51
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Deveau P, Colmet Daage L, Oldridge D, Bernard V, Bellini A, Chicard M, Clement N, Lapouble E, Combaret V, Boland A, Meyer V, Deleuze JF, Janoueix-Lerosey I, Barillot E, Delattre O, Maris JM, Schleiermacher G, Boeva V. QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. Bioinformatics 2019; 34:1808-1816. [PMID: 29342233 PMCID: PMC5972665 DOI: 10.1093/bioinformatics/bty016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/10/2018] [Indexed: 01/13/2023] Open
Abstract
Motivation In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants. Results We present a framework for defining cancer clones using most reliable variants of high depth of coverage and assigning functional mutations to the detected clones. The key element of our framework is QuantumClone, a method for variant clustering into clones based on VAFs, genotypes of corresponding regions and information about tumor purity. We validated QuantumClone and our framework on simulated data. We then applied our framework to whole genome sequencing data for 19 neuroblastoma trios each including constitutional, diagnosis and relapse samples. We confirmed an enrichment of damaging variants within such pathways as MAPK (mitogen-activated protein kinases), neuritogenesis, epithelial-mesenchymal transition, cell survival and DNA repair. Most pathways had more damaging variants in the expanding clones compared to shrinking ones, which can be explained by the increased total number of variants between these two populations. Functional mutational rate varied for ancestral clones and clones shrinking or expanding upon treatment, suggesting changes in clone selection mechanisms at different time points of tumor evolution. Availability and implementation Source code and binaries of the QuantumClone R package are freely available for download at https://CRAN.R-project.org/package=QuantumClone. Contact gudrun.schleiermacher@curie.fr or valentina.boeva@inserm.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Paul Deveau
- Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
- Département de Recherche Translationnelle, Institut Curie, PSL Research University, INSERM U830, Laboratoire RTOP (Recherche Translationelle en Oncologie Pédiatrique), SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Paris, France
- University of Paris-Sud, Orsay, France
| | - Leo Colmet Daage
- Département de Recherche Translationnelle, Institut Curie, PSL Research University, INSERM U830, Laboratoire RTOP (Recherche Translationelle en Oncologie Pédiatrique), SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Paris, France
| | - Derek Oldridge
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginie Bernard
- Institut Curie, PSL Research University, NGS platform ICGex, Paris, France
| | - Angela Bellini
- Département de Recherche Translationnelle, Institut Curie, PSL Research University, INSERM U830, Laboratoire RTOP (Recherche Translationelle en Oncologie Pédiatrique), SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Paris, France
| | - Mathieu Chicard
- Département de Recherche Translationnelle, Institut Curie, PSL Research University, INSERM U830, Laboratoire RTOP (Recherche Translationelle en Oncologie Pédiatrique), SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Paris, France
| | - Nathalie Clement
- Département de Recherche Translationnelle, Institut Curie, PSL Research University, INSERM U830, Laboratoire RTOP (Recherche Translationelle en Oncologie Pédiatrique), SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Paris, France
| | - Eve Lapouble
- Unité de Génétique Somatique, Institut Curie, PSL Research University, Paris, France
| | - Valerie Combaret
- Centre Léon-Bérard Laboratoire de Recherche Translationnelle, Lyon, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de biologie François Jacob, CEA, Evry, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de biologie François Jacob, CEA, Evry, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de biologie François Jacob, CEA, Evry, France
| | - Isabelle Janoueix-Lerosey
- Institut Curie, PSL Research University, INSERM U830, SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Olivier Delattre
- Institut Curie, PSL Research University, INSERM U830, SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - John M Maris
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gudrun Schleiermacher
- Département de Recherche Translationnelle, Institut Curie, PSL Research University, INSERM U830, Laboratoire RTOP (Recherche Translationelle en Oncologie Pédiatrique), SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), Paris, France
- Département de Pédiatrie, Institut Curie, PSL Research University, Paris, France
- To whom correspondence should be addressed. or
| | - Valentina Boeva
- Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, Paris, France
- To whom correspondence should be addressed. or
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52
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De Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda OM, Chin SF, Contente-Cuomo T, Mayor R, Arias A, Ali HR, Cope W, Tiezzi D, Dariush A, Dias Amarante T, Reshef D, Ciriaco N, Martinez-Saez E, Peg V, Ramon Y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, Caldas C. The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer. Cell Rep 2019; 27:2690-2708.e10. [PMID: 31141692 PMCID: PMC6546974 DOI: 10.1016/j.celrep.2019.04.098] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 12/13/2018] [Accepted: 04/22/2019] [Indexed: 02/07/2023] Open
Abstract
The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer.
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Affiliation(s)
- Leticia De Mattos-Arruda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain
| | - Stephen-John Sammut
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Edith M Ross
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Havell Markus
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Sandro Morganella
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yvonne Teng
- Cancer Molecular Diagnosis Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Yosef Maruvka
- The Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA 02129, USA
| | - Bernard Pereira
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Tania Contente-Cuomo
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Regina Mayor
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - Alexandra Arias
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - H Raza Ali
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Wei Cope
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Daniel Tiezzi
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Aliakbar Dariush
- Institute of Astronomy, University of Cambridge, Cambridge CB3 0HA, UK
| | - Tauanne Dias Amarante
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Dan Reshef
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nikaoly Ciriaco
- Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Elena Martinez-Saez
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Vicente Peg
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Santiago Ramon Y Cajal
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Department of Pathology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain; Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Javier Cortes
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Ramon y Cajal Hospital, 28034 Madrid, Spain
| | - George Vassiliou
- Cancer Molecular Diagnosis Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust/MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Gad Getz
- The Broad Institute, Cambridge, MA 02142, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Charlestown, MA 02129, USA
| | - Serena Nik-Zainal
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; Mayo Clinic Center for Individualized Medicine, Scottsdale, AZ, USA
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Florian Markowetz
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Joan Seoane
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona 08035, Spain; Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 2QQ, UK.
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53
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Ramazzotti D, Graudenzi A, De Sano L, Antoniotti M, Caravagna G. Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinformatics 2019; 20:210. [PMID: 31023236 PMCID: PMC6485126 DOI: 10.1186/s12859-019-2795-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 04/08/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the same method can support both data types. RESULTS We introduce TRaIT, a computational framework to infer mutational graphs that model the accumulation of multiple types of somatic alterations driving tumour evolution. Compared to other tools, TRaIT supports multi-region and single-cell sequencing data within the same statistical framework, and delivers expressive models that capture many complex evolutionary phenomena. TRaIT improves accuracy, robustness to data-specific errors and computational complexity compared to competing methods. CONCLUSIONS We show that the application of TRaIT to single-cell and multi-region cancer datasets can produce accurate and reliable models of single-tumour evolution, quantify the extent of intra-tumour heterogeneity and generate new testable experimental hypotheses.
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Affiliation(s)
| | - Alex Graudenzi
- Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, Milan, 20126 Italy
- Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Viale F.lli Cervi 93, Segrate, Milan, 20090 Italy
| | - Luca De Sano
- Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, Milan, 20126 Italy
| | - Marco Antoniotti
- Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, Milan, 20126 Italy
- Milan Center for Neuroscience, Università degli Studi di Milano-Bicocca, San Gerardo Hospital, Via Pergolesi 33, Monza, 20052 Italy
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
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54
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Hodzic E, Shrestha R, Zhu K, Cheng K, Collins CC, Cenk Sahinalp S. Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. Gigascience 2019; 8:giz024. [PMID: 30978274 PMCID: PMC6458499 DOI: 10.1093/gigascience/giz024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/12/2018] [Accepted: 02/21/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Advances in large-scale tumor sequencing have led to an understanding that there are combinations of genomic and transcriptomic alterations specific to tumor types, shared across many patients. Unfortunately, computational identification of functionally meaningful and recurrent alteration patterns within gene/protein interaction networks has proven to be challenging. FINDINGS We introduce a novel combinatorial method, cd-CAP (combinatorial detection of conserved alteration patterns), for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not) and simultaneously detects multiple alteration profile conserved subnetworks. CONCLUSIONS In a number of The Cancer Genome Atlas datasets, cd-CAP identified large biologically significant subnetworks with conserved alteration patterns, shared across many tumor samples.
