Combining multi-dimensional data to identify key genes and pathways in gastric cancer

Carcinoembryonic Antigen Related Cell Adhesion Molecule 6 Promotes Carcinogenesis of Gastric Cancer and Anti-CEACAM6 Fluorescent Probe Can Diagnose the Precancerous Lesions

The diagnosis of precancerous lesions or early gastric cancer (EGC) is very important for patient survival. Molecular imaging is a visualized method that can easily and precisely diagnose tumors. However, there are currently few studies about molecular imaging diagnosis of EGC. Here, we studied the expression of carcinoembryonic antigen related cell adhesion molecule 6 (CEACAM6) in the progression of GC. Then, the regulatory roles of CEACAM6 in GC cells were investigated. Furthermore, both the fluorescent-labeled and near infrared molecular-labeled probes were synthesized, and the diagnostic value of anti-CEACAM6 probes in GC was evaluated in vivo using a GC mice model as well as in vitro using fresh dysplastic gastric mucosa obtained from endoscopic submucosal dissection (ESD) operations. Our study showed that CEACAM6 was over expressed in GC tissues compared to adjacent tissues, and the patients with higher CEACAM6 expression had lower survival time. Moreover, the CEACAM6 expression was higher in the dysplastic gastric mucosa than in the adjacent normal mucosa. CEACAM6 accelerated the growth, proliferation, and invasion of GC cells in the in vitro and in vivo studies. Moreover, up regulated CEACAM6 can induce the expression of proteins related to GC progression. Furthermore, the anti-CEACAM6 probes exhibited good affinity with GC cell lines. The probes can track tumors as well as metastases in the mice model in vivo, and can precisely identify the area of dysplastic gastric mucosa using specimens obtained from ESD operations by wide field fluorescent endoscopy. The surface micro features of the mucosa can also be observed using fluorescent micro endoscopy, and the degree of atypia can be distinguished by both the signal intensity and surface micro morphology. CEACAM6 is a key molecular marker in GC progression, and the anti-CEACAM6 probe-assisted fluorescent endoscopy may be a potential option for the diagnosis of precancerous lesions.

A predictive model for assessing prognostic risks in gastric cancer patients using gene expression and methylation data

Background

The role(s) of epigenetic reprogramming in gastric cancer (GC) remain obscure. This study was designed to identify methylated gene markers with prognostic potential for GC.

Methods

Five datasets containing gene expression and methylation profiles from GC samples were collected from the GEO database, and subjected to meta-analysis. All five datasets were subjected to quality control and then differentially expressed genes (DEGs) and differentially expressed methylation genes (DEMGs) were selected using MetaDE. Correlations between gene expression and methylation status were analysed using Pearson coefficient correlation. Then, enrichment analyses were conducted to identify signature genes that were significantly different at both the gene expression and methylation levels. Cox regression analyses were performed to identify clinical factors and these were combined with the signature genes to create a prognosis-related predictive model. This model was then evaluated for predictive accuracy and then validated using a validation dataset.

Results

This study identified 1565 DEGs and 3754 DEMGs in total. Of these, 369 were differentially expressed at both the gene and methylation levels. We identified 12 signature genes including VEGFC, FBP1, NR3C1, NFE2L2, and DFNA5 which were combined with the clinical data to produce a novel prognostic model for GC. This model could effectively split GC patients into two groups, high- and low-risk with these observations being confirmed in the validation dataset.

Conclusion

The differential methylation of the 12 signature genes, including VEGFC, FBP1, NR3C1, NFE2L2, and DFNA5, identified in this study may help to produce a functional predictive model for evaluating GC prognosis in clinical samples.

Relationship between MTHFR Gene Polymorphisms and Gastrointestinal Tumors Development: Perspective from Eastern Part of Turkey

BACKGROUND

Gastric and esophageal cancers are 2 of the most prevalent cancer types worldwide. Polymorphisms in the genes that code the methylenetetrahydrofolate reductase (MTHFR) enzyme increase the formation of both cancer types. In this study, it was aimed to research the relationship between the existence of MTHFR C677T and A1298C polymorphisms in patients with gastric and esophageal cancer and the lifespans of patients.

