The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates
Authors: Buhigas Claudia , Warren Anne Y. , Leung Wing-Kit , Whitaker Hayley C. , Luxton Hayley J. , Hawkins Steve , Kay Jonathan , Butler Adam , Xu Yaobo , Woodcock Dan J. , Merson Sue , Frame Fiona M. , Sahli Atef , Abascal Federico ,   CRUK-ICGC Prostate Cancer Group, Gihawi Abraham , Lambert Adam , Thompson Alan , Futreal Andrew , Menzies Andrew , Baddage Anne , Ng Anthony , Sahil Atef , Kremeyer Barbara , Al-Lazikani Bissan , Massie Charlie , Greenman Christopher , Ogden Christopher , Verrill Clare , Fisher Cyril , Berney Dan , Burns Dan , Leongamornlert Daniel , Jones David , Nicol David , Wedge David , Cahill Declan , Easton Douglas , Rowe Edward , Riabchenko Ekaterina , Bancroft Elizabeth , Mayer Erik , Anokian Ezequiel , Hamdy Freddie , Park Gahee , Pelvender Gill , Leeman Gregory , Gundem Gunes , Zhang Hongwei , Mills Ian G. , Zhang Jingjing , Teague Jon , Zamora Jorge , Karaszi Katalin , Raine Kieran , Matthews Lucy , Stebbings Lucy , Alexandrov Ludmil B. , Marsden Luke , Ahmed Mahbubl , Nykter Matti , Ghori Mohammed , Livni Naomi , Dennis Nening , Van As Nicholas , Camacho Niedzica , Shah Nimish , Kumar Pardeep , Van Loo Peter , Lach Radoslaw , Edwards Sandra , Pita Sara , Field Sarah J. , Thomas Sarah , Tavaré Simon , Scalabrino Stefania , Hazell Steven , McLaren Stuart , Visakorpi Tapio , Mitchell Thomas J. , Dudderidge Tim , Dadaev Tokhir , McDermott Ultan , Bo Valeria , Haberland Valeriia , Gnanapragasam Vincent , Khoo Vincent , Howat William , Jie-Lu Yong , Yu Yongwei , Kote-Jarai Zsofia , Martincorena Iñigo , Bova G. Steven , Foster Christopher S. , Campbell Peter , Maitland Norman J. , Neal David E. , Massie Charlie E. , Lynch Andy G. , Eeles Rosalind A. , Cooper Colin S. , Wedge David C. , Brewer Daniel S. 
Published: September 2022

Abstract
Background
Up to 80% of cases of prostate cancer present with multifocal independent tumour lesions leading to the concept of a field effect present in the normal prostate predisposing to cancer development. In the present study we applied Whole Genome DNA Sequencing (WGS) to a group of morphologically normal tissue (n = 51), including benign prostatic hyperplasia (BPH) and non-BPH samples, from men with and men without prostate cancer. We assess whether the observed genetic changes in morphologically normal tissue are linked to the development of cancer in the prostate.

Results
Single nucleotide variants (P = 7.0 × 10–03, Wilcoxon rank sum test) and small insertions and deletions (indels, P = 8.7 × 10–06) were significantly higher in morphologically normal samples, including BPH, from men with prostate cancer compared to those without. The presence of subclonal expansions under selective pressure, supported by a high level of mutations, were significantly associated with samples from men with prostate cancer (P = 0.035, Fisher exact test). The clonal cell fraction of normal clones was always higher than the proportion of the prostate estimated as epithelial (P = 5.94 × 10–05, paired Wilcoxon signed rank test) which, along with analysis of primary fibroblasts prepared from BPH specimens, suggests a stromal origin. Constructed phylogenies revealed lineages associated with benign tissue that were completely distinct from adjacent tumour clones, but a common lineage between BPH and non-BPH morphologically normal tissues was often observed. Compared to tumours, normal samples have significantly less single nucleotide variants (P = 3.72 × 10–09, paired Wilcoxon signed rank test), have very few rearrangements and a complete lack of copy number alterations.

Conclusions
Cells within regions of morphologically normal tissue (both BPH and non-BPH) can expand under selective pressure by mechanisms that are distinct from those occurring in adjacent cancer, but that are allied to the presence of cancer. Expansions, which are probably stromal in origin, are characterised by lack of recurrent driver mutations, by almost complete absence of structural variants/copy number alterations, and mutational processes similar to malignant tissue. Our findings have implications for treatment (focal therapy) and early detection approaches.