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Affiliation(s)
- Ermin Hodzic
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- School of Computing Science, Simon Fraser University, 8888 University Dr, Burnaby, BC, V5A 1S6, Canada
| | - Raunak Shrestha
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- Department of Urologic Sciences, University of British Columbia, 2775 Laurel St, Vancouver, BC, V5Z 1M9, Canada
| | - Kaiyuan Zhu
- Department of Computer Science, Indiana University Bloomington, 700 N. Woodlawn Ave, Bloomington, IN, 47408, USA
| | - Kuoyuan Cheng
- Center for Bioinformatics and Computational Biology, University of Maryland, 8125 Paint Branch Dr, College Park, MD, 20742, USA
| | - Colin C Collins
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- Department of Urologic Sciences, University of British Columbia, 2775 Laurel St, Vancouver, BC, V5Z 1M9, Canada
| | - S Cenk Sahinalp
- Laboratory for Advanced Genome Analysis, Vancouver Prostate Centre, 2660 Oak St, Vancouver, BC, V6H 3Z6, Canada
- Department of Computer Science, Indiana University Bloomington, 700 N. Woodlawn Ave, Bloomington, IN, 47408, USA
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Parivesh A, Barseghyan H, Délot E, Vilain E. Translating genomics to the clinical diagnosis of disorders/differences of sex development. Curr Top Dev Biol 2019; 134:317-375. [PMID: 30999980 PMCID: PMC7382024 DOI: 10.1016/bs.ctdb.2019.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The medical and psychosocial challenges faced by patients living with Disorders/Differences of Sex Development (DSD) and their families can be alleviated by a rapid and accurate diagnostic process. Clinical diagnosis of DSD is limited by a lack of standardization of anatomical and endocrine phenotyping and genetic testing, as well as poor genotype/phenotype correlation. Historically, DSD genes have been identified through positional cloning of disease-associated variants segregating in families and validation of candidates in animal and in vitro modeling of variant pathogenicity. Owing to the complexity of conditions grouped under DSD, genome-wide scanning methods are better suited for identifying disease causing gene variant(s) and providing a clinical diagnosis. Here, we review a number of established genomic tools (karyotyping, chromosomal microarrays and exome sequencing) used in clinic for DSD diagnosis, as well as emerging genomic technologies such as whole-genome (short-read) sequencing, long-read sequencing, and optical mapping used for novel DSD gene discovery. These, together with gene expression and epigenetic studies can potentiate the clinical diagnosis of DSD diagnostic rates and enhance the outcomes for patients and families.
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Affiliation(s)
- Abhinav Parivesh
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States
| | - Emmanuèle Délot
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States.
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, United States; Department of Genomics and Precision Medicine, The George Washington University, Washington, DC, United States.
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56
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Xia R, Lin Y, Zhou J, Geng T, Feng B, Tang J. Phylogenetic Reconstruction for Copy-Number Evolution Problems. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:694-699. [PMID: 29993694 DOI: 10.1109/tcbb.2018.2829698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cancer is known for its heterogeneity and is regarded as an evolutionary process driven by somatic mutations and clonal expansions. This evolutionary process can be modeled by a phylogenetic tree and phylogenetic analysis of multiple subclones of cancer cells can facilitate the study of the tumor variants progression. Copy-number aberration occurs frequently in many types of tumors in terms of segmental amplifications and deletions. In this paper, we developed a distance-based method for reconstructing phylogenies from copy-number profiles of cancer cells. We demonstrate the importance of distance correction from the edit (minimum) distance to the estimated actual number of events. Experimental results show that our approaches provide accurate and scalable results in estimating the actual number of evolutionary events between copy number profiles and in reconstructing phylogenies.
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57
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Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Ding J, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin SF, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy. Nat Commun 2019; 10:657. [PMID: 30737380 PMCID: PMC6368565 DOI: 10.1038/s41467-019-08593-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/18/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic changes observed across treatment may result from either clonal evolution or geographically disparate sampling of heterogeneous tumors. Here we use computational modeling based on analysis of fifteen primary breast tumors and find that apparent clonal change between two tumor samples can frequently be explained by pre-treatment heterogeneity, such that at least two regions are necessary to detect treatment-induced clonal shifts. To assess for clonal replacement, we devise a summary statistic based on whole-exome sequencing of a pre-treatment biopsy and multi-region sampling of the post-treatment surgical specimen and apply this measure to five breast tumors treated with neoadjuvant HER2-targeted therapy. Two tumors underwent clonal replacement with treatment, and mathematical modeling indicates these two tumors had resistant subclones prior to treatment and rates of resistance-related genomic changes that were substantially larger than previous estimates. Our results provide a needed framework to incorporate primary tumor heterogeneity in investigating the evolution of resistance.
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Affiliation(s)
- Jennifer L Caswell-Jin
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
| | - Katherine McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, 94305, CA, USA
| | - Ruping Sun
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Zheng Hu
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Zhicheng Ma
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Jie Ding
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Susanne Tilk
- Department of Biology, Stanford University, Stanford, 94305, CA, USA
| | - Akshara Raghavendra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Victoria Forte
- Maimonides Medical Center, Brooklyn, 11219, NY, USA
- Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Helen Bardwell
- Cancer Research UK Cambridge Institute, Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Elena Provenzano
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Julie Lang
- Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, 90333, CA, USA
| | - Robert West
- Department of Pathology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Michael F Press
- Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States.
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA.
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Abstract
Cancer is an evolutionary process. Recent advances in sequencing technologies have allowed us to investigate intratumor heterogeneity at the single nucleotide level. Here, we describe computational methods that use sequencing data to identify genetically distinct tumor subclones and reconstruct tumor evolutionary histories.
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59
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Sinha VC, Piwnica-Worms H. Intratumoral Heterogeneity in Ductal Carcinoma In Situ: Chaos and Consequence. J Mammary Gland Biol Neoplasia 2018; 23:191-205. [PMID: 30194658 PMCID: PMC6934090 DOI: 10.1007/s10911-018-9410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023] Open
Abstract
Ductal carcinoma in situ (DCIS) is a non-invasive proliferative growth in the breast that serves as a non-obligate precursor to invasive ductal carcinoma. The widespread adoption of screening mammography has led to a steep increase in the detection of DCIS, which now comprises approximately 20% of new breast cancer diagnoses in the United States. Interestingly, the intratumoral heterogeneity (ITH) that has been observed in invasive breast cancers may have been established early in tumorigenesis, given the vast and varied ITH that has been detected in DCIS. This review will discuss the intratumoral heterogeneity of DCIS, focusing on the phenotypic and genomic heterogeneity of tumor cells, as well as the compositional heterogeneity of the tumor microenvironment. In addition, we will assess the spatial heterogeneity that is now being appreciated in these lesions, and summarize new approaches to evaluate heterogeneity of tumor and stromal cells in the context of their spatial organization. Importantly, we will discuss how a growing understanding of ITH has led to a more holistic appreciation of the complex biology of DCIS, specifically its evolution and natural history. Finally, we will consider ways in which our knowledge of DCIS ITH might be translated in the future to guide clinical care for DCIS patients.
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Affiliation(s)
- Vidya C Sinha
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 6565 MD Anderson Blvd, Houston, TX, 77030, USA.
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60
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Nieboer MM, Dorssers LCJ, Straver R, Looijenga LHJ, de Ridder J. TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors. PLoS One 2018; 13:e0208002. [PMID: 30496231 PMCID: PMC6264523 DOI: 10.1371/journal.pone.0208002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 11/11/2018] [Indexed: 11/18/2022] Open
Abstract
Most tumors are composed of a heterogeneous population of subclones. A more detailed insight into the subclonal evolution of these tumors can be helpful to study progression and treatment response. Problematically, tumor samples are typically very heterogeneous, making deconvolving individual tumor subclones a major challenge. To overcome this limitation, reducing heterogeneity, such as by means of microdissections, coupled with targeted sequencing, is a viable approach. However, computational methods that enable reconstruction of the evolutionary relationships require unbiased read depth measurements, which are commonly challenging to obtain in this setting. We introduce TargetClone, a novel method to reconstruct the subclonal evolution tree of tumors from single-nucleotide polymorphism allele frequency and somatic single-nucleotide variant measurements. Furthermore, our method infers copy numbers, alleles and the fraction of the tumor component in each sample. TargetClone was specifically designed for targeted sequencing data obtained from microdissected samples. We demonstrate that our method obtains low error rates on simulated data. Additionally, we show that our method is able to reconstruct expected trees in a testicular germ cell cancer and ovarian cancer dataset. The TargetClone package including tree visualization is written in Python and is publicly available at https://github.com/UMCUGenetics/targetclone.
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Affiliation(s)
- Marleen M. Nieboer
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Roy Straver
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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61
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Evolution of Metastases in Space and Time under Immune Selection. Cell 2018; 175:751-765.e16. [DOI: 10.1016/j.cell.2018.09.018] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/06/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
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Evolutionary Distance Predicts Recurrence After Liver Transplantation in Multifocal Hepatocellular Carcinoma. Transplantation 2018; 102:e424-e430. [PMID: 29994984 PMCID: PMC7598094 DOI: 10.1097/tp.0000000000002356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background Liver transplantation (LTx) is a potentially curative treatment option for hepatocellular carcinoma (HCC) in cirrhosis. However, patients, where HCC is already a systemic disease, LTx may be individually harmful and has a negative impact on donor organ usage. Thus, there is a need for improved selection criteria beyond nodule morphology to select patients with a favorable outcome for LTx in multifocal HCC. Evolutionary distance measured from genome-wide single-nucleotide polymorphism data between tumor nodules and the cirrhotic liver may be a prognostic marker of survival after LTx for multifocal HCC. Methods In a retrospective multicenter study, clinical data and formalin-fixed paraffin-embedded specimens of the liver and 2 tumor nodules were obtained from explants of 30 patients in the discovery and 180 patients in the replication cohort. DNA was extracted from formalin-fixed paraffin-embedded specimens followed by genome wide single-nucleotide polymorphism genotyping. Results Genotype quality criteria allowed for analysis of 8 patients in the discovery and 17 patients in the replication set. DNA concentrations of a total of 25 patients fulfilled the quality criteria and were included in the analysis. Both, in the discovery (P = 0.04) and in the replication data sets (P = 0.01), evolutionary distance was associated with the risk of recurrence of HCC after transplantation (combined P = 0.0002). In a univariate analysis, evolutionary distance (P = 7.4 × 10−6) and microvascular invasion (P = 1.31 × 10−5) were significantly associated with survival in a Cox regression analysis. Conclusions Evolutionary distance allows for the determination of a high-risk group of recurrence if preoperative liver biopsy is considered. The authors of this multicenter retrospective study assess whether the evolutionary distance measured from genome-wide single nucleotide polymorphism (SNP) data between tumor nodules and the cirrhotic liver may be a prognostic marker of survival after liver transplantation for multifocal hepatocellular carcinoma. Supplemental digital content is available in the text.
