Investigating Isoform Switching in RHBDF2 for its Role in human Neoplastic Growth in Breast

Abstract

Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing day by day. One major reason is the assumption that a “one gene leads to one protein” approach in most studies undergoing predicting therapeutic drug targets for cancer therapy. Therefore, there is always an immense need to find promising and novel anti-cancer drug targets. Proteases have an integral role in cell proliferation and growth because the proteolysis mechanism is an irreversible process that aids in regulating cellular growth during tumorigenesis. Therefore, they can be considered an important target for cancer treatment. Apart classifying rhomboids into active and inactive rhomboids, alternative splicing tends to produce more transcript isoforms of inactive rhomboids “iRhom2”. Speculatively, previous studies on gene expression analysis of RHBDF2 gene encoding iRhom2 showed heterogenous behaviour during tumorigenesis. Consistent with this, several studies have reported the antagonistic role of iRhom2 in tumorigenesis, i.e. either they are involved in negative regulation of EGFR ligands via ERAD pathway or positively regulate EGFR ligands via EGFR signalling pathway. Additionally, different opinions suggest iRhom2 mediated cleavage of EGFR ligands takes place TACE dependently or TACE independently. However, how to reconcile these seemingly opposing roles is still unclear and might be attributed to more than one transcript isoform of iRhom2. To observe the differences at isoform resolution, the current strategy identified isoform switching in RHBDF2 via differential transcript usage using RNA-seq data during breast cancer initiation and progression. Furthermore, interacting partners were found via correlation and enriched to explain its antagonistic role. Isoform switching was observed at DCIS, grade 2 and grade 3 from canonical to the cub isoform. Neither EGFR nor ERAD was found enriched. However, pathways leading to TACE dependent EGFR signalling pathways were more observant, specifically MAPK signalling pathways, GPCR signalling pathways, and Toll-like receptor pathways. Nevertheless, it was noteworthy that during CTCs, the cub isoform switches back to the canonical isoform, the proteasomal degradation pathway and cytoplasmic ribosomal protein pathways were found significantly enriched. Therefore, it could be inferred that both the isoforms have separate physiological roles to play during tumorigenesis.