Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations

Area of Science:

• Oncology
• Molecular Biology
• Structural Biology

Background:

• Cancer mutations can create novel protein-protein interactions driving aberrant cellular functions.
• KBTBD4, a substrate receptor in the CULLIN3-RING E3 ubiquitin ligase complex, is frequently mutated in medulloblastoma, leading to gain-of-function.
• These KBTBD4 mutations induce the degradation of the transcriptional corepressor CoREST, but the underlying mechanism was unclear.

Purpose of the Study:

• To elucidate the mechanism by which KBTBD4 mutations promote CoREST degradation.
• To characterize the structural and functional consequences of KBTBD4 mutations in medulloblastoma.
• To identify potential therapeutic strategies targeting the KBTBD4-HDAC1 interaction.

Main Methods:

• Deep mutational scanning to map the KBTBD4 cancer hotspot.
• Cryo-electron microscopy to determine the structure of KBTBD4 mutants bound to LSD1-HDAC1-CoREST.
• In vitro assays to assess the impact of mutations on protein interactions and cellular proliferation.

Main Results:

• KBTBD4 mutations promote CoREST degradation by engaging HDAC1/2 as a direct target.
• Deep mutational scanning revealed specific mutation preferences driving gain-of-function.
• Cryo-EM structures showed KBTBD4 homodimers asymmetrically binding HDAC1, with mutations stabilizing the interface by inserting into the HDAC1 active site.
• Molecular glue UM171 and HDAC1/2 inhibitors demonstrated therapeutic potential by disrupting the mutant KBTBD4-HDAC1 interaction and inhibiting cancer cell proliferation.

Conclusions:

• KBTBD4 mutations drive medulloblastoma through neomorphic interactions with HDAC1/2, leading to CoREST degradation.
• Structural and mutational analyses provide a mechanistic basis for targeting this aberrant interaction.
• Targeting the KBTBD4-HDAC1 interface with inhibitors or molecular glues represents a promising therapeutic avenue for KBTBD4-mutant medulloblastoma.