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Updated: Aug 8, 2026
A Method for Screening and Validation of Resistant Mutations Against Kinase Inhibitors
Published on: December 7, 2014
Integrated CRISPR screening and drug profiling identifies combination opportunities for EGFR, ALK, and BRAF/MEK
Ralph Tiedt1, Frederick J King2, Christelle Stamm1
1Novartis Institutes for BioMedical Research, Oncology Disease Area, Basel, Switzerland.
Abstract:
Anti-tumor efficacy of targeted therapies is variable across patients and cancer types. Even in patients with initial deep response, tumors are typically not eradicated and eventually relapse. To address these challenges, we present a systematic screen for targets that limit the anti-tumor efficacy of EGFR and ALK inhibitors in non-small cell lung cancer and BRAF/MEK inhibitors in colorectal cancer. Our approach includes genome-wide CRISPR screens with or without drugs targeting the oncogenic driver ("anchor therapy"), and large-scale pairwise combination screens of anchor therapies with 351 other drugs. Interestingly, targeting of a small number of genes, including MCL1, BCL2L1, and YAP1, sensitizes multiple cell lines to the respective anchor therapy. Data from drug combination screens with EGF816 and ceritinib indicate that dasatinib and agents disrupting microtubules act synergistically across many cell lines. Finally, we show that a higher-order-combination screen with 26 selected drugs in two resistant EGFR-mutant lung cancer cell lines identified active triplet combinations.
Insights
This study identifies key genes like MCL1, BCL2L1, and YAP1 that can overcome resistance to targeted cancer therapies. Combining drugs, including dasatinib, shows synergistic effects, improving anti-tumor efficacy in lung and colorectal cancers.
Area of Science:
- Oncology
- Genomics
- Pharmacology
Background:
- Targeted therapies for EGFR and ALK in non-small cell lung cancer (NSCLC), and BRAF/MEK in colorectal cancer (CRC), show variable efficacy and lead to tumor relapse.
- Identifying novel targets and drug combinations is crucial to enhance anti-tumor responses and overcome therapeutic resistance.
Purpose of the Study:
- To systematically screen for genetic targets that limit the efficacy of EGFR, ALK, BRAF, and MEK inhibitors.
- To identify synergistic drug combinations that enhance the anti-tumor activity of these targeted therapies in NSCLC and CRC.
Main Methods:
- Genome-wide CRISPR screens were performed with and without anchor therapies (EGFR, ALK, BRAF/MEK inhibitors).
- Large-scale pairwise combination screens were conducted using anchor therapies with 351 additional drugs.
- Higher-order combination screens with 26 selected drugs were performed in resistant EGFR-mutant lung cancer cell lines.
Main Results:
- Targeting genes such as MCL1, BCL2L1, and YAP1 sensitized multiple cell lines to anchor therapies.
- Dasatinib and microtubule-disrupting agents demonstrated synergistic activity with EGFR and ALK inhibitors across numerous cell lines.
- Active triplet combinations were identified in resistant EGFR-mutant lung cancer models.
Conclusions:
- MCL1, BCL2L1, and YAP1 are key regulators of sensitivity to targeted therapies in NSCLC and CRC.
- Combinatorial approaches involving dasatinib and microtubule agents hold promise for improving targeted cancer therapy efficacy.
- Multi-drug combinations can overcome resistance mechanisms in advanced lung and colorectal cancers.
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