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Zaccaria S, El-Kebir M, Klau GW, Raphael BJ. Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J Comput Biol 2018; 25:689-708. [PMID: 29658782 PMCID: PMC6067108 DOI: 10.1089/cmb.2017.0253] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy-number data from multiple samples of a tumor. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that either perform deconvolution/factorization of mixed tumor samples or build phylogenetic trees assuming homogeneous tumor samples. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher resolution view of copy-number evolution of this cancer than published analyses.
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Affiliation(s)
- Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, New Jersey
- Dipartimento di Informatica Sistemistica e Comunicazione (DISCo), Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Mohammed El-Kebir
- Department of Computer Science, Princeton University, Princeton, New Jersey
| | - Gunnar W. Klau
- Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
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Zeira R, Shamir R. Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. Bioinformatics 2018; 37:1489-1496. [PMID: 29726899 DOI: 10.1093/bioinformatics/bty381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/15/2018] [Accepted: 05/02/2018] [Indexed: 01/30/2023] Open
Abstract
Motivation Problems of genome rearrangement are central in both evolution and cancer research. Most genome rearrangement models assume that the genome contains a single copy of each gene and the only changes in the genome are structural, i.e., reordering of segments. In contrast, tumor genomes also undergo numerical changes such as deletions and duplications, and thus the number of copies of genes varies. Dealing with unequal gene content is a very challenging task, addressed by few algorithms to date. More realistic models are needed to help trace genome evolution during tumorigenesis. Results Here we present a model for the evolution of genomes with multiple gene copies using the operation types double-cut-and-joins, duplications and deletions. The events supported by the model are reversals, translocations, tandem duplications, segmental deletions, and chromosomal amplifications and deletions, covering most types of structural and numerical changes observed in tumor samples. Our goal is to find a series of operations of minimum length that transform one karyotype into the other. We show that the problem is NP-hard and give an integer linear programming formulation that solves the problem exactly under some mild assumptions. We test our method on simulated genomes and on ovarian cancer genomes. Our study advances the state of the art in two ways: It allows a broader set of operations than extant models, thus being more realistic, and it is the first study attempting to reconstruct the full sequence of structural and numerical events during cancer evolution. Availability Code and data are available in https://github.com/Shamir-Lab/Sorting-Cancer-Karyotypes. Contact ronzeira@post.tau.ac.il, rshamir@tau.ac.il. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv university, Tel Aviv, 6997801, Israel
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65
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Federer-Gsponer JR, Quintavalle C, Müller DC, Dietsche T, Perrina V, Lorber T, Juskevicius D, Lenkiewicz E, Zellweger T, Gasser T, Barrett MT, Rentsch CA, Bubendorf L, Ruiz C. Delineation of human prostate cancer evolution identifies chromothripsis as a polyclonal event and FKBP4 as a potential driver of castration resistance. J Pathol 2018; 245:74-84. [PMID: 29484655 DOI: 10.1002/path.5052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/09/2018] [Accepted: 01/26/2018] [Indexed: 12/30/2022]
Abstract
Understanding the evolutionary mechanisms and genomic events leading to castration-resistant (CR) prostate cancer (PC) is key to improve the outcome of this otherwise deadly disease. Here, we delineated the tumour history of seven patients progressing to castration resistance by analysing matched prostate cancer tissues before and after castration. We performed genomic profiling of DNA content-based flow-sorted populations in order to define the different evolutionary patterns. In one patient, we discovered that a catastrophic genomic event, known as chromothripsis, resulted in multiple CRPC tumour populations with distinct, potentially advantageous copy number aberrations, including an amplification of FK506 binding protein 4 (FKBP4, also known as FKBP52), a protein enhancing the transcriptional activity of androgen receptor signalling. Analysis of FKBP4 protein expression in more than 500 prostate cancer samples revealed increased expression in CRPC in comparison to hormone-naïve (HN) PC. Moreover, elevated FKBP4 expression was associated with poor survival of patients with HNPC. We propose FKBP4 amplification and overexpression as a selective advantage in the process of tumour evolution and as a potential mechanism associated with the development of CRPC. Furthermore, FKBP4 interaction with androgen receptor may provide a potential therapeutic target in PC. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Cristina Quintavalle
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
| | - David C Müller
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland.,Department of Urology, University Hospital Basel, University of Basel, Switzerland
| | - Tanja Dietsche
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Valeria Perrina
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Thomas Lorber
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Darius Juskevicius
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
| | | | | | - Thomas Gasser
- Department of Urology, University Hospital Basel, University of Basel, Switzerland
| | - Michael T Barrett
- Department of Research, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Cyrill A Rentsch
- Department of Urology, University Hospital Basel, University of Basel, Switzerland
| | - Lukas Bubendorf
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
| | - Christian Ruiz
- Institute for Pathology, University Hospital Basel, University of Basel, Switzerland
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66
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Watkins TBK, Schwarz RF. Phylogenetic Quantification of Intratumor Heterogeneity. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a028316. [PMID: 28710259 DOI: 10.1101/cshperspect.a028316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased. Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions in ways impractical with single samples alone. In this article, we discuss and show the benefits of such multisample studies. We describe how multiple samples can guide tree inference through accurate phasing of germline variants and copy-number profiles. We show their relevance in detecting clonal expansions and deriving summary statistics quantifying the overall degree of ITH, and discuss how the relationship of metastatic clades might give us insight into the dominant mode of cancer progression. We further outline how multisample studies might help us better understand selective processes acting on cancer genomes and help to detect neutral evolution and mutator phenotypes.
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Affiliation(s)
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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67
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Integrating Analysis of Cellular Heterogeneity in High-Content Dose-Response Studies. Methods Mol Biol 2018. [PMID: 29476461 DOI: 10.1007/978-1-4939-7680-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Heterogeneity is a complex property of cellular systems and therefore presents challenges to the reliable identification and characterization. Large-scale biology projects may span many months, requiring a systematic approach to quality control to track reproducibility and correct for instrumental variation and assay drift that could mask biological heterogeneity and preclude comparisons of heterogeneity between runs or even between plates. However, presently there is no standard approach to the tracking and analysis of heterogeneity. Previously, we demonstrated the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in a screen and described the use of three heterogeneity indices as a means to characterize, filter, and browse cellular heterogeneity in big data sets (Gough et al., Methods 96:12-26, 2016). In this chapter, we present a detailed method for integrating the analysis of cellular heterogeneity in assay development, validation, screening, and post screen. Importantly, we provide a detailed method for quality control, to normalize cellular data, track heterogeneity over time, and analyze heterogeneity in big data sets, along with software tools to assist in that process. The example screen for this method is from an HCS project, but the approach applies equally to other experimental methods that measure populations of cells.
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Genetic alterations driving metastatic colony formation are acquired outside of the primary tumour in melanoma. Nat Commun 2018; 9:595. [PMID: 29426936 PMCID: PMC5807512 DOI: 10.1038/s41467-017-02674-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023] Open
Abstract
Mouse models indicate that metastatic dissemination occurs extremely early; however, the timing in human cancers is unknown. We therefore determined the time point of metastatic seeding relative to tumour thickness and genomic alterations in melanoma. Here, we find that lymphatic dissemination occurs shortly after dermal invasion of the primary lesion at a median thickness of ~0.5 mm and that typical driver changes, including BRAF mutation and gained or lost regions comprising genes like MET or CDKNA2, are acquired within the lymph node at the time of colony formation. These changes define a colonisation signature that was linked to xenograft formation in immunodeficient mice and death from melanoma. Thus, melanoma cells leave primary tumours early and evolve at different sites in parallel. We propose a model of metastatic melanoma dormancy, evolution and colonisation that will inform direct monitoring of adjuvant therapy targets.
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69
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Wen Y, Wei Y, Zhang S, Li S, Liu H, Wang F, Zhao Y, Zhang D, Zhang Y. Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature. Brief Bioinform 2017; 18:426-440. [PMID: 27016391 DOI: 10.1093/bib/bbw028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Tumour heterogeneity describes the coexistence of divergent tumour cell clones within tumours, which is often caused by underlying epigenetic changes. DNA methylation is commonly regarded as a significant regulator that differs across cells and tissues. In this study, we comprehensively reviewed research progress on estimating of tumour heterogeneity. Bioinformatics-based analysis of DNA methylation has revealed the evolutionary relationships between breast cancer cell lines and tissues. Further analysis of the DNA methylation profiles in 33 breast cancer-related cell lines identified cell line-specific methylation patterns. Next, we reviewed the computational methods in inferring clonal evolution of tumours from different perspectives and then proposed a deconvolution strategy for modelling cell subclonal populations dynamics in breast cancer tissues based on DNA methylation. Further analysis of simulated cancer tissues and real cell lines revealed that this approach exhibits satisfactory performance and relative stability in estimating the composition and proportions of cellular subpopulations. The application of this strategy to breast cancer individuals of the Cancer Genome Atlas's identified different cellular subpopulations with distinct molecular phenotypes. Moreover, the current and potential future applications of this deconvolution strategy to clinical breast cancer research are discussed, and emphasis was placed on the DNA methylation-based recognition of intra-tumour heterogeneity. The wide use of these methods for estimating heterogeneity to further clinical cohorts will improve our understanding of neoplastic progression and the design of therapeutic interventions for treating breast cancer and other malignancies.
