Circular ecDNA promotes accessible chromatin and high oncogene - PowerPoint PPT Presentation

Circular ecDNA promotes accessible chromatin and high oncogene expression Wu, S. et. al (2019). Nature , 575(7784), 699-703. Marissa Di

Extrachromosomal DNA (ecDNA) ● Known as double minutes ● Large (1-3 Mb) ● Contain 1 or more full genes and regulatory regions ● Visible by light microscopy Hilgenfeld, E. et al (2001). Spectral karyotyping and fluorescence in situ hybridization detect novel chromosomal aberrations. British journal of haematology , 113(2), 305-317.

ecDNA in tumors ● Amplifies oncogenes ● Widespread in cancer ● Selective advantages ● Promote intratumoral genetic heterogeneity Verhaak, R. G., Bafna, V., & Mischel, P. S. (2019). Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nature Reviews Cancer , 19(5), 283-288.

Topics ● ecDNA is circular ● ecDNA drives massive oncogene expression ● ecDNA contains highly accessible chromatin ● ecDNA enables ultra-long-range chromatin contacts

Workflow: ecDNA structure and function

Topics ● ecDNA is circular ● ecDNA drives massive oncogene expression ● ecDNA contains highly accessible chromatin ● ecDNA enables ultra-long-range chromatin contacts

Amplicon Architect pipeline

Microscopy shows ecDNA circularity

3D ecDNA reconstruction structures

Topics ● ecDNA is circular ● ecDNA drives massive oncogene expression ● ecDNA contains highly accessible chromatin ● ecDNA enables ultra-long-range chromatin contacts

ecDNA-encoded genes are highly expressed

Copy number is greater in circular AMPs

Proposed mechanism of increased copy number

Circular genes are amplified

Topics ● ecDNA is circular ● ecDNA drives massive oncogene expression ● ecDNA contains highly accessible chromatin ● ecDNA enables ultra-long-range chromatin contacts

ecDNA has active histone marks

ecDNA has few repressive histone marks

ecDNA has periodic fragments but fewer long fragments

Circular regions contain more ATAC-seq peaks

More peaks in circular regions (after normalizing)

Assay interpretation

Topics ● ecDNA is circular ● ecDNA drives massive oncogene expression ● ecDNA contains highly accessible chromatin ● ecDNA enables ultra-long-range chromatin contacts

Organization and circularity in ecDNA

4C-seq shows higher distal interaction in ecDNA

ecDNA has increased distal interactions

Key points ● ecDNA has higher oncogene expression, increased transcription ○ circular structure (stability) ○ accessible chromatin ○ increased copy number ● ecDNA has long-range chromatin contacts which may affect distal gene expression ● Future ○ investigate ecDNA for cancer mechanisms ○ potential therapeutic targets