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Updated: Oct 2, 2025
Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
Published on: June 27, 2020
Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations
H Nayanga Thirimanne1,2,3, Feinan Wu4, Derek H Janssens5
1Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
Abstract:
The Fbw7 ubiquitin ligase targets many proteins for proteasomal degradation, which include oncogenic transcription factors (TFs) (e.g., c-Myc, c-Jun, and Notch). Fbw7 is a tumor suppressor and tumors often contain mutations in FBXW7, the gene that encodes Fbw7. The complexity of its substrate network has obscured the mechanisms of Fbw7-associated tumorigenesis, yet this understanding is needed for developing therapies. We used an integrated approach employing RNA-Seq and high-resolution mapping (cleavage under target and release using nuclease) of histone modifications and TF occupancy (c-Jun and c-Myc) to examine the combinatorial effects of misregulated Fbw7 substrates in colorectal cancer (CRC) cells with engineered tumor-associated FBXW7 null or missense mutations. Both Fbw7 mutations caused widespread transcriptional changes associated with active chromatin and altered TF occupancy: some were common to both Fbw7 mutant cell lines, whereas others were mutation specific. We identified loci where both Jun and Myc were coregulated by Fbw7, suggesting that substrates may have synergistic effects. One coregulated gene was CIITA, the master regulator of MHC Class II gene expression. Fbw7 loss increased MHC Class II expression and Fbw7 mutations were correlated with increased CIITA expression in TCGA colorectal tumors and cell lines, which may have immunotherapeutic implications for Fbw7-associated cancers. Analogous studies in neural stem cells in which FBXW7 had been acutely deleted closely mirrored the results in CRC cells. Gene set enrichment analyses revealed Fbw7-associated pathways that were conserved across both cell types that may reflect fundamental Fbw7 functions. These analyses provide a framework for understanding normal and neoplastic context-specific Fbw7 functions.
Insights
Fbw7 mutations in colorectal cancer alter gene expression and transcription factor binding, impacting pathways like MHC Class II expression. This provides a framework for understanding Fbw7
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- The Fbw7 ubiquitin ligase is a tumor suppressor, and its mutations are common in various cancers, including colorectal cancer (CRC).
- Fbw7 regulates numerous oncoproteins, but the complex substrate network has hindered understanding of Fbw7-associated tumorigenesis and therapeutic development.
- Targeting Fbw7's complex substrate network is crucial for developing effective cancer therapies.
Purpose of the Study:
- To investigate the combinatorial effects of misregulated Fbw7 substrates in colorectal cancer cells with engineered FBXW7 mutations.
- To elucidate the transcriptional and epigenetic alterations driven by FBXW7 loss or mutation.
- To identify potential therapeutic targets and implications, particularly regarding immune response.
Main Methods:
- Utilized RNA-sequencing (RNA-Seq) to analyze global gene expression changes.
- Employed high-resolution mapping (cleavage under target and release using nuclease - CUT&RUN) to assess histone modifications and transcription factor (TF) occupancy (c-Jun, c-Myc).
- Engineered colorectal cancer (CRC) cell lines with tumor-associated FBXW7 null or missense mutations and performed analogous studies in neural stem cells.
Main Results:
- FBXW7 mutations induced widespread transcriptional changes and altered TF binding, with both common and mutation-specific effects.
- Identified co-regulation of specific loci by Fbw7, c-Jun, and c-Myc, suggesting synergistic substrate effects.
- Demonstrated that Fbw7 loss increases MHC Class II expression via CIITA upregulation, correlating with FBXW7 mutations in TCGA colorectal tumors and cell lines.
Conclusions:
- FBXW7 mutations significantly alter the transcriptional landscape and TF dynamics in colorectal cancer cells.
- The identified coregulation of CIITA by Fbw7, c-Jun, and c-Myc has potential immunotherapeutic implications for Fbw7-associated cancers.
- The study provides a foundational framework for understanding context-specific Fbw7 functions in both normal and neoplastic settings.
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