SLIDE 1
Circular ecDNA promotes accessible chromatin and high oncogene expression
Wu, S. et. al (2019). Nature, 575(7784), 699-703. Marissa Di
SLIDE 2 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.
SLIDE 3 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.
SLIDE 4 Topics
- ecDNA is circular
- ecDNA drives massive oncogene expression
- ecDNA contains highly accessible chromatin
- ecDNA enables ultra-long-range chromatin contacts
SLIDE 5
Workflow: ecDNA structure and function
SLIDE 6 Topics
- ecDNA is circular
- ecDNA drives massive oncogene expression
- ecDNA contains highly accessible chromatin
- ecDNA enables ultra-long-range chromatin contacts
SLIDE 7
Amplicon Architect pipeline
SLIDE 8
Microscopy shows ecDNA circularity
SLIDE 9
3D ecDNA reconstruction structures
SLIDE 10 Topics
- ecDNA is circular
- ecDNA drives massive oncogene expression
- ecDNA contains highly accessible chromatin
- ecDNA enables ultra-long-range chromatin contacts
SLIDE 11
ecDNA-encoded genes are highly expressed
SLIDE 12
Copy number is greater in circular AMPs
SLIDE 13
Proposed mechanism of increased copy number
SLIDE 14
Circular genes are amplified
SLIDE 15 Topics
- ecDNA is circular
- ecDNA drives massive oncogene expression
- ecDNA contains highly accessible chromatin
- ecDNA enables ultra-long-range chromatin contacts
SLIDE 16
ecDNA has active histone marks
SLIDE 17
ecDNA has few repressive histone marks
SLIDE 18
ecDNA has periodic fragments but fewer long fragments
SLIDE 19
SLIDE 20
Circular regions contain more ATAC-seq peaks
SLIDE 21
More peaks in circular regions (after normalizing)
SLIDE 22
Assay interpretation
SLIDE 23 Topics
- ecDNA is circular
- ecDNA drives massive oncogene expression
- ecDNA contains highly accessible chromatin
- ecDNA enables ultra-long-range chromatin contacts
SLIDE 24
Organization and circularity in ecDNA
SLIDE 25
4C-seq shows higher distal interaction in ecDNA
SLIDE 26
ecDNA has increased distal interactions
SLIDE 27 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
○ investigate ecDNA for cancer mechanisms ○ potential therapeutic targets