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70
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Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies. Sci Rep 2017; 7:16943. [PMID: 29208983 PMCID: PMC5717219 DOI: 10.1038/s41598-017-16813-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/17/2017] [Indexed: 11/20/2022] Open
Abstract
A comprehensive characterization of tumor genetic heterogeneity is critical for understanding how cancers evolve and escape treatment. Although many algorithms have been developed for capturing tumor heterogeneity, they are designed for analyzing either a single type of genomic aberration or individual biopsies. Here we present THEMIS (Tumor Heterogeneity Extensible Modeling via an Integrative System), which allows for the joint analysis of different types of genomic aberrations from multiple biopsies taken from the same patient, using a dynamic graphical model. Simulation experiments demonstrate higher accuracy of THEMIS over its ancestor, TITAN. The heterogeneity analysis results from THEMIS are validated with single cell DNA sequencing from a clinical tumor biopsy. When THEMIS is used to analyze tumor heterogeneity among multiple biopsies from the same patient, it helps to reveal the mutation accumulation history, track cancer progression, and identify the mutations related to treatment resistance. We implement our model via an extensible modeling platform, which makes our approach open, reproducible, and easy for others to extend.
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71
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Graf JF, Zavodszky MI. Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures. PLoS One 2017; 12:e0188878. [PMID: 29190747 PMCID: PMC5708750 DOI: 10.1371/journal.pone.0188878] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/14/2017] [Indexed: 11/18/2022] Open
Abstract
Background Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity. It enables the quantification of both the concentration and spatial distribution of 60+ proteins across a tissue section. Upon bioimage processing, protein expression data can be generated for each cell from a tissue field of view. Results The Multi-Omics Heterogeneity Analysis (MOHA) tool was developed to compute tissue heterogeneity metrics from MxIF spatially resolved tissue imaging data. This technique computes the molecular state of each cell in a sample based on a pathway or gene set. Spatial states are then computed based on the spatial arrangements of the cells as distinguished by their respective molecular states. MOHA computes tissue heterogeneity metrics from the distributions of these molecular and spatially defined states. A colorectal cancer cohort of approximately 700 subjects with MxIF data is presented to demonstrate the MOHA methodology. Within this dataset, statistically significant correlations were found between the intratumor AKT pathway state diversity and cancer stage and histological tumor grade. Furthermore, intratumor spatial diversity metrics were found to correlate with cancer recurrence. Conclusions MOHA provides a simple and robust approach to characterize molecular and spatial heterogeneity of tissues. Research projects that generate spatially resolved tissue imaging data can take full advantage of this useful technique. The MOHA algorithm is implemented as a freely available R script (see supplementary information).
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Affiliation(s)
- John F. Graf
- GE Global Research, Niskayuna, New York, United States of America
- * E-mail: (JFG); (MIZ)
| | - Maria I. Zavodszky
- GE Global Research, Niskayuna, New York, United States of America
- * E-mail: (JFG); (MIZ)
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Kato M, Vasco DA, Sugino R, Narushima D, Krasnitz A. Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171060. [PMID: 28989791 PMCID: PMC5627131 DOI: 10.1098/rsos.171060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Single-cell sequencing is a promising technology that can address cancer cell evolution by identifying genetic alterations in individual cells. In a recent study, genome-wide DNA copy numbers of single cells were accurately quantified by single-cell sequencing in breast cancers. Phylogenetic-tree analysis revealed genetically distinct populations, each consisting of homogeneous cells. Bioinformatics methods based on population genetics should be further developed to quantitatively analyse the single-cell sequencing data. We developed a bioinformatics framework that was combined with molecular-evolution theories to analyse copy-number losses. This analysis revealed that most deletions in the breast cancers at the single-cell level were generated by simple stochastic processes. A non-standard type of coalescent theory, the multiple-merger coalescent model, aided by approximate Bayesian computation fit well with the data, allowing us to estimate the population-genetic parameters in addition to false-positive and false-negative rates. The estimated parameters suggest that the cancer cells underwent sweepstake evolution, where only one or very few parental cells produced a descendent cell population. We conclude that breast cancer cells successively substitute in a tumour mass, and the high reproduction of only a portion of cancer cells may confer high adaptability to this cancer.
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Affiliation(s)
- Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuuoo-ku, Tokyo 104-0045, Japan
| | - Daniel A. Vasco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Ryuichi Sugino
- School of Advanced Sciences, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Daichi Narushima
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuuoo-ku, Tokyo 104-0045, Japan
| | - Alexander Krasnitz
- Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
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Zeira R, Zehavi M, Shamir R. A Linear-Time Algorithm for the Copy Number Transformation Problem. J Comput Biol 2017; 24:1179-1194. [PMID: 28837352 DOI: 10.1089/cmb.2017.0060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Problems of genome rearrangement are central in both evolution and cancer. Most evolutionary scenarios have been studied under the assumption that the genome contains a single copy of each gene. In contrast, tumor genomes undergo deletions and duplications, and thus, the number of copies of genes varies. The number of copies of each segment along a chromosome is called its copy number profile (CNP). Understanding CNP changes can assist in predicting disease progression and treatment. To date, questions related to distances between CNPs gained little scientific attention. Here we focus on the following fundamental problem, introduced by Schwarz et al.: given two CNPs, u and v, compute the minimum number of operations transforming u into v, where the edit operations are segmental deletions and amplifications. We establish the computational complexity of this problem, showing that it is solvable in linear time and constant space.
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Affiliation(s)
- Ron Zeira
- 1 Blavatnik School of Computer Science, Tel-Aviv University , Tel-Aviv, Israel
| | - Meirav Zehavi
- 2 Department of Informatics, University of Bergen , Bergen, Norway
| | - Ron Shamir
- 1 Blavatnik School of Computer Science, Tel-Aviv University , Tel-Aviv, Israel
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Mohan S, Chemi F, Brady G. Challenges and unanswered questions for the next decade of circulating tumour cell research in lung cancer. Transl Lung Cancer Res 2017; 6:454-472. [PMID: 28904889 DOI: 10.21037/tlcr.2017.06.04] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Since blood borne circulating tumour cells (CTCs) initially shed from the primary tumour can seed and initiate metastasis at distant sites a better understanding of the biology of CTCs and their dissemination could provide valuable information that could guide therapeutic intervention and real time monitoring of disease progression. Although CTC enumeration has provided a reliable prognostic readout for a number of cancers, including lung cancer, the precise clinical utility of CTCs remains to be established. The rarity of CTCs together with the vanishingly small amounts of nucleic acids present in a single cell as well as cell to cell heterogeneity has stimulated the development of a wide range of powerful cellular and molecular methodologies applied to CTCs. These technical developments are now enabling researchers to focus on understanding the biology of CTCs and their clinical utility as a predictive and pharmacodynamics markers. This review summarises recent advances in the field of CTC research with focus on technical and biological challenges as well the progress made towards clinical utility of characterisation of CTCs with emphasis on studies in lung cancer.
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Affiliation(s)
- Sumitra Mohan
- Clinical and Experimental Pharmacology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Francesca Chemi
- Clinical and Experimental Pharmacology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Ged Brady
- Clinical and Experimental Pharmacology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
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Martinez P, Kimberley C, BirkBak NJ, Marquard A, Szallasi Z, Graham TA. Quantification of within-sample genetic heterogeneity from SNP-array data. Sci Rep 2017; 7:3248. [PMID: 28607403 PMCID: PMC5468233 DOI: 10.1038/s41598-017-03496-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/03/2017] [Indexed: 01/17/2023] Open
Abstract
Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley's L statistic of spatial homogeneity, to quantify ITH in single SNP-array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p < 0.001) and moderate associations in-vitro (p = 0.015 and p = 0.085). Our scores were also correlated to previous ITH estimates from sequencing data but heterogeneity in the fraction of tumour cells present across samples hampered accurate quantification. The prognostic potential of both scores was moderate but significantly predictive of survival in several tumour types (corrected p = 0.03). Our work thus shows how individual SNP-arrays reveal intra-sample clonal diversity with moderate accuracy.
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Affiliation(s)
- Pierre Martinez
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France.
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK.
| | - Christopher Kimberley
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK
| | - Nicolai J BirkBak
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Andrea Marquard
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
- Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Harvard Medical School, Boston, MA, USA
| | - Trevor A Graham
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK
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76
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El-Kebir M, Raphael BJ, Shamir R, Sharan R, Zaccaria S, Zehavi M, Zeira R. Complexity and algorithms for copy-number evolution problems. Algorithms Mol Biol 2017; 12:13. [PMID: 28515774 PMCID: PMC5433102 DOI: 10.1186/s13015-017-0103-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome's copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis. RESULTS We model the evolution of a tumor by segmental deletions and amplifications, and gauge distance from profile [Formula: see text] to [Formula: see text] by the minimum number of events needed to transform [Formula: see text] into [Formula: see text]. Given two profiles, our first problem aims to find a parental profile that minimizes the sum of distances to its children. Given k profiles, the second, more general problem, seeks a phylogenetic tree, whose k leaves are labeled by the k given profiles and whose internal vertices are labeled by ancestral profiles such that the sum of edge distances is minimum. CONCLUSIONS For the former problem we give a pseudo-polynomial dynamic programming algorithm that is linear in the profile length, and an integer linear program formulation. For the latter problem we show it is NP-hard and give an integer linear program formulation that scales to practical problem instance sizes. We assess the efficiency and quality of our algorithms on simulated instances. AVAILABILITY https://github.com/raphael-group/CNT-ILP.
