Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition

Area of Science:

• Genomics
• Cancer Biology
• Epigenetics

Background:

• Targeted cancer therapies inhibiting oncokinases like BRAF are crucial but face innate drug resistance.
• Upregulation of the MET receptor tyrosine kinase is a key mechanism mediating this resistance.
• The genomic mechanisms driving MET upregulation in response to targeted therapy remain largely unknown.

Purpose of the Study:

• To identify and functionally characterize lineage-specific enhancers regulating MET expression in cancer.
• To investigate the role of these enhancers in mediating drug resistance to oncokinase inhibitors.
• To explore therapeutic strategies targeting regulatory DNA to overcome resistance.

Main Methods:

• Epigenomic analysis to identify enhancers at the MET locus.
• Chromatin looping assays to assess enhancer-promoter interactions.
• CRISPR-based targeted genomic deletion of transcription factor motifs.
• Functional assays measuring MET expression, cell differentiation, and drug response.

Main Results:

• A melanoma lineage-specific enhancer 63 kb downstream of the MET transcription start site (TSS) was identified.
• This enhancer mediates inducible chromatin looping to the MET promoter, upregulating MET expression upon BRAF inhibition.
• The melanocyte-specific transcription factor MITF was identified as the key regulator of this enhancer.
• Targeted deletion of the MITF motif in the enhancer abolished inducible looping and drug resistance, while preserving MITF-dependent differentiation.

Conclusions:

• Lineage-specific enhancers can drive oncogene upregulation and mediate innate drug resistance in cancer.
• Epigenomic analysis can identify functional regulatory elements that contribute to therapeutic resistance.
• Targeting regulatory DNA offers a strategy to decouple oncogenic and anti-oncogenic functions of transcription factors, potentially blocking resistance to targeted therapies.