKGROUND

Almost all of the extracellular matrix (ECM) components can be degraded by the endoproteinases matrix metalloproteinases (MMPs). Important regulators of MMPs, and thereby of the extracellular environment, are tissue inhibitors of metalloproteinases (TIMPs), and especially TIMP-1. Early tumor development, as well as distant metastasis, may be results of an MMP/TIMP ratio imbalance altering the ECM. MMPs are elevated in several inflammatory conditions. Our aim is to investigate the prognostic role of MMP-8, - 9, and TIMP-1 in colorectal cancer (CRC) and their relationship to inflammation.

METHODS

We included 337 colorectal cancer patients and 47 controls undergoing surgery at Helsinki University Hospital in Finland, 1998-2011. Serum levels of MMP-8 and plasma levels of C-reactive protein (CRP) were determined with a time-resolved immunofluorometric assay (IFMA), and MMP-9 and TIMP-1 with commercial enzyme-linked immunosorbent assay (ELISA) kits. Association and correlation analyses were performed with the Mann-Whitney U, Kruskal-Wallis, and Spearman rank correlation tests. Survival curves were constructed according to the Kaplan-Meier method and compared with the log-rank test.

RESULTS

Among patients with advanced disease, serum levels of MMP-8 and TIMP-1 were elevated. CRC patients with high MMP-8 (HR (hazard ratio) 1.72, 95% confidence interval (CI) 1.17-2.52, P = 0.005) and those with high TIMP-1 (HR 1.80, 95% CI 1.23-2.64, P = 0.002) had worse prognoses. MMP-9 level failed to serve as a prognostic factor. In multivariable survival analysis, Dukes stage, and low MMP-9/TIMP-1 molar ratio (HR 0.46, 95% CI 0.33-0.98, P = 0.042) were independently predicted prognosis. A weak correlation between CRP and MMP-8 (r_S = 0.229, P < 0.001), and TIMP-1 (r_S = 0.280, P < 0.001) was noted. Among patients showing no systemic inflammatory response, MMP-8 (HR 1.66, 95% CI 1.10-2.53, P = 0.017) and TIMP-1 (HR 1.59, 95% CI 1.05-2.42, P = 0.029) were prognostic factors.

CONCLUSIONS

MMP-8 and TIMP-1 in serum, but not MMP-9, identified CRC patients with bad prognosis. Among patients showing no systemic inflammatory response, MMP-8 and TIMP-1 may associate with poor prognosis.

Serum tissue inhibitor of metalloproteinase 1 (TIMP-1) and vascular endothelial growth factor A (VEGF-A) are associated with prognosis in esophageal cancer patients

PURPOSE

The matrix metalloproteinases, tissue inhibitors of metalloproteinases and angiogenesis contribute to growth and spread of cancer. We investigated the correlation between pretreatment serum levels of tissue inhibitor of metalloproteinase 1 (TIMP-1) and vascular endothelial growth factor A (VEGF-A), and clinicopathologic features and survival in patients with esophageal cancer (EC).

MATERIAL/METHODS

Serum TIMP-1 and VEGF-A were measured by enzyme-linked immunosorbent assay (ELISA) in 89 patients with EC, and 30 healthy controls.

RESULTS

Serum TIMP-1 and VEGF-A levels were significantly higher in patients with esophageal carcinoma than in the control group (p=0.001 and p<0.001, respectively). High levels of TIMP-1 were associated with histological type (p<0.001), tumor depth (p<0.001), stage (p<0.001) and lymph node metastases (p=0.001). Subgroup analysis showed that tumor size (p<0.001), tumor depth (p<0.001), stage (p<0.001), lymph node metastases (p=0.002), distant metastases (p=0.009) and resectability (p=0.003), were correlated with an elevated level of VEGF-A. Patients with elevated levels of TIMP-1 and VEGF-A had a significantly lower overall survival (p=0.02 and p=0.048, respectively), and disease-free survival (TIMP-1, p<0.001).

CONCLUSION

High serum levels of TIMP-1 and VEGF-A were found to be associated with tumor progression and unfavorable prognosis in patients with EC.