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Updated: Nov 17, 2025
A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis
Published on: March 8, 2022
Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen
Corinna Jie Hui Goh1, Jin Huei Wong1, Chadi El Farran2
1Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore.
Abstract:
Vemurafenib is a BRAF kinase inhibitor (BRAFi) that is used to treat melanoma patients harboring the constitutively active BRAF-V600E mutation. However, after a few months of treatment patients often develop resistance to vemurafenib leading to disease progression. Sequence analysis of drug-resistant tumor cells and functional genomic screens has identified several genes that regulate vemurafenib resistance. Reactivation of mitogen-activated protein kinase (MAPK) pathway is a recurrent feature of cells that develop resistance to vemurafenib. We performed a genome-scale CRISPR-based knockout screen to identify modulators of vemurafenib resistance in melanoma cells with a highly improved CRISPR sgRNA library called Brunello. We identified 33 genes that regulate resistance to vemurafenib out of which 14 genes have not been reported before. Gene ontology enrichment analysis showed that the hit genes regulate histone modification, transcription and cell cycle. We discuss how inactivation of hit genes might confer resistance to vemurafenib and provide a framework for follow-up investigations.
Insights
Vemurafenib resistance in melanoma is common. Researchers used a CRISPR screen to find new genes involved in this resistance, offering potential new therapeutic targets for BRAF-mutant melanoma.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Vemurafenib is a BRAF kinase inhibitor (BRAFi) effective against BRAF-V600E mutated melanoma.
- Acquired resistance to vemurafenib frequently occurs, leading to disease progression.
- Reactivation of the mitogen-activated protein kinase (MAPK) pathway is a common mechanism of resistance.
Purpose of the Study:
- To identify novel genetic modulators of vemurafenib resistance in melanoma using a genome-scale CRISPR knockout screen.
- To discover previously unreported genes associated with vemurafenib resistance.
Main Methods:
- Utilized a genome-scale CRISPR-based knockout screen with the Brunello sgRNA library in melanoma cells.
- Performed sequence analysis of drug-resistant tumor cells and functional genomic screens.
- Conducted gene ontology enrichment analysis on identified hit genes.
Main Results:
- Identified 33 genes that regulate vemurafenib resistance.
- 14 of the identified genes have not been previously reported in the context of vemurafenib resistance.
- Enrichment analysis revealed that hit genes are involved in histone modification, transcription, and cell cycle regulation.
Conclusions:
- Inactivation of identified genes may confer resistance to vemurafenib.
- These findings provide a framework for future investigations into overcoming vemurafenib resistance.
- Discovery of novel resistance mechanisms could lead to improved therapeutic strategies for melanoma.