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Affiliation(s)
- Mohammed El-Kebir
- Department of Computer Science, Princeton University, Princeton, NJ 08540 USA
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA
| | - Benjamin J. Raphael
- Department of Computer Science, Princeton University, Princeton, NJ 08540 USA
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA
| | - Ron Shamir
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Simone Zaccaria
- Department of Computer Science, Princeton University, Princeton, NJ 08540 USA
- Department of Computer Science, Center for Computational Molecular Biology, Brown University, Providence, RI 02912 USA
- Dipartimento di Informatica Sistemistica e Comunicazione (DISCo), Univ. degli Studi di Milano-Bicocca, Milan, Italy
| | - Meirav Zehavi
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ron Zeira
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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77
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Abstract
BACKGROUND Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. CONCLUSIONS While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances.
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Affiliation(s)
- Ian H. Holmes
- 0000 0001 2181 7878grid.47840.3fDept of Bioengineering, University of California, Berkeley, 94720 USA
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78
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Brown D, Smeets D, Székely B, Larsimont D, Szász AM, Adnet PY, Rothé F, Rouas G, Nagy ZI, Faragó Z, Tőkés AM, Dank M, Szentmártoni G, Udvarhelyi N, Zoppoli G, Pusztai L, Piccart M, Kulka J, Lambrechts D, Sotiriou C, Desmedt C. Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations. Nat Commun 2017; 8:14944. [PMID: 28429735 PMCID: PMC5474888 DOI: 10.1038/ncomms14944] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 02/15/2017] [Indexed: 01/06/2023] Open
Abstract
Several studies using genome-wide molecular techniques have reported various degrees of genetic heterogeneity between primary tumours and their distant metastases. However, it has been difficult to discern patterns of dissemination owing to the limited number of patients and available metastases. Here, we use phylogenetic techniques on data generated using whole-exome sequencing and copy number profiling of primary and multiple-matched metastatic tumours from ten autopsied patients to infer the evolutionary history of breast cancer progression. We observed two modes of disease progression. In some patients, all distant metastases cluster on a branch separate from their primary lesion. Clonal frequency analyses of somatic mutations show that the metastases have a monoclonal origin and descend from a common 'metastatic precursor'. Alternatively, multiple metastatic lesions are seeded from different clones present within the primary tumour. We further show that a metastasis can be horizontally cross-seeded. These findings provide insights into breast cancer dissemination.
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Affiliation(s)
- David Brown
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - Dominiek Smeets
- Laboratory of Translational Genetics, Vesalius Research Center, VIB, Campus Gasthuisberg, O&N IV Herestraat 49, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Oncology, Katholieke Universiteit Leuven, O&N IV Herestraat 49, 3000 Leuven, Belgium
| | - Borbála Székely
- Second Department of Pathology, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
| | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - A. Marcell Szász
- Second Department of Pathology, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
| | - Pierre-Yves Adnet
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - Ghizlane Rouas
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - Zsófia I. Nagy
- Second Department of Pathology, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
| | - Zsófia Faragó
- Second Department of Pathology, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
| | - Anna-Mária Tőkés
- Second Department of Pathology, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
- 2 Department of Pathology, MTA-SE Tumor Progression Research Group, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
| | - Magdolna Dank
- Semmelweis University Cancer Center, Semmelweis University, Tömő u. 25-29, 1083 Budapest, Hungary
| | - Gyöngyvér Szentmártoni
- Semmelweis University Cancer Center, Semmelweis University, Tömő u. 25-29, 1083 Budapest, Hungary
| | - Nóra Udvarhelyi
- Surgical and Molecular Tumor Pathology Centre, National Institute of Oncology, Ráth György u. 7-9, 1122 Budapest, Hungary
| | - Gabriele Zoppoli
- University of Genova and Istituto di Cura a Carattere Clinico e Scientifico Azienda Ospedaliera Universitaria San Martino—Instituto Nazionale Tumori, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Lajos Pusztai
- Yale University, Cedar Street 333, New Haven, Connecticut 05620, USA
| | - Martine Piccart
- Department of Medical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - Janina Kulka
- Second Department of Pathology, Semmelweis University, Üllői út 93, 1091 Budapest, Hungary
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Vesalius Research Center, VIB, Campus Gasthuisberg, O&N IV Herestraat 49, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Oncology, Katholieke Universiteit Leuven, O&N IV Herestraat 49, 3000 Leuven, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bld de Waterloo 121, 1000 Brussels, Belgium
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Abstract
Rapid advances in high-throughput sequencing and a growing realization of the importance of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies of tumour progression. These studies have yielded not only new insights but also a plethora of experimental approaches, sometimes reaching conflicting or poorly supported conclusions. Here, we consider this body of work in light of the key computational principles underpinning phylogenetic inference, with the goal of providing practical guidance on the design and analysis of scientifically rigorous tumour phylogeny studies. We survey the range of methods and tools available to the researcher, their key applications, and the various unsolved problems, closing with a perspective on the prospects and broader implications of this field.
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Affiliation(s)
- Russell Schwartz
- Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania 15217, USA
| | - Alejandro A Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20892, USA
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80
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Kuipers J, Jahn K, Beerenwinkel N. Advances in understanding tumour evolution through single-cell sequencing. Biochim Biophys Acta Rev Cancer 2017; 1867:127-138. [PMID: 28193548 PMCID: PMC5813714 DOI: 10.1016/j.bbcan.2017.02.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 12/14/2022]
Abstract
The mutational heterogeneity observed within tumours poses additional challenges to the development of effective cancer treatments. A thorough understanding of a tumour's subclonal composition and its mutational history is essential to open up the design of treatments tailored to individual patients. Comparative studies on a large number of tumours permit the identification of mutational patterns which may refine forecasts of cancer progression, response to treatment and metastatic potential. The composition of tumours is shaped by evolutionary processes. Recent advances in next-generation sequencing offer the possibility to analyse the evolutionary history and accompanying heterogeneity of tumours at an unprecedented resolution, by sequencing single cells. New computational challenges arise when moving from bulk to single-cell sequencing data, leading to the development of novel modelling frameworks. In this review, we present the state of the art methods for understanding the phylogeny encoded in bulk or single-cell sequencing data, and highlight future directions for developing more comprehensive and informative pictures of tumour evolution. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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MESH Headings
- Adaptation, Physiological
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Evolution, Molecular
- Gene Expression Regulation, Neoplastic
- Genetic Fitness
- Genetic Heterogeneity
- Genetic Predisposition to Disease
- Heredity
- Humans
- Models, Genetic
- Mutation
- Neoplasms/drug therapy
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Pedigree
- Phenotype
- Phylogeny
- Sequence Analysis, DNA
- Signal Transduction/genetics
- Single-Cell Analysis/methods
- Time Factors
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Affiliation(s)
- Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
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81
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Hu Z, Sun R, Curtis C. A population genetics perspective on the determinants of intra-tumor heterogeneity. Biochim Biophys Acta Rev Cancer 2017; 1867:109-126. [PMID: 28274726 DOI: 10.1016/j.bbcan.2017.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
Abstract
Cancer results from the acquisition of somatic alterations in a microevolutionary process that typically occurs over many years, much of which is occult. Understanding the evolutionary dynamics that are operative at different stages of progression in individual tumors might inform the earlier detection, diagnosis, and treatment of cancer. Although these processes cannot be directly observed, the resultant spatiotemporal patterns of genetic variation amongst tumor cells encode their evolutionary histories. Such intra-tumor heterogeneity is pervasive not only at the genomic level, but also at the transcriptomic, phenotypic, and cellular levels. Given the implications for precision medicine, the accurate quantification of heterogeneity within and between tumors has become a major focus of current research. In this review, we provide a population genetics perspective on the determinants of intra-tumor heterogeneity and approaches to quantify genetic diversity. We summarize evidence for different modes of evolution based on recent cancer genome sequencing studies and discuss emerging evolutionary strategies to therapeutically exploit tumor heterogeneity. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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Affiliation(s)
- Zheng Hu
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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82
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Davis A, Gao R, Navin N. Tumor evolution: Linear, branching, neutral or punctuated? Biochim Biophys Acta Rev Cancer 2017; 1867:151-161. [PMID: 28110020 DOI: 10.1016/j.bbcan.2017.01.003] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/14/2017] [Accepted: 01/16/2017] [Indexed: 02/08/2023]
Abstract
Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of how this genetic diversity emerges over time remains limited. A central challenge in studying tumor evolution is the difficulty in collecting longitudinal samples from cancer patients. Consequently, most studies have inferred tumor evolution from single time-point samples, providing very indirect information. These data have led to several competing models of tumor evolution: linear, branching, neutral and punctuated. Each model makes different assumptions regarding the timing of mutations and selection of clones, and therefore has different implications for the diagnosis and therapeutic treatment of cancer patients. Furthermore, emerging evidence suggests that models may change during tumor progression or operate concurrently for different classes of mutations. Finally, we discuss data that supports the theory that most human tumors evolve from a single cell in the normal tissue. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.
