78P - Exploring ecDNA heterogeneity and evolution in non-small cell lung cancer

Background

During progression, tumours accumulate aberrations such as circular extra chromosomal DNA (ecDNA). These ecDNA elements often harbour proto-oncogenes or oncogenic regulatory elements, giving cells where they are found in higher number an advantage for proliferation or survival. Due to the lack of centromeres, ecDNA segregates unequally into daughter cells during cell division, making rapid accumulation in a single cell possible. However, our understanding of ecDNA biology remains limited, and further exploration of its contribution to intra-tumour heterogeneity and impact on cancer progression is needed.

Methods

In this work, we investigate the heterogeneity of ecDNA in primary NSCLC tumours and its evolution during disease course using multi-region and multi-time point whole genome sequencing data from 407 samples of 130 patients enrolled in the TRACERx and PEACE studies. Amplicon Architect, a computational tool designed to identify and characterize focal amplifications from sequencing data, was used to assess the presence of ecDNA in each sample.

Results

We identify ecDNA in 29% of tumours in our cohort. Multi-region sampling shows that the number of detected ecDNAs is positively correlated with the number of sampled regions. Around 50% of detected ecDNA contained at least one known oncogene, however, recurrence of oncogenes across the cohort was low, displaying a diverse range of oncogenes that can be amplified on ecDNA. When sampling multiple regions of the primary tumour, ecDNA is often only detected in a subset of regions, indicating intra-tumour heterogeneity. Patients with ecDNA detected in their primary tumour consistently exhibited ecDNA presence in samples obtained at autopsy, underscoring the persistent nature of ecDNA throughout tumour evolution. Lastly, autopsy samples exhibited the highest number of distinct ecDNA detected per sample, compared to relapse and primary tumour samples.

Conclusions

In conclusion, longitudinal sampling offered valuable insights into the persistence of ecDNA during tumour progression. Gaining insights into how ecDNA in metastatic samples may promote metastasis and foster drug resistance will be valuable for potential clinical intervention.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

TRACERxConsortium.

Funding

Francis Crick Institute which receives its core funding from Cancer Research UK (CC2008, CC2041), the UK Medical Research Council (CC2008, CC2041), and the Wellcome Trust (CC2008, CC2041).

Disclosure

N. Kanu: Financial Interests, Personal, Research Grant, grant support: AstraZeneca; Financial Interests, Personal, Funding: The Rosetree Trust and CRUK. M. Jamal-Hanjani: Financial Interests, Personal, Invited Speaker, Invited speaker honorarium: Oslo Cancer Cluster, Astex Pharmaceutical; Financial Interests, Personal, Invited Speaker, Speaker honorarium: Pfizer, Bristol Myers Squibb; Financial Interests, Personal, Advisory Board, Cancer cachexia research advisory board: Pfizer; Non-Financial Interests, Personal, Advisory Role, Scientific Advisory Board and Steering Committee member: Achilles Therapeutics; Other, Personal, Other, I am named as co-inventor on patent PCT/US2017/028013 relating to methods for lung cancer detection: Patent. C. Swanton: Financial Interests, Personal, Invited Speaker, Activity took place in 2016: Pfizer, Celgene; Financial Interests, Personal, Invited Speaker, October 26th 2020: Novartis; Financial Interests, Personal, Invited Speaker: Roche/Ventana, BMS, AstraZeneca, MSD, Illumina, GSK; Financial Interests, Personal, Advisory Board, Ad Board - November 12th, 2020: Amgen; Financial Interests, Personal, Advisory Board, Current - since 2018: Genentech; Financial Interests, Personal, Advisory Board: Sarah Canon Research Institute; Financial Interests, Personal, Advisory Board, Joined October 2020. Also have stock options: Bicycle Therapeutics; Financial Interests, Personal, Other, Consultancy: Medicxi; Financial Interests, Personal, Advisory Board, Member of the Science Advisory Board. Also had stock options until June 2021: GRAIL; Financial Interests, Personal, Other, Consultancy agreement: Roche Innovation Centre Shanghai; Financial Interests, Personal, Advisory Board, 29 November - 1 December 2022: Novartis; Financial Interests, Personal, Invited Speaker, Oncology Collective - 2nd Nov - 4 Nov 2022 - Atlanta, USA: Roche; Financial Interests, Personal, Advisory Board, ctDNA advisory Board - 24th March 2023: AstraZeneca; Financial Interests, Personal, Invited Speaker, Pfizer Oncology 'Leading the revolution for the future: Pfizer; Financial Interests, Personal, Advisory Board, Scientific Advisory Board and Stock options from September 2023: Relay Therapeutics; Financial Interests, Personal, Advisory Board, Member of the Scientific Advisory Board: SAGA Diagnostics; Financial Interests, Personal, Full or part-time Employment, Chief Clinician since October 2017: Cancer Research UK; Financial Interests, Personal, Ownership Interest, Co-Founder of Achilles Therapeutics. Also, have stock options in this company: Achilles Therapeutics; Financial Interests, Personal, Stocks/Shares, Stocks owned until June 2021: GRAIL, Apogen Biotechnologies; Financial Interests, Personal, Stocks/Shares: Epic Biosciences, Bicycle Therapeutics; Financial Interests, Personal, Stocks/Shares, Stock options: Relay Therapeutics; Financial Interests, Institutional, Research Grant, Funded RUBICON grant - October 2018 - April 2021: Bristol Myers Squibb; Financial Interests, Institutional, Research Grant, Collaboration in minimal residual disease sequencing technologies: Archer Dx Inc; Financial Interests, Institutional, Research Grant: Pfizer, Boehringer Ingelheim; Financial Interests, Institutional, Invited Speaker, Chief Investigator for the MeRmaiD 1and 2 clinical trials and chair of the steering committee: AstraZeneca; Financial Interests, Institutional, Research Grant, Research grant from Oct 2019 - July 2023 - Genetics of CIN and SCNAs for Targeted Discovery (SCEPTRE): Ono Pharmaceutical; Financial Interests, Institutional, Research Grant, Research Grants from 2015: Roche; Financial Interests, Personal, Other, Co-chief investigator: NHS-Galleri Clinical Trial; Financial Interests, Institutional, Research Grant, from October 2022: Personalis; Non-Financial Interests, Personal, Principal Investigator, Chief Investigator for MeRmaiD 1 and 2 clinical trials: AstraZeneca; Non-Financial Interests, Personal, Member of Board of Directors, From 2019-2022: AACR; Non-Financial Interests, Personal, Other, Board of Directors: AACR; Non-Financial Interests, Personal, Advisory Role, EACR Advisory Council member: EACR. All other authors have declared no conflicts of interest.