Christopher Abbosh

Tracking the Evolution of Non–Small-Cell Lung Cancer

BACKGROUND Among patients with non‐small‐cell lung cancer (NSCLC), data on intratumor heterogeneity and cancer genome evolution have been limited to small retrospective cohorts. We wanted to prospectively investigate intratumor heterogeneity in relation to clinical outcome and to determine the clonal nature of driver events and evolutionary processes in early‐stage NSCLC. METHODS In this prospective cohort study, we performed multiregion whole‐exome sequencing on 100 early‐stage NSCLC tumors that had been resected before systemic therapy. We sequenced and analyzed 327 tumor regions to define evolutionary histories, obtain a census of clonal and subclonal events, and assess the relationship between intratumor heterogeneity and recurrence‐free survival. RESULTS We observed widespread intratumor heterogeneity for both somatic copy‐number alterations and mutations. Driver mutations in EGFR, MET, BRAF, and TP53 were almost always clonal. However, heterogeneous driver alterations that occurred later in evolution were found in more than 75% of the tumors and were common in PIK3CA and NF1 and in genes that are involved in chromatin modification and DNA damage response and repair. Genome doubling and ongoing dynamic chromosomal instability were associated with intratumor heterogeneity and resulted in parallel evolution of driver somatic copy‐number alterations, including amplifications in CDK4, FOXA1, and BCL11A. Elevated copy‐number heterogeneity was associated with an increased risk of recurrence or death (hazard ratio, 4.9; P=4.4×10‐4), which remained significant in multivariate analysis. CONCLUSIONS Intratumor heterogeneity mediated through chromosome instability was associated with an increased risk of recurrence or death, a finding that supports the potential value of chromosome instability as a prognostic predictor. (Funded by Cancer Research UK and others; TRACERx ClinicalTrials.gov number, NCT01888601.)

Circulating tumour DNA analyses reveal novel resistance mechanisms to CDK inhibition in metastatic breast cancer

1. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144(5): 646–674. 2. McAllister SS, Weinberg RA. The tumour-induced systemic environment as a critical regulator of cancer progression and metastasis. Nat Cell Biol 2014; 16(8): 717–727. 3. Guinney J, Dienstmann R, Wang X et al. The consensus molecular subtypes of colorectal cancer. Nat Med 2015; 21(11): 1350–1356. 4. Huijbers A, Tollenaar RA, v Pelt GW et al. The proportion of tumorstroma as a strong prognosticator for stage II and III colon cancer patients: validation in the VICTOR trial. Ann Oncol 2013; 24(1): 179–185. 5. Park JH, Richards CH, McMillan DC et al. The relationship between tumour stroma percentage, the tumour microenvironment and survival in patients with primary operable colorectal cancer. Ann Oncol 2014; 25(3): 644–651. 6. Danielsen HE, Hveem TS, Domingo E et al. Prognostic markers for colorectal cancer: estimating ploidy and stroma. Ann Oncol 2018; 29(3): 616–623. 7. Dekker TJ, van de Velde CJ, van Pelt GW et al. Prognostic significance of the tumor-stroma ratio: validation study in node-negative premenopausal breast cancer patients from the EORTC perioperative chemotherapy (POP) trial (10854). Breast Cancer Res Treat 2013; 139(2): 371–379. 8. Courrech Staal EF, Wouters MW, van Sandick JW et al. The stromal part of adenocarcinomas of the oesophagus: does it conceal targets for therapy? Eur J Cancer 2010; 46(4): 720–728. 9. Roxburgh CSD, McMillan DC. The role of the in situ local inflammatory response in predicting recurrence and survival in patients with primary operable colorectal cancer. Cancer Treat Rev 2012; 38(5): 451–466. 10. Galon J, Mlecnik B, Marliot F et al. Validation of the immunoscore (IM) as a prognostic marker in stage I/II/III colon cancer: results of a worldwide consortium-based analysis of 1,336 patients. J Clin Oncol 2016; 34(suppl): 3500. 11. Mlecnik B, Van den Eynde M, Bindea G et al. Comprehensive intrametastatic immune quantification and major impact of immunoscore on survival. J Natl Cancer Inst 2018; 110(1): 97–108. 12. Park JH, McMillan DC, Powell AG et al. Evaluation of a tumor microenvironment-based prognostic score in primary operable colorectal cancer. Clin Cancer Res 2015; 21(4): 882–888. 13. Hynes SO, Coleman HG, Kelly PJ et al. Back to the future: routine morphological assessment of the tumour microenvironment is prognostic in stage II/III colon cancer in a large population-based study. Histopathology 2017; 71(1): 12–26. 14. Le DT, Uram JN, Wang H et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med 2015; 372(26): 2509–2520. 15. Roseweir AK, McMillan DC, Horgan PG, Edwards J. Colorectal cancer subtypes: translation to routine clinical pathology. Cancer Treat Rev 2017; 57: 1–7.

