Mapping Single Cell Transcriptomes in the Intra-Tumoural and Associated Territories of Kidney Cancer

Tumour behaviour is intricately dependent on the oncogenic properties of cancer cells and their multi-cellular interactions. To better understand these dependencies within the wider micro-environment, we studied over 270,000 single cell transcriptomes and 100 micro-dissected whole exomes from 12 patients with kidney tumours, prior to validation through the use of spatial transcriptomics. Tissues were sampled from multiple regions of the tumour core, the tumour-normal interface, normal surrounding tissues, and peripheral blood. We found the tissue-type location of CD8+ T cell clonotypes largely defined their exhaustion state, with intra-tumoural spatial heterogeneity that is not well-explained by somatic heterogeneity. De novo mutation calling from single cell RNA sequencing data allows us to broadly infer the clonality of stromal cells and lineage-trace myeloid cell development. We discovered six conserved meta-programmes that distinguish tumour cell function. An epithelial-mesenchymal transition meta-programme, highly enriched at the tumour-normal interface appears co-localised with IL1B expressing macrophages, which could represent a plausible therapeutic target.Funding Information: This work was supported by Cancer Research UK/Royal College of Surgeons Clinician Scientist Fellowship (T.J.M: C63474/A27176), British Heart Foundation (R.L), the National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre and the NIHR Blood and Transplant Research Unit (J.R.F. and M.R.C), Kidney Research UK Clinical PhD Fellowship (K.W.L.: TF_013_20171124), Wellcome Science Strategic Award for the Human Cell Atlas (G.S.B), Medical Research Council Human Cell Atlas Research Grant (M.R.C.: MR/S035842/1), Cancer Research UK Cambridge Centre (A.W.: C9685/A25177), Kidney Cancer UK and Facingup2Kidney cancer (M.G.B.T). The Wellcome Sanger Institute is supported by core funding from the Wellcome Trust (206194).Conflict of Interests:In the past 3 years, S.A.T has consulted for Roche and Genentech and is a Scientific Advisory Board member of Qiagen, Foresite labs, Biogen and GSK, as well as a consultant and equity holder as co-founder of Transition Bio. All other authors declare no competing interests.Ethical Approval: Human kidney and tumour tissues were collected through studies approved by UK NHS research ethics committees. All adult kidneys samples, except PD44967 were collected from patients enrolled in the DIAMOND study; Evaluation of biomarkers in urological disease (NHS National Research Ethics Service reference 03/018). Tumour PD44967 was collected from a patient enrolled in Characterisation of the immunological and biological markers of Renal cancer progression (NHS National Research Ethics Service reference 16/WS/0039).