The mammalian target of rapamycin (mTOR) pathway is critical in regulating cell proliferation/growth and is deregulated in cancer and many metabolic diseases. Thus, studying the mTOR pathway at a molecular level is fundamental to understand disease pathogenesis. These researchers recently discovered genome-wide alterations of polyadenylation sites in mRNAs when mTOR is experimentally activated in mouse embryonic fibroblast cells (MEFs). One striking outcome from this molecular event is an early termination of mRNA transcription to produce truncated mRNAs with polyadenylation in upstream introns/exons. Truncated mRNAs contain distinct molecular signatures at both RNA and protein levels: the new 3’end of mRNAs is from introns (intronic 3’end) and it generates a brand new C-terminus protein sequence encoded from introns. Preliminary data using a custom-developed data mining procedure revealed unknown truncated mRNAs in the mTOR-activated transcriptome, suggesting the likelihood of such new mRNA existence in cancer transcriptome. All truncated proteins that would be synthesized from truncated mRNAs lack catalytic or regulatory domains present in their full-length proteins, suggesting that they are functionally compromised or deregulated, and could be pathogenic “super isoforms.” The researchers found that specific knockdown of truncated mRNAs in mTOR-activated cells drastically impairs cell proliferation, indicating functional consequences of their protein products and a major biological role. Together, they propose that truncated isoforms of mRNAs and proteins are new molecular features of mTOR-activated cancer cells and they create undiscovered complexities in cancer transcriptome and proteome. Strikingly, interrogation of The Cancer Genome Atlas (TCGA) datasets revealed that truncated mRNAs are highly enriched in breast cancer patient tumors and they cluster in distinct clinical features, suggesting their in vivo functions in mTOR-deregulated cancer mechanisms. Based on these data, a systemic identification of clinically relevant truncated mRNAs and understanding the importance of those transcripts in cancer pathogenesis are needed. Thus, this group has initiated studies to identify cancer-enriched truncated mRNAs using a new data mining procedure and to uncover the mechanism of truncated mRNA production. Their central hypothesis is that truncation of mRNAs and consequent alterations in proteome are a major cause of cellular deregulation associated with carcinogenesis.
The goals of this project are to discover truncated mRNA isoforms using an mTOR inhibitor-driven high-throughput profiling experiments and to assess their pathogenic functions in cell proliferation. If the group's hypothesis proves true, they will reveal a brand-new class of biological molecules (truncated mRNAs and proteins) as well as new pathogenic mechanisms wherein super isoforms of proteins are expressed from gene units with altered functions. These findings will uncover a hidden layer of gene expression regulating cellular function, establishing a new paradigm for understanding cancer mechanisms.