Abstract PO-018: Single cell whole genome sequencing reveals the dynamics of copy number instability at the earliest stages of cancer evolution
Authors: Alexander M. Frankell, Sebastian Hobor, Maise Al-bakir, Eva Grönroos, Charles Swanton
Journal: Cancer Research (2020)

Abstract Background: Cancer evolution occurs though a Darwinian process of natural selection. Selective sweeps occur in most human tumours which obscure early, unsuccessful lineages. In addition, analysis of bulk samples has limited phylogenies to SNVs and Indels, due to methodological difficulties in bulk clonal deconvolution of copy number aberrations (CNAs). Using single cell whole genome sequencing we construct phylogenies of CNAs for murine models of the early stages in lung adenocarcinoma evolution and define features of unsuccessful lineages not yet obscured by full selective sweeps. Methods: Non-invasive tumour tissue was homogenised from EGFRL858R and EGFRL858R/TP53 knock out (KO) mice and subject to 0.1X single cell WGS. Bowtie and AnneuFinder were used to align FASTQ files and call CNAs respectively. A strict quality control step was step applied using read depth and coverage variability, removing 15% of cells. MEDDIC was used to construct phylogenetic trees and ancestral CN states at each node. These ancestral CN states were translated into distinct CN events in the evolutionary history of each tumour. Results: We reconstructed tumour CNA phylogenies using scWGS to determine phylogenetic relationships and time CN events. CNAs in these data were far more heterogenous than in previously published human studies. We noted small populations of progenitor cells which branched off early in evolutionary time, containing far fewer copy number aberrations and which were not genome doubled. These populations allow us to more accurately time CN events such as would be obscured after a full selective sweep. Whole chromosomal events were significantly more likely to occur earlier in evolutionary history than intra-chromosomal events (Wilcoxon test, P &amp;lt; 1e-16, OR = 2.24) and chromosomal gains were also significantly more common at the earlier stages of tumour evolution (Wilcoxon test, P &amp;lt; 1e-16, OR = 1.44). Within whole chromosomal events, gains were significantly more enriched for early timing (Wilcoxon test, P &amp;lt; 1e-16, OR = 7.11). Progenitor cell populations also contained a small number of additional events, which were usually unique to a single cell. We reasoned these events may represent evolutionary dead ends. We found these events were highly enriched for losses in TP53 wild type tumours (Wilcoxon test, P &amp;lt; 1e-16, OR = 11.9) but much less so in TP53 mutant tumours (Wilcoxon test, P = 1e-6, OR = 1.14) suggesting early negative selection against loss of heterozygosity, particularly when TP53 is intact. Discussion: The observed depletion of intrachromosomal events may be caused by a more intact DNA damage response system which is therefore less permissive to chromosomal breaks. Heterozygous losses may be negatively selected due to resultant decreased dosage of a large numbers of genes, upon which the cells become less reliant as cancer progresses. These data are consistent with a recent report of spontaneous CNAs in culture of normal hTERT lines which have a strong preference for gains in a TP53 WT context but not upon TP53 KO. Citation Format: Alexander M. Frankell, Sebastian Hobor, Maise Al-bakir, Eva Grönroos, Charles Swanton. Single cell whole genome sequencing reveals the dynamics of copy number instability at the earliest stages of cancer evolution [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-018.