Using single cell data to validate the cellular origins of a clonal expression biomarker in lung cancer

Abstract

Abstract Background Molecular biomarkers aim to stratify cancer patients into disease subtypes predictive of outcome, improving diagnostic precision beyond clinical descriptors such as tumour stage. Transcriptomic intra-tumour heterogeneity (RNA-ITH) has been shown to confound existing expression-based biomarkers across multiple cancer types. Methods Here, we analyse multi-region whole-exome and RNA sequencing data for 156 tumour regions from 48 TRACERx patients to explore and control for RNA-ITH in non-small cell lung cancer (NSCLC). Results We find that chromosomal instability (CIN) is a major driver of RNA-ITH, and existing prognostic gene expression signatures are vulnerable to tumour sampling bias. To address this, we identify genes expressed homogeneously within individual tumours that encode expression modules of cancer cell proliferation and are often driven by DNA copy-number gains selected early in tumour evolution. Leveraging single-cell data, we examine the origins of the expression signals, and relate our findings to published biological and clinical gene expression signatures. Conclusions Clonal transcriptomic biomarkers overcome tumour sampling bias, associate with survival independently of clinicopathological risk factors, and may provide a general strategy to refine biomarker design across cancer types. Clinical trial identification NCT0188860. Legal entity responsible for the study University College London (UCL/12/0279) and has been approved by an independent Research Ethics Committee (13/LO/1546). Funding Francis Crick Institute that receives its core funding from Cancer Research UK (FC001169, FC001202), the UK Medical Research Council (FC001169, FC001202), and the Wellcome Trust (FC001169, FC001202). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) Consolidator Grant (FP7-THESEUS-617844), European Commission ITN (FP7-PloidyNet 607722), ERC Advanced Grant (PROTEUS) has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 835297), Chromavision – this project has received funding from the European’s Union Horizon 2020 research and innovation programme (grant agreement No. 665233). Disclosure D. Biswas: Non-remunerated activity/ies, patent co-inventor: CRUK; Studentship: Jean Shanks Foundation MBPhD; Funding (self): MBPhD programme at University College London; Funding (institution): the NIHR BRC at University College London Hospitals. N.J. Birkbak: Non-remunerated activity/ies, patent co-inventor: CRUK; Fellow: Lundbeck Foundation; Funding (self): the Aarhus University Research Foundation; Funding (institution): Danish Cancer Society. N. McGranahan: Non-remunerated activity/ies, patent co-inventor: CRUK. Fellow: Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant Number 211179/Z/18/Z); Funding (institution): CRUK, Rosetrees, the NIHR BRC at University College London Hospitals. C. Swanton: Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca; Advisory / Consultancy, Research grant / Funding (institution): BMS; Advisory / Consultancy, Research grant / Funding (institution): Roche; Advisory / Consultancy, Research grant / Funding (institution): Ventana; Advisory / Consultancy: Novartis; Advisory / Consultancy: GlaxoSmithKline; Advisory / Consultancy: MSD; Advisory / Consultancy: Celgene; Advisory / Consultancy: Illumina; Advisory / Consultancy: Genentech; Advisory / Consultancy, Shareholder / Stockholder / Stock options: GRAIL; Advisory / Consultancy: Medicxi; Advisory / Consultancy: Sarah Cannon Research Institute; Advisory / Consultancy: Dynamo Therapeutics; Shareholder / Stockholder / Stock options: ApoGen Biotechnologies; Shareholder / Stockholder / Stock options: Epic Bioscience; Shareholder / Stockholder / Stock options: Achilles Therapeutics. Funding (institution) Cancer Research UK (TRACERx and CRUK Cancer Immunotherapy Catalyst Network), the CRUK Lung Cancer Centre of Excellence, Stand Up 2 Cancer (SU2C), the Rosetrees Trust, Butterfield and Stoneygate Trusts, NovoNordisk Foundation (ID16584), the Prostate Cancer Foundation, the Breast Cancer Research Foundation (BCRF), National Institute for Health Research, the University College London Hospitals Biomedical Research Centre, and the Cancer Research UK University College London Experimental Cancer Medicine Centre.