Abstract PR011: Comprehensive longitudinal tracking of lung cancer evolutionary clonal dynamics during therapy using circulating tumour DNA
Authors: Frankell Alexander M. , Abbosh Christopher , Grigoriadis Kristiana , Lim Emilia , Veeriah Selvaraju , Ward Sophia , Karasaki Tak , Black James R. M. , Jamal-Hanjani Mariam , McGranahan Nicholas , Swanton Charles 
Published: February 2024

Abstract
Background: Outgrowth of resistance cancer cell populations is a common mechanism of therapy failure in oncology. Effective personalised medicine relies on targeting of ubiquitous aberrations; however, tumours are highly heterogenous. Liquid biopsies have the potential to provide representative tumour sampling at regular intervals through disease course, but extensive interrogation of longitudinal clonal evolution through therapy has been lacking, particularly for patients on a curative disease pathway. Methods: We analysed 1102 plasma samples from 202 early-stage non-small cell lung cancer patients who underwent multiregional whole exome sequencing of primary tumour, relapse and, where available, comprehensive post-mortem samples. We designed personalised panels targeting a median of 200 mutations for each patient and sequenced cell-free DNA (cfDNA) around these variant sites to saturation. For four patients we designed personalised panels including all clonal and subclonal mutations discovered (up to 600). One of these four patients received a personalised neoantigen vaccine. We used ECLIPSE to determine the clonal composition of low tumour fraction ctDNA. Results: We found a directly proportional correlation between the cancer cell fraction (CCF) of subclones estimated in plasma and multiregional tissue samples at surgery. Lower plasma CCFs were observed for clonal illusion mutations from randomly selected single samples, one for each TRACERx patient, when compared to truly clonal mutations (P &lt; 0.001, OR = 0.44), distinguishing appropriate therapeutic targets without multiregional sampling. In 24 patients with both cfDNA and tissue available at relapse we detected 28/29 relapse tissue subclones in the cfDNA with an additional 8 cfDNA unique subclones. We found a strong bias for cfDNA unique subclones to be present in only subset of cells (P = 0.008, OR = 5.5), consistent with insufficient tissue sampling. We observed longitudinal clonal dynamics which were often, but not always, associated with treatment. Metastatic competent subclones had higher CCFs in the primary tumour, as measured in pre-operative plasma (P &lt; 0.001, OR = 4.5). Upon receiving a personalised neoantigen vaccine a patient had regression of clones harbouring a targeted EGFR mutation. However, copy number loss of the targeted EGFR mutation occurred in a liver lesion which grew over the treatment period on surveillance radiology alongside a novel ctDNA subclone. Upon cessation vaccine treatment the resistance-associated subclone and liver lesion underwent regression. EGFR mutant clones become dominant in the tumour thereafter suggesting a fitness cost associated with vaccine resistant EGFR mutation loss in this patient, measured using ctDNA. Conclusions: We find evidence that comprehensive tracking of subclonal mutations in plasma can accurately profile the clonal structure of tumours over time, revealing clonal dynamics in response to treatment and biological determinants of metastasis with the potential to guide personalised medicine.
Citation Format: Alexander M. Frankell, Christopher Abbosh, Kristiana Grigoriadis, Emilia Lim, Selvaraju Veeriah, Sophia Ward, Tak Karasaki, James R. M. Black, Mariam Jamal-Hanjani, Nicholas McGranahan, Charles Swanton. Comprehensive longitudinal tracking of lung cancer evolutionary clonal dynamics during therapy using circulating tumour DNA [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr PR011.