Overexpressions of RHOA, CSNK1A1, DVL2, FZD8, and LRP5 genes enhance gastric cancer development in the presence of Helicobacter pylori

Demirci, Ufuk; Orenay-Boyacioglu, Seda; Kasap, Elmas; Gerçeker, Emre; Bilgiç, Fahri; Yüceyar, Hakan; Yıldırım, Hatice; Baykan, Ahmed Ramiz; Ellidokuz, Ender; Korkmaz, Mehmet Emin

doi:10.1016/j.ajg.2023.01.004

Cited by 2 publications

(1 citation statement)

References 39 publications

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“…Though the role of CCND2 in apoptosis in humans has already been published [32], no studies have implicated its role in apoptosis in gastric cancer. Another study by Demirci et al, suggests that CCND2, along with RHOA, LRP5, FZD8, and DVL2, may be a potential target for gastric cancer therapy due to their significant overexpression in tumor tissues and their potential role in early carcinogenesis [33]. The miRNA, miR-141 targets and inhibits YAP1 gene expression thereby inducing apoptosis in GC [34].…”

Section: Cerna Network and Apoptosismentioning

confidence: 99%

Integrated Bioinformatics Analysis Reveals ceRNA Triplet Related to Apoptosis in Gastric Cancer

Nath,

Natarajan

2024

MEDIN

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Apoptosis is a form of programmed cell death and evading the apoptosis is a milestone in gastric cancer (GC) tumorigenesis. Various RNAs such as miRNA (microRNA), mRNA (messenger RNA), lncRNA (long non-coding RNA), circRNA (circular RNA), play crucial roles in the apoptosis mechanism. In this present study, we aimed to understand the role played by these RNAs in apoptosis in GC. We constructed a ceRNA (competitive endogenous RNA) network using the expression profiles obtained from SRA (Sequence Read Archive) and GEO (Gene Expression Omnibus) datasets. After network construction, the differentially expressed mRNAs were used for gene prioritization. The prioritized genes and the RNAs interacting with them were analyzed to study their role in GC apoptosis. Then, we performed functional and pathway analysis to understand the role played by these genes in gastric cancer. This resulted in 37 miRNA-mRNA interactions, one miRNA-lncRNA interaction, and 17 miRNA-circRNA interactions. The binding site analysis resulted in 10 miRNAs that share common MRE (miRNA Response Elements) among mRNA, lncRNAs, circRNA. Besides, we found 33 miRNA-mRNA-circRNA and two miRNA-mRNA-lncRNA valid interactions. Integration of multiple omics datasets revealed dysregulated genes, including IGF1, MME, CCND2, CDH2, and COL1A1, implicated in GC apoptosis. Functional enrichment analysis highlighted pathways related to apoptosis, with CCND2 emerging as a key player. The integrative methodology has revealed a new potential diagnostic biomarker for the regulation of gastric cancer (GC) apoptosis: the CCND2-miR-141-3p-hsa_circ_0008035 ceRNA triplet. This discovery offers fresh perspectives into the intricate regulatory pathways governing gene expression in GC, promising significant insights into its pathology.

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Section: Cerna Network and Apoptosismentioning

confidence: 99%

Integrated Bioinformatics Analysis Reveals ceRNA Triplet Related to Apoptosis in Gastric Cancer

Nath,

Natarajan

2024

MEDIN

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Identification of differentially expressed genes and enriched pathways in inflammatory bowel disease using bioinformatics and next generation sequencing data analysis

Vastrad¹,

Vastrad²

2023

Preprint

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Inflammatory bowel disease (IBD) is the most common chronic digestive disorders and inflammation in the gastrointestinal tract globally that is characterized by episodes of abdominal pain, diarrhea, bloody stools and weight loss. However, the pathophysiologic mechanisms of IBD have not been thoroughly investigated. To explore potential targets for treatment of IBD, we reorganized and analyzed next generation sequencing (NGS) dataset (GSE186507). The R package DESeq2 tool was used to screen for differentially expressed genes (DEGs) between IBD and normal control samples. We used the g:Profiler database to perform Gene Ontology (GO) enrichment analysis and the REACTOME for pathway enrichment analysis. Protein-protein interaction (PPI) network construction and module analysis were performed to elucidate molecular mechanisms of DEGs and screen hub genes. Then miRNA-hub gene regulatory network and TF-hub gene regulatory network of these hub genes were visualized by Cytoscape. We also validated the identified hub genes via receiver operating characteristic (ROC) curve analysis. A total of 957 DEGs (478 up regulated genes and 479 down regulated genes) were detected in NGS dataset. And they were mainly enriched in the terms of multicellular organismal process, response to stimulus, GPCR ligand binding and immune system. Based on the data of PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network the top hub genes were ranked, including IL7R, ERBB2, SMAD1, RPS26, TLE1, HNF4A, CDKN1A, SRPK1, H3C12 and SFN. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the development and progression of IDB, and certain novel genes might be used as candidate target molecules to diagnose, monitor and treat IDB.

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Overexpressions of RHOA, CSNK1A1, DVL2, FZD8, and LRP5 genes enhance gastric cancer development in the presence of Helicobacter pylori

Cited by 2 publications

References 39 publications

Integrated Bioinformatics Analysis Reveals ceRNA Triplet Related to Apoptosis in Gastric Cancer

Integrated Bioinformatics Analysis Reveals ceRNA Triplet Related to Apoptosis in Gastric Cancer

Identification of differentially expressed genes and enriched pathways in inflammatory bowel disease using bioinformatics and next generation sequencing data analysis

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