Nadeem Shaikh1, Alice Mazzagatti1, Simone De Angelis1, Sarah C Johnson1, Bjorn Bakker2,3, Diana C J Spierings2, René Wardenaar2, Eleni Maniati1, Jun Wang1, Michael A Boemo4, Floris Foijer2, Sarah E McClelland5. 1. Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK. 2. European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, AV, the Netherlands. 3. Current address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. 4. Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK. 5. Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK. s.mcclelland@qmul.ac.uk.
Abstract
BACKGROUND: A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induced replication stress induces breakages at common fragile sites, but the exact causes of fragility are debated, and acute genomic consequences of replication stress are not fully explored. RESULTS: We characterize DNA copy number alterations (CNAs) in single, diploid non-transformed cells, caused by one cell cycle in the presence of either aphidicolin or hydroxyurea. Multiple types of CNAs are generated, associated with different genomic regions and features, and observed copy number landscapes are distinct between aphidicolin and hydroxyurea-induced replication stress. Coupling cell type-specific analysis of CNAs to gene expression and single-cell replication timing analyses pinpointed the causative large genes of the most recurrent chromosome-scale CNAs in aphidicolin. These are clustered on chromosome 7 in RPE1 epithelial cells but chromosome 1 in BJ fibroblasts. Chromosome arm level CNAs also generate acentric lagging chromatin and micronuclei containing these chromosomes. CONCLUSIONS: Chromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution. Different inducers of replication stress lead to distinctive CNA landscapes providing the opportunity to derive copy number signatures of specific replication stress mechanisms. Single-cell CNA analysis thus reveals the impact of replication stress on the genome, providing insights into the molecular mechanisms which fuel chromosomal instability in cancer.
BACKGROUND: A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induced replication stress induces breakages at common fragile sites, but the exact causes of fragility are debated, and acute genomic consequences of replication stress are not fully explored. RESULTS: We characterize DNA copy number alterations (CNAs) in single, diploid non-transformed cells, caused by one cell cycle in the presence of either aphidicolin or hydroxyurea. Multiple types of CNAs are generated, associated with different genomic regions and features, and observed copy number landscapes are distinct between aphidicolin and hydroxyurea-induced replication stress. Coupling cell type-specific analysis of CNAs to gene expression and single-cell replication timing analyses pinpointed the causative large genes of the most recurrent chromosome-scale CNAs in aphidicolin. These are clustered on chromosome 7 in RPE1 epithelial cells but chromosome 1 in BJ fibroblasts. Chromosome arm level CNAs also generate acentric lagging chromatin and micronuclei containing these chromosomes. CONCLUSIONS: Chromosomal instability driven by replication stress occurs via focal CNAs and chromosome arm scale changes, with the latter confined to a very small subset of chromosome regions, potentially heavily skewing cancer genome evolution. Different inducers of replication stress lead to distinctive CNA landscapes providing the opportunity to derive copy number signatures of specific replication stress mechanisms. Single-cell CNA analysis thus reveals the impact of replication stress on the genome, providing insights into the molecular mechanisms which fuel chromosomal instability in cancer.
Authors: Anne Letessier; Gaël A Millot; Stéphane Koundrioukoff; Anne-Marie Lachagès; Nicolas Vogt; R Scott Hansen; Bernard Malfoy; Olivier Brison; Michelle Debatisse Journal: Nature Date: 2011-01-23 Impact factor: 49.962
Authors: Bjorn Bakker; Aaron Taudt; Mirjam E Belderbos; David Porubsky; Diana C J Spierings; Tristan V de Jong; Nancy Halsema; Hinke G Kazemier; Karina Hoekstra-Wakker; Allan Bradley; Eveline S J M de Bont; Anke van den Berg; Victor Guryev; Peter M Lansdorp; Maria Colomé-Tatché; Floris Foijer Journal: Genome Biol Date: 2016-05-31 Impact factor: 13.583
Authors: Iosifina P Foskolou; Christian Jorgensen; Katarzyna B Leszczynska; Monica M Olcina; Hanna Tarhonskaya; Bauke Haisma; Vincenzo D'Angiolella; William K Myers; Carmen Domene; Emily Flashman; Ester M Hammond Journal: Mol Cell Date: 2017-04-13 Impact factor: 17.970
Authors: Rebecca A Burrell; Sarah E McClelland; David Endesfelder; Petra Groth; Marie-Christine Weller; Nadeem Shaikh; Enric Domingo; Nnennaya Kanu; Sally M Dewhurst; Eva Gronroos; Su Kit Chew; Andrew J Rowan; Arne Schenk; Michal Sheffer; Michael Howell; Maik Kschischo; Axel Behrens; Thomas Helleday; Jiri Bartek; Ian P Tomlinson; Charles Swanton Journal: Nature Date: 2013-02-28 Impact factor: 49.962