Multi-omics data-based analysis characterizes molecular alterations of the vesicle genes in human colorectal cancer

Abstract

Abstract Background: Vesicular genes are crucial to the development of colorectal cancer. Understanding the molecular pathways behind colorectal carcinogenesis and identifying possible treatment targets can be accomplished by analyzing alterations in vesicle genes at multi-omics. Studies on the overall alteration of vesicle genes in colorectal cancer are still lacking, nevertheless. Methods: In order to identify a potential association between vesicle genetic alterations and CRC progression, we analyzed molecular alterations in CRC vesicle genes at eight levels in this study, including mRNA, protein, and epigenetic levels. We also analyzed CRC overall survival related genes that were obtained from public database. Results: The analysis of the chromatin structural variants, DNA methylation, chromatin accessibility, proteins, protein phosphorylation, ubiquitination, and malonylation of our collected CRC tissues in combination with the RNA-seq data from the TCGA database revealed the presence of multiple levels of alterations in CRC vesicle genes. We progressively examined the alterations of vesicle genes in mRNA and protein levels in CRC and discovered the hub genes COL5A1 and HSPA8. Further investigation identified the probable essential transcription factors YY1, CDX2, and CBX3. Conclusions: This study contributes to a thorough knowledge of the connection between vesicle genes alterations in multiple level and the development of CRC and offers a theoretical framework for the identification of novel treatment targets.