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Affiliation(s)
- Alexander Davis
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruli Gao
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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83
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Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla C, Schurdak ME, Haney SA, Taylor DL. Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS DISCOVERY 2017; 22:213-237. [PMID: 28231035 DOI: 10.1177/2472555216682725] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.
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Affiliation(s)
- Albert Gough
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Andrew M Stern
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - John Maier
- 3 Department of Family Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy Lezon
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Tong-Ying Shun
- 2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Chakra Chennubhotla
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA
| | - Mark E Schurdak
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Steven A Haney
- 5 Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
| | - D Lansing Taylor
- 1 Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.,2 University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.,4 University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
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84
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Graham TA, Sottoriva A. Measuring cancer evolution from the genome. J Pathol 2017; 241:183-191. [PMID: 27741350 DOI: 10.1002/path.4821] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 12/30/2022]
Abstract
The temporal dynamics of cancer evolution remain elusive, because it is impractical to longitudinally observe cancers unperturbed by treatment. Consequently, our knowledge of how cancers grow largely derives from inferences made from a single point in time - the endpoint in the cancer's evolution, when it is removed from the body and studied in the laboratory. Fortuitously however, the cancer genome, by virtue of ongoing mutations that uniquely mark clonal lineages within the tumour, provides a rich, yet surreptitious, record of cancer development. In this review, we describe how a cancer's genome can be analysed to reveal the temporal history of mutation and selection, and discuss why both selective and neutral evolution feature prominently in carcinogenesis. We argue that selection in cancer can only be properly studied once we have some understanding of what the absence of selection looks like. We review the data describing punctuated evolution in cancer, and reason that punctuated phenotype evolution is consistent with both gradual and punctuated genome evolution. We conclude that, to map and predict evolutionary trajectories during carcinogenesis, it is critical to better understand the relationship between genotype change and phenotype change. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrea Sottoriva
- Cancer Evolutionary Genomics and Modelling Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
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85
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Abstract
Cancer genome sequences contain footprints of somatic mutational processes, whose analysis in large tumor sequencing datasets has revealed novel mutational signatures, correlative features of variant topography, and complex events. Many of these analytic results have yet to reconciled with decades of mechanistic genome integrity research performed in controlled model systems. However, a new generation of genome-integrity experiments combining computational modeling, data analytics, and high-throughput sequencing are emerging to link mechanisms to patterns. Conversely, analytic studies evaluating quantitative footprints of specific genome integrity hypotheses will be critical in fitting naturally occurring mutational patterns to the predictions of a particular mechanistic model. Such quantitative and mechanistic studies will form the foundation of an emerging systems biology of genome integrity.
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Affiliation(s)
- John Maciejowski
- Rockefeller University, New York, USA.,New York Genome Center, New York, USA
| | - Marcin Imielinski
- New York Genome Center, New York, USA.,Weill Cornell Medicine, New York, USA
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86
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Mangiola S, Hong MKH, Cmero M, Kurganovs N, Ryan A, Costello AJ, Corcoran NM, Macintyre G, Hovens CM. Comparing nodal versus bony metastatic spread using tumour phylogenies. Sci Rep 2016; 6:33918. [PMID: 27653089 PMCID: PMC5031992 DOI: 10.1038/srep33918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/31/2016] [Indexed: 02/07/2023] Open
Abstract
The role of lymph node metastases in distant prostate cancer dissemination and lethality is ill defined. Patients with metastases restricted to lymph nodes have a better prognosis than those with distant metastatic spread, suggesting the possibility of distinct aetiologies. To explore this, we traced patterns of cancer dissemination using tumour phylogenies inferred from genome-wide copy-number profiling of 48 samples across 3 patients with lymph node metastatic disease and 3 patients with osseous metastatic disease. Our results show that metastatic cells in regional lymph nodes originate from evolutionary advanced extraprostatic tumour cells rather than less advanced central tumour cell populations. In contrast, osseous metastases do not exhibit such a constrained developmental lineage, arising from either intra or extraprostatic tumour cell populations, at early and late stages in the evolution of the primary. Collectively, this comparison suggests that lymph node metastases may not be an intermediate developmental step for distant osseous metastases, but rather represent a distinct metastatic lineage.
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Affiliation(s)
- Stefano Mangiola
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,Centre for Neural Engineering, 203 Bouverie St, Carlton 3053, Victoria, Australia
| | - Matthew K H Hong
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia
| | - Marek Cmero
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,Centre for Neural Engineering, 203 Bouverie St, Carlton 3053, Victoria, Australia
| | - Natalie Kurganovs
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia
| | - Andrew Ryan
- TissuPath Specialist Pathology, Mount Waverley 3149, Victoria, Australia
| | - Anthony J Costello
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Niall M Corcoran
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
| | - Geoff Macintyre
- Centre for Neural Engineering, 203 Bouverie St, Carlton 3053, Victoria, Australia.,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Christopher M Hovens
- Departments of Urology and Surgery, Royal Melbourne Hospital and University of Melbourne, Parkville 3050 Victoria, Australia.,The Epworth Prostate Centre, Epworth Hospital, Richmond 3121, Victoria, Australia
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87
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Cresswell GD, Apps JR, Chagtai T, Mifsud B, Bentley CC, Maschietto M, Popov SD, Weeks ME, Olsen ØE, Sebire NJ, Pritchard-Jones K, Luscombe NM, Williams RD, Mifsud W. Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications. EBioMedicine 2016; 9:120-129. [PMID: 27333041 PMCID: PMC4972528 DOI: 10.1016/j.ebiom.2016.05.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 11/30/2022] Open
Abstract
The evolution of pediatric solid tumors is poorly understood. There is conflicting evidence of intra-tumor genetic homogeneity vs. heterogeneity (ITGH) in a small number of studies in pediatric solid tumors. A number of copy number aberrations (CNA) are proposed as prognostic biomarkers to stratify patients, for example 1q+ in Wilms tumor (WT); current clinical trials use only one sample per tumor to profile this genetic biomarker. We multisampled 20 WT cases and assessed genome-wide allele-specific CNA and loss of heterozygosity, and inferred tumor evolution, using Illumina CytoSNP12v2.1 arrays, a custom analysis pipeline, and the MEDICC algorithm. We found remarkable diversity of ITGH and evolutionary trajectories in WT. 1q+ is heterogeneous in the majority of tumors with this change, with variable evolutionary timing. We estimate that at least three samples per tumor are needed to detect >95% of cases with 1q+. In contrast, somatic 11p15 LOH is uniformly an early event in WT development. We find evidence of two separate tumor origins in unilateral disease with divergent histology, and in bilateral WT. We also show subclonal changes related to differential response to chemotherapy. Rational trial design to include biomarkers in risk stratification requires tumor multisampling and reliable delineation of ITGH and tumor evolution.
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Affiliation(s)
| | - John R Apps
- UCL Institute of Child Health, London, United Kingdom; Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital, London, United Kingdom
| | | | | | - Christopher C Bentley
- The Francis Crick Institute, London, United Kingdom; UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, United Kingdom
| | | | - Sergey D Popov
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Mark E Weeks
- UCL Institute of Child Health, London, United Kingdom
| | - Øystein E Olsen
- Department of Radiology, Great Ormond Street Hospital, London, United Kingdom
| | - Neil J Sebire
- UCL Institute of Child Health, London, United Kingdom; Department of Histopathology, Great Ormond Street Hospital, London, United Kingdom
| | - Kathy Pritchard-Jones
- UCL Institute of Child Health, London, United Kingdom; Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital, London, United Kingdom
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, United Kingdom; UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, United Kingdom; Okinawa Institute of Science & Technology, Okinawa, Japan
| | | | - William Mifsud
- UCL Institute of Child Health, London, United Kingdom; Department of Histopathology, Great Ormond Street Hospital, London, United Kingdom.
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88
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Affiliation(s)
- Jeffrey B. Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- University of British Columbia, Department of Medicine, Vancouver, British Columbia, Canada
| | - Richard H. Liang
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - T. Nguyen
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Art F. Y. Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- University of British Columbia, Department of Medicine, Vancouver, British Columbia, Canada
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89
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Ross EM, Markowetz F. OncoNEM: inferring tumor evolution from single-cell sequencing data. Genome Biol 2016; 17:69. [PMID: 27083415 PMCID: PMC4832472 DOI: 10.1186/s13059-016-0929-9] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 11/17/2022] Open
Abstract
Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships. In simulation studies, we assess OncoNEM's robustness and benchmark its performance against competing methods. Finally, we show its applicability in case studies of muscle-invasive bladder cancer and essential thrombocythemia.
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Affiliation(s)
- Edith M Ross
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK.
