title: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing.
abstract: Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer.
  
  
  
  We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients. By comparing the cells' DNA copy number aberration (CNA) landscapes with those of the primary tumors and lymph node metastasis, we establish that 53% of the single cells morphologically classified as tumor cells are DTCs disseminating from the observed tumor. The remaining cells represent either non-aberrant "normal" cells or "aberrant cells of unknown origin" that have CNA landscapes discordant from the tumor. Further analyses suggest that the prevalence of aberrant cells of unknown origin is age-dependent and that at least a subset is hematopoietic in origin. Evolutionary reconstruction analysis of bulk tumor and DTC genomes enables ordering of CNA events in molecular pseudo-time and traced the origin of the DTCs to either the main tumor clone, primary tumor subclones, or subclones in an axillary lymph node metastasis.
  
  
  
  Single-cell sequencing of bone marrow epithelial-like cells, in parallel with intra-tumor genetic heterogeneity profiling from bulk DNA, is a powerful approach to identify and study DTCs, yielding insight into metastatic processes. A heterogeneous population of CNA-positive cells is present in the bone marrow of non-metastatic breast cancer patients, only part of which are derived from the observed tumor lineages.
authors.affiliation: The Francis Crick Institute, London, UK.|Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.
authors.forename: Jonas
authors.identifier: 0000-0002-2660-2478
authors.initials: J
authors.lastname: Demeulemeester
authors.affiliation: Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.|Single-cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Parveen
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
authors.forename: Elen K
authors.initials: EK
authors.lastname: Møller
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
authors.forename: Silje
authors.initials: S
authors.lastname: Nord
authors.affiliation: Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: David C
authors.initials: DC
authors.lastname: Wedge
authors.affiliation: Institute for Genomics & Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL, USA.|Present address: Laboratory of Genetics, University of Wisconsin, Madison, WI, USA.
authors.forename: April
authors.initials: A
authors.lastname: Peterson
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.|Department of Oncology, Division of Surgery and Cancer Medicine, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.|Present address: Department of Oncology, Akershus University Hospital, Lørenskog, Norway.
authors.forename: Randi R
authors.initials: RR
authors.lastname: Mathiesen
authors.affiliation: Department of Pathology, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
authors.forename: Renathe
authors.initials: R
authors.lastname: Fjelldal
authors.affiliation: Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.
authors.forename: Masoud
authors.initials: M
authors.lastname: Zamani Esteki
authors.affiliation: Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.
authors.forename: Koen
authors.initials: K
authors.lastname: Theunis
authors.affiliation: Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.
authors.forename: Elia
authors.initials: E
authors.lastname: Fernandez Gallardo
authors.affiliation: Institute for Genomics & Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL, USA.
authors.forename: A Jason
authors.initials: AJ
authors.lastname: Grundstad
authors.affiliation: Department of Pathology, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
authors.forename: Elin
authors.initials: E
authors.lastname: Borgen
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.|Present address: Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
authors.forename: Lars O
authors.initials: LO
authors.lastname: Baumbusch
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
authors.affiliation: Institute for Genomics & Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL, USA. kpwhite@uchicago.edu.|Tempus Labs, Chicago, IL, 60654, USA. kpwhite@uchicago.edu.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.affiliation: Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway. v.n.kristensen@medisin.uio.no.|Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital, Lørenskog, Norway. v.n.kristensen@medisin.uio.no.
authors.forename: Vessela N
authors.initials: VN
authors.lastname: Kristensen
authors.affiliation: The Francis Crick Institute, London, UK. Peter.VanLoo@crick.ac.uk.|Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium. Peter.VanLoo@crick.ac.uk.
authors.forename: Peter
authors.initials: P
authors.lastname: Van Loo
authors.affiliation: Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium. Thierry.Voet@med.kuleuven.be.|Single-cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, UK. Thierry.Voet@med.kuleuven.be.
authors.forename: Thierry
authors.initials: T
authors.lastname: Voet
authors.affiliation: Department of Oncology, Division of Surgery and Cancer Medicine, Oslo University Hospital, Radiumhospitalet, Oslo, Norway. bjorn.naume@medisin.uio.no.|Institute of Clinical Medicine, University of Oslo, Oslo, Norway. bjorn.naume@medisin.uio.no.
authors.forename: Bjørn
authors.initials: B
authors.lastname: Naume
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D019943:Amino Acid Substitution; D001365:Axilla; D014408:Biomarkers, Tumor; D001854:Bone Marrow Cells / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D056915:DNA Copy Number Variations; D006801:Humans; D007150:Immunohistochemistry; D008198:Lymph Nodes / Q000473:pathology; D008875:Middle Aged; D009154:Mutation; D060787:Neoplasm Grading; D009362:Neoplasm Metastasis; D009367:Neoplasm Staging; D009360:Neoplastic Cells, Circulating / Q000378:metabolism* / Q000473:pathology; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods
chemical_list: D014408:Biomarkers, Tumor
keywords: Disseminated tumor cells; Intra-tumor genetic heterogeneity; Metastasis; Phylogeny; Single-cell sequencing