Certification of novel lncRNA based on analysis of ceRNA network in digestive system pan-cancer and characteristics of tumor immune microenvironment

Abstract

AbstractBackground:Based on analysis of competitive endogenous RNA (ceRNA) and immune microenvironment, we screened their specific Long non-coding RNA (lncRNA) from the perspective of digestive system pan-cancer, and performed preliminary experimental validation.Methods:The transcriptome data of were downloaded from The Cancer Genome Atlas (TCGA) database, including esophageal carcinoma(ESCA), stomach adenocarcinoma (STAD), colorectal carcinoma (CRC) and liver hepatocellular adenocarcinoma (LIHC). We screened and predicted co-expressed differentially lncRNAs, miRNAs, and mRNAs of four tumors using R language. CeRNA networks were constructed by Cytoscape software.LASSO and Cox regression analysis were used to construct prognostic model. The application value of the prognostic model was assessed by combining clinicopathological features. The relationship between prognostic models and immune micro-environment was evaluated using Wilcoxon signed rank test. CCK8, scratch and Transwell assays were performed to analyze the effects of overexpression of lncRNA on CRC cells lines SW837 and SW620. The effect of overexpression of lncRNA on target proteins was detected using western blot.Results:Co-expressed lncRNAs 256, miRNAs 36, mRNAs 921 were obtained to construct the ceRNA network. LncRNA (WDFY3-AS2 and HOTAIR), miRNA (hsa-miR-21), and mRNA (OSR1) were screened using LASSO and Cox regression analysis to construct prognostic model. The survival rate of patients in the low-risk group was better than that in the high-risk group (P<0.001). The risk score and clinical stage could be used as independent prognostic factors for the digestive system pan-cancer. The risk score was positively correlated with the infiltration of multiple immune cells. The high-risk groups of CRC and LIHC were positively correlated with the expression of CD274, CTLA4, PDCD1, and HAVCR2 (P<0.05). Cellular experiments showed that the overexpression of WDFY3-AS2 reduced the survival rates of colorectal cancer cells, increased the healing time of scratched cells, and decreased the passage rate of transwell cells. Western blot assay suggested that WDFY3- AS2 can positively regulated the expression of OSR1.Conclusions:The prognostic model constructed based on the WDFY3-AS2/HOTAIR /hsa-miR-21/OSR1 ceRNA regulatory axis was able to assess the prognosis of pan-cancer of the digestive system, and the specific LncRNA WDFY3-AS2 inhibited the proliferation, invasion and metastasis of colon cancer cells.