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90
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Beerenwinkel N, Greenman CD, Lagergren J. Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput Biol 2016; 12:e1004717. [PMID: 26845763 PMCID: PMC4742235 DOI: 10.1371/journal.pcbi.1004717] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail: (NB); (CDG); (JL)
| | - Chris D. Greenman
- School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
- * E-mail: (NB); (CDG); (JL)
| | - Jens Lagergren
- Science for Life Laboratory, School of Computer Science and Communication, Swedish E-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
- * E-mail: (NB); (CDG); (JL)
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91
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Gough A, Shun TY, Lansing Taylor D, Schurdak M. A metric and workflow for quality control in the analysis of heterogeneity in phenotypic profiles and screens. Methods 2015; 96:12-26. [PMID: 26476369 DOI: 10.1016/j.ymeth.2015.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
Heterogeneity is well recognized as a common property of cellular systems that impacts biomedical research and the development of therapeutics and diagnostics. Several studies have shown that analysis of heterogeneity: gives insight into mechanisms of action of perturbagens; can be used to predict optimal combination therapies; and can be applied to tumors where heterogeneity is believed to be associated with adaptation and resistance. Cytometry methods including high content screening (HCS), high throughput microscopy, flow cytometry, mass spec imaging and digital pathology capture cell level data for populations of cells. However it is often assumed that the population response is normally distributed and therefore that the average adequately describes the results. A deeper understanding of the results of the measurements and more effective comparison of perturbagen effects requires analysis that takes into account the distribution of the measurements, i.e. the heterogeneity. However, the reproducibility of heterogeneous data collected on different days, and in different plates/slides has not previously been evaluated. Here we show that conventional assay quality metrics alone are not adequate for quality control of the heterogeneity in the data. To address this need, we demonstrate the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in an SAR screen, describe a workflow for quality control in heterogeneity analysis. One major challenge in high throughput biology is the evaluation and interpretation of heterogeneity in thousands of samples, such as compounds in a cell-based screen. In this study we also demonstrate that three heterogeneity indices previously reported, capture the shapes of the distributions and provide a means to filter and browse big data sets of cellular distributions in order to compare and identify distributions of interest. These metrics and methods are presented as a workflow for analysis of heterogeneity in large scale biology projects.
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Affiliation(s)
- Albert Gough
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA; Dept. of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, USA.
| | - Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA; Dept. of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, USA
| | - Mark Schurdak
- University of Pittsburgh Drug Discovery Institute, 3501 Fifth Avenue, Pittsburgh, PA, USA; Dept. of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, USA
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92
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Hong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Res 2015; 75:4021-5. [PMID: 26260528 PMCID: PMC4833389 DOI: 10.1158/0008-5472.can-15-1889] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/04/2015] [Indexed: 01/06/2023]
Abstract
Determining the evolutionary history of metastases is a key problem in cancer biology. Several recent studies have presented inferences regarding the origin of metastases based on phylogenies of cancer lineages. Many of these studies have concluded that the observed monophyly of metastatic subclones favored metastasis-to-metastasis spread ("a metastatic cascade" rather than parallel metastases from the primary tumor). In this article, we argue that identifying a monophyletic clade of metastatic subclones does not provide sufficient evidence to unequivocally establish a history of metastatic cascades. In the absence of a complete phylogeny of the subclones within the primary tumor, a scenario of parallel metastatic events from the primary tumor is an equally plausible interpretation. Future phylogenetic studies on the origin of metastases should obtain a complete phylogeny of subclones within the primary tumor. This complete phylogeny may be obtainable by ultra-deep sequencing and phasing of large sections or by targeted sequencing of many small, spatially heterogeneous sections, followed by phylogenetic reconstruction using well-established molecular evolutionary models. In addition to resolving the evolutionary history of metastases, a complete phylogeny of subclones within the primary tumor facilitates the identification of driver mutations by application of phylogeny-based tests of natural selection.
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Affiliation(s)
| | - Max Shpak
- NeuroTexas Institute, St. David's Medical Center, Austin, Texas. Center for Systems and Synthetic Biology, University of Texas, Austin, Texas. Fresh Pond Research Institute, Cambridge, Massachusetts.
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut. Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut. Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
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93
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Kim TM, Jung SH, An CH, Lee SH, Baek IP, Kim MS, Park SW, Rhee JK, Lee SH, Chung YJ. Subclonal Genomic Architectures of Primary and Metastatic Colorectal Cancer Based on Intratumoral Genetic Heterogeneity. Clin Cancer Res 2015; 21:4461-72. [PMID: 25979483 DOI: 10.1158/1078-0432.ccr-14-2413] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/22/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE The intratumoral heterogeneity (ITH) and the evolution of genomic architectures associated with the development of distant metastases are not well understood in colorectal cancers. EXPERIMENTAL DESIGN We performed multiregion biopsies of primary and liver metastatic regions from five colorectal cancers with whole-exome sequencing and copy number profiling. RESULTS In addition to a substantial level of genetic ITH, multiregion genetic profiling identifies the subclonal mutational architecture, leading to the region-based or spatial categorization of somatic mutations and the inference of intratumoral evolutionary history of cancers. The universal mutations (those observed in all the regional biopsies) are enriched in known cancer genes such as APC and TP53 with distinct mutational spectra compared with biopsy- or region-specific mutations, suggesting that major operative mutational mechanisms and their selective pressures are not constant across the metastatic progression. The phylogenies inferred from genomic data show branching evolutionary patterns where some primary biopsies are often segregated with metastastic lesions. Our analyses also revealed that copy number changes such as the chromosomal gains of c-MYC and chromothripsis can be region specific and the potential source of genetic ITH. CONCLUSIONS Our data show that the genetic ITH is prevalent in colorectal cancer serving as a potential driving force to generate metastasis-initiating clones and also as a means to infer the intratumoral evolutionary history of cancers. The paucity of recurrent metastasis-clonal events suggests that colorectal cancer distant metastases may not follow a uniform course of genomic evolution, which should be considered in the genetic diagnosis and the selection of therapeutic targets for the advanced colorectal cancer.
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Affiliation(s)
- Tae-Min Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Seung-Hyun Jung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Chang Hyeok An
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sung Hak Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Pyo Baek
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Min Sung Kim
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sung-Won Park
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Je-Keun Rhee
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sug-Hyung Lee
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.
| | - Yeun-Jun Chung
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, South Korea. Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.
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94
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Affiliation(s)
- Florian Markowetz
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
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95
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Turning the headlights on novel cancer biomarkers: Inspection of mechanics underlying intratumor heterogeneity. Mol Aspects Med 2015; 45:3-13. [PMID: 26024970 DOI: 10.1016/j.mam.2015.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/20/2015] [Indexed: 01/20/2023]
Abstract
Although the existence of intratumoral heterogeneity (ITH) in the expression of common biomarkers has been described by pathologists since the late 1890s, we have only recently begun to fathom the staggering extent and near ubiquity of this phenomenon. From the tumor's perspective, ITH provides a stabilizing diversity that allows for the evolution of aggressive cancer phenotypes. As the weight of the evidence correlating ITH to poor prognosis burgeons, it has become increasingly important to determine the mechanisms by which a tumor acquires ITH, find clinically-adaptable means to quantify ITH and design strategies to deal with the numerous profound clinical ramifications that ITH forces upon us. Elucidation of the drivers of ITH could enable development of novel biomarkers whose interrogation might permit quantitative evaluation of the ITH inherent in a tumor in order to predict the poor prognosis risk associated with that tumor. This review proposes centrosome amplification (CA), aided and abetted by centrosome clustering mechanisms, as a critical driver of chromosomal instability (CIN) that makes a key contribution to ITH generation. Herein we also evaluate how a tumor's inherent mitotic propensity, which reflects the cell cycling kinetics within the tumor's proliferative cells, functions as the indispensable engine underpinning CIN, and determines the rate of CIN. We thus expound how the forces of centrosome amplification and mitotic propensity collaborate to sculpt the genetic landscape of a tumor and spawn extensive subclonal diversity. As such, centrosome amplification and mitotic propensity profiles could serve as clinically facile and powerful prognostic biomarkers that would enable more accurate risk segmentation of patients and design of individualized therapies.
