Recent work has documented that change in alternative pre-mRNA processing associate with colon cancer. These observations suggest that aberrant pre-mRNA processing may contribute to tumorigenesis. We have demonstrated that the expression levels of several RNA processing factors are misregulated in colon cancer and that generation of alternative mRNA isoforms of the Wnt-signaling LEF/TCF transcription factors activates cell growth. These observations strongly suggest that alternative pre-mRNA processing participates in establishing altered gene expression programs that are characteristic for colon cancer. Here we propose to determine the extent of alternative pre- mRNA processing in colon cancer and to test whether colon cancer-specific mRNA isoforms provide a functional advantage for tumor growth and progression. We will combine experimental analyses with bioinformatics to characterize colon cancer-specific alternative pre-mRNA processing (splicing and polyadenylation). (1) Using high throughput sequencing approaches and computational analyses we will generate a comprehensive list of colon cancer-specific alternative pre-mRNA processing events. (2) Using mRNA isoform-specific knockdown and overexpression approaches we will test the hypothesis that the misexpression of mRNA isoforms changes the colon cancer cell phenotype and alters the ability of normal colon to maintain proper cell cycle control. We will also test the hypothesis that the altered expression of candidate mRNA isoforms triggers tumor formation using colon cancer xenograft models in nude mice. (3) Using cell-based assays and xenograft models we will test the hypothesis that misregulated pre-mRNA processing factors influence proteomic diversity and colon tumorigenesis. The experiments described will highlight colon cancer-specific alternative pre-mRNA processing events that may be crucial for the development of additional screening and outcome predictions. Furthermore, understanding the mechanisms involved in colon cancer-specific alternative pre-mRNA processing may pave the way for novel therapies of human colon cancer. Throughout this project we will rely on our expertise in cancer biology, RNA biology, and bioinformatics to obtain snapshots of gene expression patterns in colon cancer, thus producing a wealth of data useful to the colon cancer research community. The identification of colon cancer-specific alternative pre-mRNA processing events coupled with differential gene expression patterns will be valuable for early detection and improved prediction of colon cancer prognosis. Ultimately, the alternative pre-mRNA processing analysis may uncover new targets for colon cancer therapy.
Alternative pre-mRNA processing is a hallmark of many colon cancer genes, suggesting that aberrant pre-mRNA processing may be beneficial for tumorigenesis. Here, we propose to determine the extent of alternative pre-mRNA processing in colon cancer and to test whether colon cancer-specific mRNA isoforms provide a functional advantage for tumor growth and progression. The value of the molecular insights gained is realized when applying such analyses to colon cancer patients of various stage groupings, as they are likely to provide novel screening, outcome prediction, and therapeutic possibilities.