Evolutionary dynamics in pre-invasive neoplasia

Mutational processes occur in normal tissues from conception throughout life. Field cancerization describes the preconditioning of an area of epithelium to tumor growth. Pre-invasive lesions may arise in these fields, however only a minority of pre-invasive neoplasia progresses to overt malignancy. Within this review we discuss recent advances in our understanding of genomic instability processes in normal tissue, describe evolutionary dynamics in pre-invasive disease and highlight current evidence describing how increasing genomic instability may drive the transition from pre-invasive to invasive disease. Appreciation of the evolutionary rulebooks that operate in pre-invasive neoplasia may facilitate screening strategies, risk-stratification of pre-invasive lesions and precipitate novel preventative treatments in at-risk patient populations.

Early stage NSCLC — challenges to implementing ctDNA-based screening and MRD detection

Circulating tumour DNA (ctDNA) refers to the fraction of cell-free DNA in a patient’s blood that originates from a tumour. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumours have resulted in increased interest in exploiting ctDNA as a tool to facilitate earlier detection of cancer and thereby improve therapeutic outcomes by enabling early intervention. ctDNA analysis might also have utility in the adjuvant therapeutic setting by enabling the identification of patients at a high risk of disease recurrence on the basis of the detection of post-surgical minimal (or molecular) residual disease (MRD). This approach could provide the capability to adapt clinical trials in the adjuvant setting in order to optimize risk stratification, and we argue that this objective is achievable with current technologies. Herein, we evaluate contemporary next-generation sequencing (NGS) approaches to ctDNA detection with a focus on non-small-cell lung cancer. We explain the technical and analytical challenges to low-frequency mutation detection using NGS-based ctDNA profiling and evaluate the feasibility of ctDNA profiling in both screening and MRD assessment contexts.Liquid biopsy approaches hold great promise in early cancer diagnosis or minimal residual disease monitoring for cancer recurrence. Herein, the authors evaluate contemporary next-generation sequencing approaches to circulating tumour DNA detection in these contexts, with a focus on studies in patients with non-small-cell lung cancer. They discuss the feasibility of introducing these strategies into the clinic, highlighting the technical and analytical challenges, as well as possible solutions.

Abstract IA14: Circulating tumor DNA in early-stage NSCLC: A lung TRACERx study

The Cancer Research UK-funded study TRACERx (TRAcking Cancer Evolution through therapy [Rx]) aims to recruit patients undergoing surgery for early-stage non-small cell lung cancer (NSCLC). Patients donate blood pre- and postoperatively alongside multi-region sampled primary tumor tissue. Up to 40% of patients undergoing surgery for NSCLC experience relapse of their disease. At this point patients are approached for relapse tissue sampling. TRACERx therefore provides a strong platform for evaluating circulating tumor DNA (ctDNA) in early-stage NSCLC and a minimal residual disease (MRD) setting. In this presentation we will describe data arising from a phylogenetic, patient-specific approach to ctDNA evaluation in the first 100 patients analyzed as part of TRACERx. We will discuss clinicopathologic factors associated with ctDNA detection in early-stage NSCLC and suggest the existence of distinct tumor phenotypic characteristics that predict the presence of ctDNA at measurable quantities in plasma. Additionally, we will discuss tumor volume limit of detection analyses and highlight potential implications of our findings within the context of early cancer detection. We will then examine data arising from the ctDNA profiling of postoperative plasma samples taken in the adjuvant setting. These data demonstrate that ctDNA detection is specific for NSCLC relapse and that ctDNA detection precedes clinical diagnosis of NSCLC relapse (median lead-time of 77 days, range 10 to 346 days). We will provide examples of using phylogenetic ctDNA profiling to characterize the subclonal nature of relapsing NSCLC as a potential method to personalize relapse therapeutic intervention. Finally, we will highlight potential advantages of patient-specific ctDNA profiling in an adjuvant MRD setting and suggest ways that this technology can be used to fuel adjuvant drug development in NSCLC by driving novel study designs. Citation Format: Christopher Abbosh. Circulating tumor DNA in early-stage NSCLC: A lung TRACERx study [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA14.