Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

Samra Turajlic; Hang Xu; Kevin Litchfield; Andrew Rowan; Stuart Horswell; Tim Chambers; Tim O'Brien; Jose I Lopez; Thomas B K Watkins; David Nicol; Mark Stares; Ben Challacombe; Steve Hazell; Ashish Chandra; Thomas J Mitchell; Lewis Au; Claudia Eichler-Jonsson; Faiz Jabbar; Aspasia Soultati; Simon Chowdhury; Sarah Rudman; Joanna Lynch; Archana Fernando; Gordon Stamp; Emma Nye; Aengus Stewart; Wei Xing; Jonathan C Smith; Mickael Escudero; Adam Huffman; Nik Matthews; Greg Elgar; Ben Phillimore; Marta Costa; Sharmin Begum; Sophia Ward; Max Salm; Stefan Boeing; Rosalie Fisher; Lavinia Spain; Carolina Navas; Eva Grönroos; Sebastijan Hobor; Sarkhara Sharma; Ismaeel Aurangzeb; Sharanpreet Lall; Alexander Polson; Mary Varia; Catherine Horsfield; Nicos Fotiadis; Lisa Pickering; Roland F Schwarz; Bruno Silva; Javier Herrero; Nick M Luscombe; Mariam Jamal-Hanjani; Rachel Rosenthal; Nicolai J Birkbak; Gareth A Wilson; Orsolya Pipek; Dezso Ribli; Marcin Krzystanek; Istvan Csabai; Zoltan Szallasi; Martin Gore; Nicholas McGranahan; Peter Van Loo; Peter Campbell; James Larkin; Charles Swanton; TRACERx Renal Consortium

doi:10.1016/j.cell.2018.03.043

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

Cell. 2018 Apr 19;173(3):595-610.e11. doi: 10.1016/j.cell.2018.03.043. Epub 2018 Apr 12.

Authors

Samra Turajlic¹, Hang Xu², Kevin Litchfield², Andrew Rowan², Stuart Horswell³, Tim Chambers², Tim O'Brien⁴, Jose I Lopez⁵, Thomas B K Watkins², David Nicol⁶, Mark Stares², Ben Challacombe⁴, Steve Hazell⁷, Ashish Chandra⁸, Thomas J Mitchell⁹, Lewis Au¹⁰, Claudia Eichler-Jonsson², Faiz Jabbar², Aspasia Soultati¹¹, Simon Chowdhury¹¹, Sarah Rudman¹¹, Joanna Lynch¹⁰, Archana Fernando⁴, Gordon Stamp¹², Emma Nye¹², Aengus Stewart³, Wei Xing¹³, Jonathan C Smith¹³, Mickael Escudero³, Adam Huffman¹³, Nik Matthews¹⁴, Greg Elgar¹⁴, Ben Phillimore¹⁴, Marta Costa¹⁴, Sharmin Begum¹⁴, Sophia Ward¹⁵, Max Salm³, Stefan Boeing³, Rosalie Fisher², Lavinia Spain¹⁰, Carolina Navas², Eva Grönroos², Sebastijan Hobor², Sarkhara Sharma², Ismaeel Aurangzeb², Sharanpreet Lall¹¹, Alexander Polson⁸, Mary Varia⁸, Catherine Horsfield⁸, Nicos Fotiadis¹⁶, Lisa Pickering¹⁰, Roland F Schwarz¹⁷, Bruno Silva¹³, Javier Herrero¹⁸, Nick M Luscombe¹⁹, Mariam Jamal-Hanjani²⁰, Rachel Rosenthal²¹, Nicolai J Birkbak²², Gareth A Wilson²², Orsolya Pipek²³, Dezso Ribli²³, Marcin Krzystanek²⁴, Istvan Csabai²³, Zoltan Szallasi²⁵, Martin Gore¹⁰, Nicholas McGranahan²⁰, Peter Van Loo²⁶, Peter Campbell²⁷, James Larkin²⁸, Charles Swanton²⁹; TRACERx Renal Consortium

Affiliations

¹ Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
² Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK.
³ Department of Bioinformatics and Biostatistics, the Francis Crick Institute, London NW1 1AT, UK.
⁴ Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK.
⁵ Department of Pathology, Cruces University Hospital, Biocruces Institute, University of the Basque Country, Barakaldo, Spain.
⁶ Department of Urology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
⁷ Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
⁸ Department of Pathology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK.
⁹ Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Department of Surgery, Addenbrooke's Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.
¹⁰ Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
¹¹ Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK.
¹² Experimental Histopathology Laboratory, the Francis Crick Institute, London NW1 1AT, UK.
¹³ Department of Scientific Computing, the Francis Crick Institute, London NW1 1AT, UK.
¹⁴ Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK.
¹⁵ Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK.
¹⁶ Department of Radiology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
¹⁷ Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany.
¹⁸ Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK.
¹⁹ Bioinformatics and Computational Biology Laboratory, the Francis Crick Institute, London NW1 1AT, UK.
²⁰ Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK.
²¹ Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK.
²² Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK.
²³ Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary.
²⁴ Department of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby 2800, Denmark.
²⁵ Department of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
²⁶ Cancer Genomics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium.
²⁷ Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
²⁸ Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK. Electronic address: [email protected].
²⁹ Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK. Electronic address: [email protected].

Abstract

The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of driver event ordering, co-occurrence, and mutual exclusivity at clone level, we show the deterministic nature of clonal evolution. ccRCC can be grouped into seven evolutionary subtypes, ranging from tumors characterized by early fixation of multiple mutational and copy number drivers and rapid metastases to highly branched tumors with >10 subclonal drivers and extensive parallel evolution associated with attenuated progression. We identify genetic diversity and chromosomal complexity as determinants of patient outcome. Our insights reconcile the variable clinical behavior of ccRCC and suggest evolutionary potential as a biomarker for both intervention and surveillance.

Trial registration: ClinicalTrials.gov NCT03226886.

Keywords: branched evolution; cancer evolution; chromosome instability; deterministic evolution; intratumor heterogeneity; linear evolution; metastasis; punctuated evolution; renal cell cancer; tumor diversity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Aged
Aged, 80 and over
Alleles
Biomarkers, Tumor
Carcinoma, Renal Cell / genetics*
Carcinoma, Renal Cell / pathology*
Chromosomes
Clonal Evolution
Disease Progression
Evolution, Molecular
Female
Genetic Heterogeneity
Genetic Variation
Humans
Kidney Neoplasms / genetics*
Kidney Neoplasms / pathology*
Longitudinal Studies
Male
Middle Aged
Models, Statistical
Mutation
Neoplasm Metastasis
Phenotype
Phylogeny
Prognosis
Prospective Studies
Sequence Analysis, DNA

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

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