• Downregulation of LIPF affected by hsa-miR-2277-5p, FLG-AS1, and WDFY3-AS2 in a ceRNA network promotes the development of gastric cancer
  • Ghazal Khodadoustan,1,* Mohammad Rezaei,2 Mansoureh Azadeh,3
    1. Zist Fanavari Novin Biotechnology Institute, Isfahan, Iran
    2. Zist Fanavari Novin Biotechnology Institute, Isfahan, Iran
    3. Zist Fanavari Novin Biotechnology Institute, Isfahan, Iran


  • Introduction: Gastric cancer (GC) is the fifth most common type of cancer in the world. Despite advances in medical treatment, GC is still a major cause of cancer-related deaths, ranking as the third most common cause of cancer death globally. Treatment for GC typically involves surgery to remove the tumor, followed by chemotherapy and/or radiation therapy to kill any remaining cancer cells, which is highly invasive. Therefore, finding a new biomarker can enhance monitoring and early detection. The theory of the competitive endogenous RNA (ceRNA) network suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) engage in a competitive regulatory mechanism that ultimately determines the induction or suppression of gene expression. In various cancer types, the interplay between the different constituents of this network undergoes alterations, thereby underscoring its potential utility as a biomarker for the diagnosis and treatment of cancer. The aim of this bioinformatics approach was to discover a set of genes, miRNAs, and LncRNAs that act in a biological network that remarkably impacts the progression of GC. As a potential biomarker in GC monitoring and early detection.
  • Methods: Raw data (GSE220917) was initially extracted from the NCBI Gene Expression Omnibus (GEO) for later analysis by Rstudio. The study included microarray raw data of RNA expression profiles of 23 samples (5 normal, 9 gastric cancer (GC), 9 gastroesophageal junction cancer), the 9 gastroesophageal junction cancer were later excluded and analysis was continued on GC and normal samples. Further analysis of raw data of microarray was conducted by Rstudio using “Limma” and “Affy” packages (downloaded from https://www.bioconductor.org) along with “pheatmap”, “dpylr”, “gplots”, and “ggplot2” packages (downloaded from https://cran.r-project.org) to find significant differentially expressed genes (DEGs). In this investigation, DEGs with adjusted p-value < 0.05 and |logFC| > 2 were considered significant. As a result of this analysis, LIPF was selected. Furthermore, GEPIA2 and ENCORI databases were used to validate the results of the analysis. In addition, biological pathway involvement was processed through Reactome and NRICHR databases. Moreover, STRING was utilized to find significant protein-protein interactions among LIPF and other protein-coding genes. Finally, the possible interactions among LIPF with miRNAs and LncRNAs were verified by Mirwalk and miRNet respectively.
  • Results: Results of the microarray raw data analysis by Rstudio show LIPF gene is significantly downregulated in GC samples compared to normal samples (logFC = -7, adjusted p-value = 5.2 e-9). gastric lipase (LIPF) gene, which is connected with various lipid metabolism processes, is indicated to be significantly downregulated in this investigation. Therefore, the expression level of LIPF in GC seemed to be associated with local invasion, and disease stage. possible miRNA-mRNA interactions were determined using Mirwalk. As a result, six miRNAs were candidate to have significant interaction with the LIPF gene. These six candidates were later processed through the ENCORI database for further validations of mRNA-miRNA interaction and co-expression in GC progression. As a result, hsa-miR-2277-5p was selected to be negatively co-expressed with the LIPF gene. hsa-miR-2277-5p is shown to be overly expressed in GC samples and repress the activity of LIFP mRNAs. LncRNAs can act as miRNA sponges and have a regulatory effect on their target miRNAs. Therefore, selected miRNA was searched in miRNet to find interaction between them and lncRNAs in a ceRNA network. FLG¬-AS1 and WDFY3-AS2 were identified to have strong interactions with hsa-miR-2277-5p. FLG¬-AS1 and WDFY3-AS2 were later searched in ENCORI database to validate the miRNA-lncRNA correlation. Results of this study revealed that, all of these RNAs act as a ceRNA network that influences GC progression.
  • Conclusion: In conclusion, the downregulation of LIPF mRNA forms a possible ceRNA network along with hsa-miR-2277-5p, FLG-AS1, and WDFY3-AS2 Which proved to have a significant role in GC progression. With further investigation and experiments, this finding could be identified as a potential marker in GC early detection and monitoring.
  • Keywords: gastric cancer, ceRNA, bioinformatics