Enhancing transcription-replication conflict targets ecDNA-positive cancers.

Area of Science:

• Oncology
• Molecular Biology
• Genetics

Background:

• Extrachromosomal DNA (ecDNA) is a key driver of cancer treatment resistance and poor patient outcomes due to oncogene amplification and rapid genome evolution.
• Currently, no treatments specifically target ecDNA, representing a significant unmet need in cancer therapy.
• ecDNA facilitates massive oncogene transcription and rapid genome evolution, contributing to poor patient survival.

Purpose of the Study:

• To investigate the potential of enhancing transcription-replication conflicts as a strategy for targeted elimination of ecDNA-containing cancers.
• To identify specific molecular mechanisms underlying ecDNA's role in cancer progression and treatment resistance.
• To develop and evaluate novel therapeutic approaches targeting ecDNA vulnerabilities.

Main Methods:

• Analysis of ecDNA transcription and associated single-stranded DNA to quantify transcription-replication conflicts.
• Assessment of nucleotide incorporation rates and replication stress in ecDNA-containing tumors.
• Investigating the role of pRPA2-S33 and CHK1 activation in response to ecDNA-driven stress.
• Evaluating the efficacy of CHK1 inhibition, including a novel inhibitor BBI-2779, in preclinical cancer models.

Main Results:

• ecDNA exhibits higher transcription-replication conflicts and replication stress compared to chromosomal DNA.
• CHK1 activation and DNA double-strand breaks are elevated on ecDNA in a transcription-dependent manner.
• Genetic or pharmacological inhibition of CHK1 leads to preferential death of ecDNA-containing tumor cells.
• The novel CHK1 inhibitor BBI-2779 demonstrates potent and selective killing of ecDNA-containing tumor cells and suppresses tumor growth in a gastric cancer model.

Conclusions:

• Enhancing transcription-replication conflict is a viable strategy for targeted ecDNA elimination in cancer.
• CHK1 inhibition represents a promising therapeutic avenue for treating ecDNA-driven cancers.
• BBI-2779 shows potential as a novel, orally available drug for ecDNA-targeted cancer therapy, overcoming treatment resistance.