Uncovering a highly transforming, Myc-stabilizing isoform of dipeptidase-1 in colorectal cancer

Protein isoforms play significant roles in cancer progression as they can impact localization, binding partners, and functions, especially when it comes to pro-tumorigenic properties. One protein in particular, dipeptidase-1 (DPEP1), was identified 25 years ago as a cell-surface protein upregulated in adenomas and colorectal cancers (CRCs) in comparison to normal colonic tissue. We have found that a diffuse staining pattern of DPEP1, not a cell-surface localization, leads to worse overall and progression-free survival for CRC patients. Spurred by the inconsistency of an intracellular DPEP1 staining pattern for a cell surface protein, we discovered two isoforms of DPEP1 that differ in their C-terminal sequence. This difference reflects an absence of a glycosylphosphatidylinositol anchorage signal sequence in a novel, undescribed isoform of DPEP1, that we have termed DPEP1 Isoform B. We found expression of DPEP1 Isoform B in CRC patient tissue samples which, upon immunohistochemical staining, revealed an intracellular localization of DPEP1 in cells. DPEP1 Isoform B expression transforms a non-tumorigenic cell line to form large, invasive tumors in nude mice and upregulates pro-tumorigenic gene programs including Myc targets, epithelial-to-mesenchymal transition, and angiogenesis as identified by RNA-seq. Surprisingly, in a CRC cell line, we find that DPEP1 Isoform B binds to Myc, increasing its half-life 2-fold. Utilizing TCGA data sets, we deployed a strategy to examine long transcripts and found that DPEP1 Isoform B was present in 91% of CRC patients, with 28% of patients having high expression of DPEP1 Isoform B. To contrast, DPEP1 Isoform A was present in 68% of CRC patients, having high expression in 26% of patients. Overall, our work demonstrates the discovery of a novel isoform of DPEP1, which given its high incidence in CRC, warrants further investigation as a predicative biomarker as well as a novel therapeutic target.