METHODS AND MATERIALS

This prospective study was performed at Van Yuzuncu Yil University. Included in the study were 30 patients with esophageal tumors, 70 patients with gastric tumors, and 61 healthy volunteers. From each of the patients, 5 mL of blood was drawn. DNA was isolated via kits with spin-column technology.

RESULTS

It was concluded that the risk of developing gastric cancer was 4.13 times higher in individuals who had the AC genotype of the A1298C polymorphism when compared to those who had the AA genotype, while the risk was 2.91 times higher in individuals who had the CC genotype when compared to those who had the AA genotype (P = 0.001, P = 0.027). Carriers of the AC genotype of the A1298C polymorphism had 2.89 times higher risk of developing esophageal cancer when compared to those who had the AA genotype (P = 0.033). It was determined that individuals who had the 1298 CC genotype were not at higher risk of developing esophageal cancer when compared to those with the AA genotype (P = 0.863). It was concluded that individuals who had the TT genotype of the C677T polymorphism were not at higher risk of developing gastric and esophageal cancers when compared to those who had the 677CC genotype (P > 0.05). There was no difference in terms of the life spans of the patients with regards to the genotypes (P > 0.05).

CONCLUSION

The results showed that the A1298C polymorphism on the MTHFR gene can be a risk factor for gastric and esophageal cancer in eastern Turkey. These polymorphisms may have no effect on the life spans of the patients.

Emerging functions of PRKDC in the initiation and progression of cancer

The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is encoded by the protein kinase, DNA-activated, catalytic polypeptide (PRKDC) gene. DNA-PKcs plays a major role in nonhomologous end joining DNA repair, and it has been identified to be an important factor in tumor progression and metastasis. DNA-PKcs may have opposite effects in diseases, depending on the cell and tissue types. In this review, we discuss its role in various tumors. High levels of DNA-PKcs are directly associated with prognosis, neoplasm recurrence rates, and overall survival. Our results suggest that DNA-PKcs may serve as a therapeutic target for advanced malignancies.

Identification of key genes involved in the biosynthesis of triterpenic acids in the mint family

Triterpenic acids (TAs), a large group of natural compounds with diverse biological activity, are produced by several plant taxa. Betulinic, oleanolic, and ursolic acids are the most medicinally important TAs and are mainly found in plants of the mint family. Metabolic engineering is strongly dependent on identifying the key genes in biosynthetic pathways toward the products of interest. In this study, gene expression tracking was performed by transcriptome mining, co-expression network analysis, and tissue-specific metabolite-expression analysis in order to identify possible key genes involved in TAs biosynthetic pathways. To this end, taxa-specific degenerate primers of six important genes were designed using an effective method based on the MEME algorithm in a phylogenetically related group of sequences and successfully applied in three members of the Lamiaceae (Rosmarinus officinalis, Salvia officinalis, and Thymus persicus). Based on the results of in-depth data analysis, genes encoding squalene epoxidase and oxido squalene cyclases are proposed as targets for boosting triterpene production. The results emphasize the importance of identifying key genes in triterpene biosynthesis, which may facilitate genetic manipulation or overexpression of target genes.

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis

Background and Objective: Despite striking advances in multimodality management, gastric cancer (GC) remains the third cause of cancer mortality globally and identifying novel diagnostic and prognostic biomarkers is urgently demanded. The study aimed to identify potential key genes associated with the pathogenesis and prognosis of GC.

Methods: Differentially expressed genes between GC and normal gastric tissue samples were screened by an integrated analysis of multiple gene expression profile datasets. Key genes related to the pathogenesis and prognosis of GC were identified by employing protein–protein interaction network and Cox proportional hazards model analyses.

Results: We identified nine hub genes (TOP2A, COL1A1, COL1A2, NDC80, COL3A1, CDKN3, CEP55, TPX2, and TIMP1) which might be tightly correlated with the pathogenesis of GC. A prognostic gene signature consisted of CST2, AADAC, SERPINE1, COL8A1, SMPD3, ASPN, ITGBL1, MAP7D2, and PLEKHS1 was constructed with a good performance in predicting overall survivals.

Conclusion: The findings of this study would provide some directive significance for further investigating the diagnostic and prognostic biomarkers to facilitate the molecular targeting therapy of GC.