Identification of Circular RNA-Based Immunomodulatory Networks in Colorectal Cancer

Abstract

BackgroundCircular RNAs (circRNAs) have been recently proposed as hub molecules in various diseases, especially in tumours. We found that circRNAs derived from ribonuclease P RNA component H1 (RPPH1) were highly expressed in colorectal cancer (CRC) samples from Gene Expression Omnibus (GEO) datasets.ObjectiveWe sought to identify new circRNAs derived from RPPH1 and investigate their regulation of the competing endogenous RNA (ceRNA) and RNA binding protein (RBP) networks of CRC immune infiltration.MethodsThe circRNA expression profiles miRNA and mRNA data were extracted from the GEO and The Cancer Genome Atlas (TCGA) datasets, respectively. The differentially expressed (DE) RNAs were identified using R software and online server tools, and the circRNA–miRNA–mRNA and circRNA–protein networks were constructed using Cytoscape. The relationship between targeted genes and immune infiltration was identified using the GEPIA2 and TIMER2 online server tools.ResultsA ceRNA network, including eight circRNAs, five miRNAs, and six mRNAs, was revealed. Moreover, a circRNA–protein network, including eight circRNAs and 49 proteins, was established. The targeted genes, ENOX1, NCAM1, SAMD4A, and ZC3H10, are closely related to CRC tumour-infiltrating macrophages.ConclusionsWe analysed the characteristics of circRNA from RPPH1 as competing for endogenous RNA binding miRNA or protein in CRC macrophage infiltration. The results point towards the development of a new diagnostic and therapeutic paradigm for CRC.

PROSER2 is a poor prognostic biomarker for patients with osteosarcoma and promotes proliferation, migration and invasion of osteosarcoma cells

“…Xiantao database (xiantao.love/products) is primarily used for gene expression, co-expression, enrichment and interaction network analysis and contains the RNA sequencing and microarray data from TCGA database and part of the Gene Expression Omnibus database. Numerous researchers have published articles using the Xiantao database and similar procedures to the present study (21)(22)(23)(24). GO, KEGG and GSEA analyses were performed on PROSER2 differentially expressed genes (DEGs) using Xiantao platform.…”

Interaction between diet and genetics in patients with inflammatory bowel disease

“…CircRNAs are noncoding RNAs with covalently closed loop structures[ 15 ]. CircRNAs are involved in various diseases such as metabolic disorders[ 16 ], cardiovascular diseases[ 17 ], cancer[ 18 ] and IBD[ 19 ], showing their potential role as biomarkers for diagnosis, prognosis, or even as therapeutic targets for IBD. CircRNAs act together with miRNA in various inflammatory process, acting as miRNA sponges and altering their expression, and interacting with proteins[ 19 ].…”