Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations

Abstract

Fbw7 is a ubiquitin ligase substrate receptor that targets proteins for proteasomal degradation. Most known Fbw7 substrates are transcription factors (TFs) and many are also oncoproteins (e.g., c-Myc, c-Jun, Notch). Fbw7 is an important tumor suppressor and FBXW7 mutations drive tumorigenesis through activation of oncogenic Fbw7 substrates. Defining the mechanisms of Fbw7-associated tumorigenesis is critical for developing targeted therapies. We thus determined the transcriptional consequences of oncogenic Fbw7 mutations by studying isogenic colorectal cancer cell lines with engineered FBXW7 null and heterozygous missense mutations. We used an integrated approach employing RNA-Seq and high-resolution mapping (CUT&RUN) of histone modifications and TF occupancy (c-Jun and c-Myc) to examine the combinatorial effects of mis-regulated Fbw7 substrates. Fbw7 mutations caused widespread transcriptional changes associated with active chromatin and altered TF occupancy at distal regulatory regions. Some regulatory changes were common to both FBXW7-mutant cell lines whereas others were FBXW7 mutation-specific. By comparing c-Jun and c-Myc binding sites, we also identified co-regulated elements, suggesting that Fbw7 substrates may have synergistic effects. One co-regulated gene was CIITA, a master regulator of MHC Class II gene expression, and Fbw7 loss increased CIITA and MHC Class II gene expression in colorectal cancer cells. Fbw7 mutations were also correlated with increased CIITA expression in TCGA colorectal tumors and cell lines, which may have immunologic implications for progression and treatment of Fbw7-associated cancers. This integrative analysis provides a framework for understanding normal and neoplastic context-specific Fbw7 functions.