Dynamic optimization of extrachromosomal DNA copy number drives tumour evolution

Area of Science:

• Cancer Biology
• Genetics
• Genomics

Background:

• Extrachromosomal DNA (ecDNA) is prevalent in human cancers and linked to poor prognosis.
• The mechanisms translating ecDNA-driven genetic heterogeneity into functional diversity are not well understood.

Purpose of the Study:

• To investigate how ecDNA copy number heterogeneity influences gene expression, cellular behavior, and tumor evolution.
• To explore the role of ecDNA plasticity in drug resistance and tumor adaptation.

Main Methods:

• Single-cell multiomics sequencing
• Multiplexed immunofluorescence and fluorescence in situ hybridization (IF-FISH)
• Live-cell lineage tracking
• In vivo tumor experiments

Main Results:

• Asymmetric ecDNA inheritance generates copy number heterogeneity, impacting gene expression, oncogenic signaling, and stress responses.
• ecDNA heterogeneity arises rapidly (within few cell divisions) and influences daughter cell division timing.
• An optimal ecDNA copy number range maximizes proliferative fitness, which shifts under drug pressure (CHK1 inhibition) to favor low copy numbers.
• Pre-existing and de novo generated low ecDNA copy number cells drive drug resistance.
• Shifts in ecDNA copy number optimize tumor growth within specific microenvironments, enhancing tumorigenicity.

Conclusions:

• ecDNA copy number plasticity is a key driver of tumor evolution and adaptation.
• Understanding ecDNA dynamics is crucial for developing effective cancer therapies and predicting treatment outcomes.