Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy

John M. Findlay, Francesc Castro-Giner, Seiko Makino, Emily Rayner, Christiana Kartsonaki, William Cross, Michal Kovac, Danny Ulahannan, Claire Palles, Richard S. Gillies, Thomas P. MacGregor, David Church, Nicholas D. Maynard, Francesca Buffa, Jean-Baptiste Cazier, Trevor A. Graham, Lai-Mun Wang, Ricky A. Sharma, Mark Middleton, Ian Tomlinson

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

How chemotherapy affects carcinoma genomes is largely unknown. Here we report whole-exome and deep sequencing of 30 paired oesophageal adenocarcinomas sampled before and after neo-adjuvant chemotherapy. Most, but not all, good responders pass through genetic bottlenecks, a feature associated with higher mutation burden pre-treatment. Some poor responders pass through bottlenecks, but re-grow by the time of surgical resection, suggesting a missed therapeutic opportunity. Cancers often show major changes in driver mutation presence or frequency after treatment, owing to outgrowth persistence or loss of sub-clones, copy number changes, polyclonality and/or spatial genetic heterogeneity. Post-therapy mutation spectrum shifts are also common, particularly C>A and TT>CT changes in good responders or bottleneckers. Post-treatment samples may also acquire mutations in known cancer driver genes (for example, SF3B1, TAF1 and CCND2) that are absent from the paired pre-treatment sample. Neo-adjuvant chemotherapy can rapidly and profoundly affect the oesophageal adenocarcinoma genome. Monitoring molecular changes during treatment may be clinically useful.
Original languageEnglish
Article number11111
Number of pages13
JournalNature Communications
Volume7
DOIs
Publication statusPublished - 5 Apr 2016

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