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96
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Desmedt C, Fumagalli D, Pietri E, Zoppoli G, Brown D, Nik-Zainal S, Gundem G, Rothé F, Majjaj S, Garuti A, Carminati E, Loi S, Van Brussel T, Boeckx B, Maetens M, Mudie L, Vincent D, Kheddoumi N, Serra L, Massa I, Ballestrero A, Amadori D, Salgado R, de Wind A, Lambrechts D, Piccart M, Larsimont D, Campbell PJ, Sotiriou C. Uncovering the genomic heterogeneity of multifocal breast cancer. J Pathol 2015; 236:457-66. [PMID: 25850943 PMCID: PMC4691324 DOI: 10.1002/path.4540] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/20/2015] [Accepted: 03/31/2015] [Indexed: 12/17/2022]
Abstract
Multifocal breast cancer (MFBC), defined as multiple synchronous unilateral lesions of invasive breast cancer, is relatively frequent and has been associated with more aggressive features than unifocal cancer. Here, we aimed to investigate the genomic heterogeneity between MFBC lesions sharing similar histopathological parameters. Characterization of different lesions from 36 patients with ductal MFBC involved the identification of non‐silent coding mutations in 360 protein‐coding genes (171 tumour and 36 matched normal samples). We selected only patients with lesions presenting the same grade, ER, and HER2 status. Mutations were classified as ‘oncogenic’ in the case of recurrent substitutions reported in COSMIC or truncating mutations affecting tumour suppressor genes. All mutations identified in a given patient were further interrogated in all samples from that patient through deep resequencing using an orthogonal platform. Whole‐genome rearrangement screen was further conducted in 8/36 patients. Twenty‐four patients (67%) had substitutions/indels shared by all their lesions, of which 11 carried the same mutations in all lesions, and 13 had lesions with both common and private mutations. Three‐quarters of those 24 patients shared oncogenic variants. The remaining 12 patients (33%) did not share any substitution/indels, with inter‐lesion heterogeneity observed for oncogenic mutation(s) in genes such as PIK3CA, TP53, GATA3, and PTEN. Genomically heterogeneous lesions tended to be further apart in the mammary gland than homogeneous lesions. Genome‐wide analyses of a limited number of patients identified a common somatic background in all studied MFBCs, including those with no mutation in common between the lesions. To conclude, as the number of molecular targeted therapies increases and trials driven by genomic screening are ongoing, our findings highlight the presence of genomic inter‐lesion heterogeneity in one‐third, despite similar pathological features. This implies that deeper molecular characterization of all MFBC lesions is warranted for the adequate management of those cancers. © 2015 The Authors. Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Debora Fumagalli
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Elisabetta Pietri
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumouri (IRST) - IRCCS, Meldola, Italy
| | - Gabriele Zoppoli
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium.,Department of Internal Medicine, University of Genoa and IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - David Brown
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Samira Majjaj
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Anna Garuti
- Department of Internal Medicine, University of Genoa and IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Enrico Carminati
- Department of Internal Medicine, University of Genoa and IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Sherene Loi
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium.,Translational Breast Cancer Genomics Lab, Division of Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Thomas Van Brussel
- VIB Vesalius Research Center, KU Leuven, Campus Gasthuisberg, Herestraat 49, Bus 912, Leuven, Belgium
| | - Bram Boeckx
- VIB Vesalius Research Center, KU Leuven, Campus Gasthuisberg, Herestraat 49, Bus 912, Leuven, Belgium
| | - Marion Maetens
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Laura Mudie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Delphine Vincent
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Naima Kheddoumi
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
| | - Luigi Serra
- Pathology Unit, 'G.B. Morgagni-L. Pierantoni' Hospital, Forlì, Italy
| | - Ilaria Massa
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumouri (IRST) - IRCCS, Meldola, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine, University of Genoa and IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Dino Amadori
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumouri (IRST) - IRCCS, Meldola, Italy
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium.,Breast International Group Headquarters (BIG-aisbl), Brussels, Belgium
| | - Alexandre de Wind
- Pathology Department, Jules Bordet Institute, Boulevard de Waterloo 121, Brussels, Belgium
| | - Diether Lambrechts
- VIB Vesalius Research Center, KU Leuven, Campus Gasthuisberg, Herestraat 49, Bus 912, Leuven, Belgium
| | - Martine Piccart
- Department of Medical Oncology, Jules Bordet Institute, Boulevard de Waterloo 121, Brussels, Belgium
| | - Denis Larsimont
- Pathology Department, Jules Bordet Institute, Boulevard de Waterloo 121, Brussels, Belgium
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.,Department of Haematology, University of Cambridge, Cambridge, UK.,Department of Haematology, Addenbrooke's Hospital, Cambridge, UK
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Boulevard de Waterloo 121, Brussels, Belgium
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97
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Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N. BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biol 2015; 16:36. [PMID: 25786108 PMCID: PMC4359483 DOI: 10.1186/s13059-015-0592-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/21/2015] [Indexed: 11/28/2022] Open
Abstract
Cancer has long been understood as a somatic evolutionary process, but many details of tumor progression remain elusive. Here, we present BitPhylogenyBitPhylogeny, a probabilistic framework to reconstruct intra-tumor evolutionary pathways. Using a full Bayesian approach, we jointly estimate the number and composition of clones in the sample as well as the most likely tree connecting them. We validate our approach in the controlled setting of a simulation study and compare it against several competing methods. In two case studies, we demonstrate how BitPhylogeny BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm.
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Affiliation(s)
- Ke Yuan
- />University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Thomas Sakoparnig
- />Department of Biosystems Science and Engineering, ETH Zurich, Basel Switzerland
- />SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- />Current address: Biozentrum, University of Basel, Basel, Switzerland
| | - Florian Markowetz
- />University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Niko Beerenwinkel
- />Department of Biosystems Science and Engineering, ETH Zurich, Basel Switzerland
- />SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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98
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Sottoriva A, Kang H, Ma Z, Graham TA, Salomon MP, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C. A Big Bang model of human colorectal tumor growth. Nat Genet 2015; 47:209-16. [PMID: 25665006 PMCID: PMC4575589 DOI: 10.1038/ng.3214] [Citation(s) in RCA: 715] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/12/2015] [Indexed: 12/12/2022]
Abstract
What happens in the early, still undetectable human malignancy is unknown because direct observations are impractical. Here we present and validate a “Big Bang” model, whereby tumors grow predominantly as a single expansion producing numerous intermixed sub-clones that are not subject to stringent selection, and where both public (clonal) and most detectable private (subclonal) alterations arise early during growth. Genomic profiling of 349 individual glands from 15 colorectal tumors revealed the absence of selective sweeps, uniformly high intra-tumor heterogeneity (ITH), and sub-clone mixing in distant regions, as postulated by our model. We also verified the prediction that most detectable ITH originates from early private alterations, and not from later clonal expansions, thus exposing the profile of the primordial tumor. Moreover, some tumors appear born-to-be-bad, with sub-clone mixing indicative of early malignant potential. This new model provides a quantitative framework to interpret tumor growth dynamics and the origins of ITH with significant clinical implications.
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Affiliation(s)
- Andrea Sottoriva
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Haeyoun Kang
- 1] Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA. [2] Department of Pathology, CHA University, Seongnam-si, South Korea
| | - Zhicheng Ma
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Trevor A Graham
- 1] Center for Evolution and Cancer, University of California, San Francisco, San Francisco, California, USA. [2] Centre for Tumor Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Matthew P Salomon
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Junsong Zhao
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Paul Marjoram
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Kimberly Siegmund
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Christina Curtis
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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Beck AH. Open access to large scale datasets is needed to translate knowledge of cancer heterogeneity into better patient outcomes. PLoS Med 2015; 12:e1001794. [PMID: 25710538 PMCID: PMC4339838 DOI: 10.1371/journal.pmed.1001794] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this guest editorial, Andrew Beck discusses the importance of open access to big data for translating knowledge of cancer heterogeneity into better outcomes for cancer patients.
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Affiliation(s)
- Andrew H. Beck
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Schwarz RF, Ng CKY, Cooke SL, Newman S, Temple J, Piskorz AM, Gale D, Sayal K, Murtaza M, Baldwin PJ, Rosenfeld N, Earl HM, Sala E, Jimenez-Linan M, Parkinson CA, Markowetz F, Brenton JD. Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis. PLoS Med 2015; 12:e1001789. [PMID: 25710373 PMCID: PMC4339382 DOI: 10.1371/journal.pmed.1001789] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The major clinical challenge in the treatment of high-grade serous ovarian cancer (HGSOC) is the development of progressive resistance to platinum-based chemotherapy. The objective of this study was to determine whether intra-tumour genetic heterogeneity resulting from clonal evolution and the emergence of subclonal tumour populations in HGSOC was associated with the development of resistant disease. METHODS AND FINDINGS Evolutionary inference and phylogenetic quantification of heterogeneity was performed using the MEDICC algorithm on high-resolution whole genome copy number profiles and selected genome-wide sequencing of 135 spatially and temporally separated samples from 14 patients with HGSOC who received platinum-based chemotherapy. Samples were obtained from the clinical CTCR-OV03/04 studies, and patients were enrolled between 20 July 2007 and 22 October 2009. Median follow-up of the cohort was 31 mo (interquartile range 22-46 mo), censored after 26 October 2013. Outcome measures were overall survival (OS) and progression-free survival (PFS). There were marked differences in the degree of clonal expansion (CE) between patients (median 0.74, interquartile range 0.66-1.15), and dichotimization by median CE showed worse survival in CE-high cases (PFS 12.7 versus 10.1 mo, p = 0.009; OS 42.6 versus 23.5 mo, p = 0.003). Bootstrap analysis with resampling showed that the 95% confidence intervals for the hazard ratios for PFS and OS in the CE-high group were greater than 1.0. These data support a relationship between heterogeneity and survival but do not precisely determine its effect size. Relapsed tissue was available for two patients in the CE-high group, and phylogenetic analysis showed that the prevalent clonal population at clinical recurrence arose from early divergence events. A subclonal population marked by a NF1 deletion showed a progressive increase in tumour allele fraction during chemotherapy. CONCLUSIONS This study demonstrates that quantitative measures of intra-tumour heterogeneity may have predictive value for survival after chemotherapy treatment in HGSOC. Subclonal tumour populations are present in pre-treatment biopsies in HGSOC and can undergo expansion during chemotherapy, causing clinical relapse.
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Affiliation(s)
- Roland F. Schwarz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte K. Y. Ng
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Susanna L. Cooke
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Scott Newman
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jillian Temple
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Anna M. Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Karen Sayal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Muhammed Murtaza
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Peter J. Baldwin
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Helena M. Earl
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Evis Sala
- University Department of Radiology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | | | - Christine A. Parkinson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - James D. Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
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