Systematic discovery of mutation-directed neo-protein-protein interactions in cancer

Comprehensive sequencing of patient tumors reveals genomic mutations across tumor types that enable tumorigenesis and progression. A subset of oncogenic driver mutations results in neomorphic activity where the mutant protein mediates functions not engaged by the parental molecule. Here, we identify prevalent variant-enabled neomorph-protein-protein interactions (neoPPI) with a quantitative high-throughput differential screening (qHT-dS) platform. The coupling of highly sensitive BRET biosensors with miniaturized co expression in an ultra-HTS format allows large-scale monitoring of the interactions of wild-type and mutant variant counterparts with a library of cancer-associated proteins in live cells. The screening of 17,792 interactions with 2,172,864 data points revealed a landscape of gain of interactions encompassing both oncogenic and tumor suppressor mutations. For example, the recurrent BRAF V600E lesion mediates KEAP1 neoPPI, rewiring a BRAF(V600E)/KEAP1 signaling axis and creating collateral vulnerability to NQO1 substrates, offering a combination therapeutic strategy. Thus, cancer genomic alterations can create neo-interactions, informing variant-directed therapeutic approaches for precision medicine.

Automated summary

Comprehensive sequencing of patient tumors can reveal genomic mutations that drive tumorigenesis and progression. Some of these mutations lead to neomorphic activity in the mutant proteins, resulting in functions different from the parental molecules. In this study, a quantitative high-throughput differential screening platform was used to identify prevalent variant-enabled neomorph-protein-protein interactions (neoPPI). By coupling highly sensitive BRET biosensors with miniaturized co-expression in an ultra-HTS format, the researchers were able to monitor the interactions of wild-type and mutant variant counterparts with a library of cancer-associated proteins in live cells on a large scale. The findings revealed a landscape of gain of interactions involving both oncogenic and tumor suppressor mutations, providing potential therapeutic strategies for precision medicine.