Abstract
Background: Gene expression and alternative splicing (AS) can promote cancer development via complex mechanisms. We aimed to identify and verify the hub AS events and splicing factors associated with the progression of colorectal cancer (CRC).Methods: RNA-Seq data, clinical data, and AS events of 590 CRC samples were obtained from the TCGA and TCGASpliceSeq databases. Cox univariable and multivariable analyses, KEGG, and GO pathway analyses were performed to identify hub AS events and splicing factor/spliceosome genes, which were further validated in five CRCs.Results: In this study, we first compared differentially expressed genes and gene AS events between normal and tumor tissues. Differentially expressed genes were different from genes with differentially expressed AS events. Prognostic analysis and co-expression network analysis of gene expression and gene AS events were conducted to screen five hub gene AS events involved in CRC progression: EPB41L2, CELF2, TMEM130, VCL, and SORBS2. Using qRT-PCR, we also verified that the gene AS events SORBS2 were downregulated in tumor tissue, and gene AS events EPB41L2, CELF2, TMEM130, and VCL were upregulated in tumor tissue. The genes whose mRNA levels were significantly related to the five hub gene AS events were significantly enriched in the GO term of cell division and Notch signaling pathway. Further coexpression of gene AS events and alternative splicing factor genes revealed NOVA1 as a crucial factor regulating the hub gene AS event expression in CRC. Through in vitro experiments, we found that NOVA1 inhibited gene AS event SORBS2, which induced the migration of CRC cells via the Notch pathway.Conclusion: Integrated analysis of gene expression and gene AS events and further experiments revealed that NOVA1-mediated SORBS2 promoted the migration of CRC, indicating its potential as a therapeutic target.
Highlights
Colorectal cancer is one of the most frequently diagnosed malignant cancers and the second leading cause of cancer-related deaths worldwide (Bray et al, 2018)
Using the Venn diagram, we found that most of the genes with differentially expressed mRNA levels were different from the genes with differentially expressed alternative splicing (AS) events (Figure 1C)
GO analysis revealed that pathways enriched by genes with differentially expressed mRNA levels (Figure 1D) were inconsistent with pathways enriched by genes with differentially expressed AS events (Figure 1E)
Summary
Colorectal cancer is one of the most frequently diagnosed malignant cancers and the second leading cause of cancer-related deaths worldwide (Bray et al, 2018). A single RNA precursor can be spliced in different arrangements to synthesize distinct mRNA and protein variants with different structures and functions. This may be one of the main reasons for the increased complexity of biological processes (Climente-Gonzalez et al, 2017). Using the Cancer Genome Atlas (TCGA) project data, Xiong et al (2018) performed a systematic analysis to reveal critical AS events involved in CRC progression. The splicing factor SRSF6 directly binds to exon of ZO-1 mRNA to produce the aberrant ZO-1 isoform, which functions as a tumor-promoting gene in colorectal cancer (Wan et al, 2019). We aimed to identify and verify the hub AS events and splicing factors associated with the progression of colorectal cancer (CRC)
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