Tracking Cancer Evolution through the Disease Course

Abstract

During cancer evolution, constituent tumor cells compete under dynamic selection pressures. Phenotypic variation can be observed as intratumor heterogeneity, which is propagated by genome instability leading to mutations, somatic copy-number alterations, and epigenomic changes. TRACERx was set up in 2014 to observe the relationship between intratumor heterogeneity and patient outcome. By integrating multiregion sequencing of primary tumors with longitudinal sampling of a prospectively recruited patient cohort, cancer evolution can be tracked from early- to late-stage disease and through therapy. Here we review some of the key features of the studies and look to the future of the field. SIGNIFICANCE: Cancers evolve and adapt to environmental challenges such as immune surveillance and treatment pressures. The TRACERx studies track cancer evolution in a clinical setting, through primary disease to recurrence. Through multiregion and longitudinal sampling, evolutionary processes have been detailed in the tumor and the immune microenvironment in non-small cell lung cancer and clear-cell renal cell carcinoma. TRACERx has revealed the potential therapeutic utility of targeting clonal neoantigens and ctDNA detection in the adjuvant setting as a minimal residual disease detection tool primed for translation into clinical trials.

Figure 1. Outline of TRACERx Lung and PEACE autopsy studies.

1. Following a diagnosis of early stage non-small cell lung cancer, patients undergo surgery to resect their primary tumour (with adjuvant chemotherapy, depending on disease stage). Multiple regions from the primary tumour are sampled. In the event of recurrent disease, biopsies are obtained where possible. Patients that are enrolled in the PEACE study have multiple sites of disease sampled for analysis. Tumour samples are processed for whole exome sequencing, RNA-seq and tissue microarrays. 2. Recruitment sites for TRACERx and PEACE in the UK. 3. The core analysis of tumour samples involves calling clonal and subclonal mutation and copy number alterations, with construction of phylogenetic trees. Combining tissue microarray, RNA-seq data and other techniques has facilitated the study of immune and spatial heterogeneity. PV-CTC, pulmonary vein circulating tumour cells.

Figure 2. Tumour evolution in non-small cell lung cancer.

Evolutionary processes in non-small cell lung cancer are outlined. Top, subclonal dynamics over time can be represented by a fish plot, however a single sample in time only provides a snapshot. From this snapshot tumour phylogeny can be inferred. Bottom, evolutionary processes generating immune and genomic heterogeneity are described as part of a ‘tree’. Events that occur in the ‘trunk’ are clonal; i.e. they occur within every cell in the tumour. Through tumour evolution, subclones can emerge through selection; events that occur in these subclones are known as ‘branch’ events.

Figure 3. Clinical trials in tumour evolution.

Outlined are key trials that have been associated with the TRACERx project. Top, the MERMAID-1 trial incorporates bespoke ctDNA panels as MRD detection, following on from the work by Abbosh et al (52). Left, the THETIS and CHIRON trials are first-in-man studies that look at the efficacy of autologous clonal neoantigen reactive T cells in non-small cell lung cancer and melanoma. Clonal neoantigens are identified following tumour sequencing. T cells are subsequently expanded with neo-antigenic peptides and returned to the patient. Right, the DARWIN-II trial investigates the impact of intra-tumour heterogeneity in targeted therapy response in relapsed non small cell lung cancer, combining data from primary tumours sampled in the TRACERx Lung project.