As we embark on Year 3 of Team eDyNAmiC, we reflect on Year 2’s progress and impact.

Year 2 was transformative for Team eDyNAmiC. We built on year 1 progress by further integrating powerful new technologies and learning from patients. Our team grew stronger and more integrated, and we brought in a new member to enhance our capabilities. During year 2, we addressed a key goal by developing 3 new genetic models of ecDNA, including in mice with an intact immune system. We made remarkable progress in our mechanistic understanding of ecDNA formation and function, revealing new mechanisms of non-Mendelian inheritance, and discovering that because of open ecDNA chromatin, ecDNA-containing tumours have a pharmacologically actionable vulnerability that is now being tested in a Phase I clinical trial. Our understanding of the role of ecDNA in suppressing both the innate and adaptive immune system grew by leaps and bounds, explaining why ecDNA-containing cancers are so resistant to immunotherapies and revealing potential therapeutic strategies to reverse it. We also made major advances in our unique chemistry for drugging the undruggable in ecDNA-containing cancers. Collectively, during year 2, we crossed a threshold, transitioning from ecDNA as a compelling new biology to revealing the immense potential for impact for a great many cancer patients.

We highlight the following year 2 impacts:

1. Developed 3 new genetic approaches for generating ecDNA in human and mouse cells, including 2 in vivo mouse models with an intact immune system
2. Revealed distinct repair pathways for ecDNA generation vs. chromosomal DNA breaks
3. Discovered coordinated inheritance of ecDNA species in cell division, revealing a critical role for mitotic transcription
4. Developed new technologies for ecDNA detection, including a digital droplet PCR-based method that allows us to detect ecDNA-derived breakpoints at very high sensitivity
5. Developed a single-cell ecDNA and RNA sequencing method (scEC&Tseq), identifying transcriptional signatures of ecDNA-containing tumours and revealing coordinate transcriptional immunosuppression and upregulation of DNA damage and response pathways
6. Developed a new optical mapping approach for distinguishing breakage fusion bridge-based amplification from ecDNA, revealing significantly worse prognosis and more rapid genome evolution in ecDNA-containing tumours
7. Conducted the two largest scale studies of ecDNA in patients ever accomplished, gaining critical new insight into the origin, evolution, mutational signatures, tumour suppressor, and tissue contexts of ecDNA and their impact on patients
8. Discovered that ecDNAs may suppress the innate immune system by disrupting cGAS signalling and provided mouse model data showing that the lack of response to immune checkpoint inhibitors can be reversed by genetically activating cGAS signalling
9. From patient samples, we discovered that ecDNAs amplify immunosuppressive genes potentially blocking the adaptive immune response making ecDNA-containing tumours immune cold, and suggesting potential points of intervention to overcome it
10. Discovered and characterised stereoselective and site-specific monofunctional degraders of the transcriptional regulatory protein ERCC3, for which previous inhibitors (triptolide) have been implicated in regulating ecDNA-driven cancers
11. Developed a streamlined base editing platform to allow for ‘chemistry-first’ characterisation of the contributions of covalent small molecule-protein interactions to cancer cell growth
12. Published at the highest level (Nature, Nature Genetics, Cancer Discovery, Cell Genomics, and PNAS), with two high-profile reviews on ecDNA in Nature Reviews Cancer and Annual Reviews of Cancer Biology
13. Discovered the first therapeutic strategy targeting ecDNAs in cancer, generated by highly accessible chromatin and transcription-replication collisions, now in a Phase I clinical trial.