Year 3 was a breakthrough year for Team eDyNAmiC. We developed the first mouse genetic model of ecDNA-driven tumorigenesis; gained new insight into ecDNA formation mechanisms; and discovered a critical role for mitotic transcription on ecDNA. We learned how ongoing transcription-replication conflicts on ecDNA drive replication stress, contributing to the first ecDNA-directed therapy now being tested in a Phase I clinical trial. We discovered that mitotic transcription drives coordinated inheritance of ecDNA particles during cell division, breaking Mendel’s law of independent assortment, promoting the inheritance of favorable regulatory interactions and epigenetic states on ecDNA. We conducted the largest study of the origins and impact of ecDNA across cancer, revealing origins, contents, and clinical impact. We discovered that ecDNAs amplify not only oncogenes, but also regulatory sequences and immunomodulatory elements, lowering T-cell fractions, contributing to immunosuppression. We developed chemical tools for ecDNA proteins-of-interest that have historically been considered undruggable. We built and shared new ecDNA computational tools. We published 4 papers in Nature, including 3 in one issue with the cover, as well as research papers in Nature Genetics, Cancer Discovery, and Nature Chemical Biology, amongst others. Specific highlights include:

• First mouse genetic ecDNA cancer models (Pradella et al., Nature, 2024) (WP1)
• New insight into mechanisms of ecDNA formation and repair (Rose et al., Cancer Discovery, 2024) (WP1)
• Discovery of rampant replication-transcription collisions on ecDNA and CHK1 synthetic lethality being tested in the clinic (Tang et al., Nature, 2024) (WP2)
• First ecDNA-related mutational signatures (Bailey et al., Nature, 2024) (WP3)
• Transcriptional signatures of ecDNA (Lin et al, eLife, 2024) (WP3)
• Analysed 15,000 tumour samples (GEL) cohort in collaboration with Professor Swanton and TRACERx (Bailey et al., Nature, 2024), revealing ecDNA origins, contents, mutational signatures, and adverse clinical impact (WP4)
• Companion study of Hartwig, TCGA, and PCAWG datasets, revealing association of ecDNA with metastases (Kim et al., Nature Genetics, 2024) (WP4)
• Discovery of coordinated ecDNA inheritance by mitotic transcription, breaking Mendel’s rule of independent assortment (Hung et al., Nature, 2024) (WPs2,5,7)
• Demonstrated role of MYC-paralog amplification on ecDNA in SCLC treatment failure resistance (Choudhri et al, Cancer Discovery, 2024) (WP5)
• New mechanistic insight into ecDNA-mediated cGAS-STING suppression (WP6)
• Developed stereo-and regiochemically defined spirocycle acrylamides and analysed these electrophilic “stereoprobes” in human cancer cells by activity-based protein profiling (Liu et al, JACS, 2024) providing new tool compounds to identify and target ecDNA proteins of interest (Hung et al., Nature, 2024)(WP7)
• Built new ecDNA sequence, long-read (Zhu et al, Genome Research, 2024; Giurgiu et al., Genome Research, 2024), imaging and AI-based computational tools, and built a publicly available data repository
• Ongoing discussions with DepMap and St. Jude cloud database leaders to incorporate ecDNA data and filters to lower barriers to entry to the field of ecDNA research.

The impact of Team eDyNAmiC’s progress during year 3 can be measured both by high-level publications and by how our work has helped shape the cancer research community. We are honoured and delighted to be part of the Cancer Grand Challenges community and look forward to continued discovery and growth in Year 4.