The evolution of lung cancer and impact of subclonal selection in TRACERx.
Frankell AM., Dietzen M., Al Bakir M., Lim EL., Karasaki T., Ward S., Veeriah S., Colliver E., Huebner A., Bunkum A., Hill MS., Grigoriadis K., Moore DA., Black JRM., Liu WK., Thol K., Pich O., Watkins TBK., Naceur-Lombardelli C., Cook DE., Salgado R., Wilson GA., Bailey C., Angelova M., Bentham R., Martínez-Ruiz C., Abbosh C., Nicholson AG., Le Quesne J., Biswas D., Rosenthal R., Puttick C., Hessey S., Lee C., Prymas P., Toncheva A., Smith J., Xing W., Nicod J., Price G., Kerr KM., Naidu B., Middleton G., Blyth KG., Fennell DA., Forster MD., Lee SM., Falzon M., Hewish M., Shackcloth MJ., Lim E., Benafif S., Russell P., Boleti E., Krebs MG., Lester JF., Papadatos-Pastos D., Ahmad T., Thakrar RM., Lawrence D., Navani N., Janes SM., Dive C., Blackhall FH., Summers Y., Cave J., Marafioti T., Herrero J., Quezada SA., Peggs KS., Schwarz RF., Van Loo P., Miedema DM., Birkbak NJ., Hiley CT., Hackshaw A., Zaccaria S., TRACERx Consortium None., Jamal-Hanjani M., McGranahan N., Swanton C.
Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource.