Investigation of novel regulatory mechanisms of TRIM29 in BC, GC, and CRC patients: systems biology approach to find novel non-coding interactions

Background The rising cancer mortality and increasing incidence demand further investigation, particularly for breast cancer (BC), the leading cause of cancer deaths in women, gastric cancer (GC), among the top five global cancers, and colorectal cancer (CRC), the third most common in men and second in women. Numerous studies have shown that mRNAs and lncRNAs play key roles in cancer regulation. Dysregulation of lncRNAs like NORAD, MIR497-HG, and the TRIM29 gene has been reported in various cancers. This research aimed to explore their potential as biomarkers and tumor suppressors in BC, GC, and CRC. Methods High-throughput gene expression analysis was conducted using R Studio (v4.4.1) with datasets GSE134359, GSE54129, and GSE81558 from GEO. Data normalization and visualization were done with gplots, ggplot2, factoextra, reshape2, EnhancedVolcano, VennDiagram, and pheatmap gplots. PPI networks were sourced from STRING, and pathway enrichment was analyzed via Enrichr and Reactome. Gene ontology and expression analysis were performed using Enrichr and ENCORI, while GEPIA2 was used for correlation and survival analysis. Data visualization was done through NetworkAnalyst and R Studio. qRT-PCR validated the findings in BC, GC, and CRC samples, with data analyzed via the ddCt method using GraphPad Prism (v10.3.1). Results Bioinformatics and qRT-PCR analyses revealed TRIM29 was downregulated in BC and upregulated in CRC, but It reduced in GC despite microarray data suggesting otherwise. TRIM29 showed significant interaction with hsa-miRNA-3940-5p. MIR497-HG expression was notably reduced in BC, GC, and CRC across both microarray and qRT-PCR. It also exhibited strong links with MUC2, MUC4, MUC5AC, and MUC5B. While ENCORI indicated a slight decrease in NORAD expression in BC, qRT-PCR results were not significant. However, NORAD was significantly upregulated in GC and CRC, interacting with key cancer-related genes like MUC4, MUC2, MUC16, MUC3A, and MUC5AC. Conclusion Our findings highlight TRIM29's significant involvement in interferon gamma signaling and Interferon Signaling pathways, where dysregulation can contribute to tumorigenic processes cancer in BC, GC, and CRC. MIR497-HG and NORAD seem to interact with mRNAs and indirectly contribute to signaling pathways that impact tumorigenesis in these cancers. TRIM29, NORAD, and MIR497-HG are potential diagnostic biomarkers in GC and CRC. However, for BC just TRIM29 and MIR497-HG Show diagnostic significance. Our study found strong positive correlations between TRIM29 and the lncRNAs MIR497-HG and NORAD in BC, GC, CRC. The robust associations, particularly between TRIM29 and MIR497-HG in BC and GC, suggest that these interactions may play a role in tumorigenesis.