151
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Behjati S, Lindsay S, Teichmann SA, Haniffa M. Mapping human development at single-cell resolution. Development 2018; 145:145/3/dev152561. [PMID: 29439135 DOI: 10.1242/dev.152561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human development is regulated by spatiotemporally restricted molecular programmes and is pertinent to many areas of basic biology and human medicine, such as stem cell biology, reproductive medicine and childhood cancer. Mapping human development has presented significant technological, logistical and ethical challenges. The availability of established human developmental biorepositories and the advent of cutting-edge single-cell technologies provide new opportunities to study human development. Here, we present a working framework for the establishment of a human developmental cell atlas exploiting single-cell genomics and spatial analysis. We discuss how the development atlas will benefit the scientific and clinical communities to advance our understanding of basic biology, health and disease.
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Affiliation(s)
- Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Theory of Condensed Matter, Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK .,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
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152
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Abstract
Origins of mutations in single cells during human brain development and aging are revealed
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Affiliation(s)
- Je H Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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153
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Laurenti E, Göttgens B. From haematopoietic stem cells to complex differentiation landscapes. Nature 2018; 553:418-426. [PMID: 29364285 PMCID: PMC6555401 DOI: 10.1038/nature25022] [Citation(s) in RCA: 484] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 11/08/2017] [Indexed: 12/18/2022]
Abstract
The development of mature blood cells from haematopoietic stem cells has long served as a model for stem-cell research, with the haematopoietic differentiation tree being widely used as a model for the maintenance of hierarchically organized tissues. Recent results and new technologies have challenged the demarcations between stem and progenitor cell populations, the timing of cell-fate choices and the contribution of stem and multipotent progenitor cells to the maintenance of steady-state blood production. These evolving views of haematopoiesis have broad implications for our understanding of the functions of adult stem cells, as well as the development of new therapies for malignant and non-malignant haematopoietic diseases.
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Affiliation(s)
- Elisa Laurenti
- Department of Haematology and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge UK
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154
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Garaycoechea JI, Crossan GP, Langevin F, Mulderrig L, Louzada S, Yang F, Guilbaud G, Park N, Roerink S, Nik-Zainal S, Stratton MR, Patel KJ. Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells. Nature 2018; 553:171-177. [PMID: 29323295 PMCID: PMC6047743 DOI: 10.1038/nature25154] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022]
Abstract
Haematopoietic stem cells renew blood. Accumulation of DNA damage in these cells promotes their decline, while misrepair of this damage initiates malignancies. Here we describe the features and mutational landscape of DNA damage caused by acetaldehyde, an endogenous and alcohol-derived metabolite. This damage results in DNA double-stranded breaks that, despite stimulating recombination repair, also cause chromosome rearrangements. We combined transplantation of single haematopoietic stem cells with whole-genome sequencing to show that this damage occurs in stem cells, leading to deletions and rearrangements that are indicative of microhomology-mediated end-joining repair. Moreover, deletion of p53 completely rescues the survival of aldehyde-stressed and mutated haematopoietic stem cells, but does not change the pattern or the intensity of genome instability within individual stem cells. These findings characterize the mutation of the stem-cell genome by an alcohol-derived and endogenous source of DNA damage. Furthermore, we identify how the choice of DNA-repair pathway and a stringent p53 response limit the transmission of aldehyde-induced mutations in stem cells.
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Affiliation(s)
- Juan I Garaycoechea
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Frédéric Langevin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lee Mulderrig
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sandra Louzada
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fentang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Guillaume Guilbaud
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Naomi Park
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sophie Roerink
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | | | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Rd, Cambridge CB2 0QQ, UK
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155
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Abstract
DNA mutations are inevitable. Despite proficient DNA repair mechanisms, somatic cells accumulate mutations during development and aging, generating cells with different genotypes within the same individual, a phenomenon known as somatic mosaicism. While the existence of somatic mosaicism has long been recognized, in the last five years, advances in sequencing have provided unprecedented resolution to characterize the extent and nature of somatic genetic variation. Collectively, these new studies are revealing a previously uncharacterized aging phenotype: the accumulation of clones with cancer driver mutations. Here, we summarize the most recent findings, which converge in the novel notion that cancer-associated mutations are prevalent in normal tissue and accumulate with aging.
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Affiliation(s)
- Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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156
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Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. Opportunities for organoids as new models of aging. J Cell Biol 2017; 217:39-50. [PMID: 29263081 PMCID: PMC5748992 DOI: 10.1083/jcb.201709054] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/13/2017] [Accepted: 11/27/2017] [Indexed: 01/02/2023] Open
Abstract
The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research.
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Affiliation(s)
- Jennifer L Hu
- University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA
| | - Michael E Todhunter
- Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA
| | - Mark A LaBarge
- Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA .,National Science Foundation Center for Cellular Construction, University of California San Francisco, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
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157
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Holmberg FE, Seidelin JB, Yin X, Mead BE, Tong Z, Li Y, Karp JM, Nielsen OH. Culturing human intestinal stem cells for regenerative applications in the treatment of inflammatory bowel disease. EMBO Mol Med 2017; 9:558-570. [PMID: 28283650 PMCID: PMC5412884 DOI: 10.15252/emmm.201607260] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Both the incidence and prevalence of inflammatory bowel disease (IBD) is increasing globally; in the industrialized world up to 0.5% of the population are affected and around 4.2 million individuals suffer from IBD in Europe and North America combined. Successful engraftment in experimental colitis models suggests that intestinal stem cell transplantation could constitute a novel treatment strategy to re-establish mucosal barrier function in patients with severe disease. Intestinal stem cells can be grown in vitro in organoid structures, though only a fraction of the cells contained are stem cells with regenerative capabilities. Hence, techniques to enrich stem cell populations are being pursued through the development of multiple two-dimensional and three-dimensional culture protocols, as well as co-culture techniques and multiple growth medium compositions. Moreover, research in support matrices allowing for efficient clinical application is in progress. In vitro culture is accomplished by modulating the signaling pathways fundamental for the stem cell niche with a suitable culture matrix to provide additional contact-dependent stimuli and structural support. The aim of this review was to discuss medium compositions and support matrices for optimal intestinal stem cell culture, as well as potential modifications to advance clinical use in IBD.
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Affiliation(s)
- Fredrik Eo Holmberg
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Jakob B Seidelin
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Xiaolei Yin
- Division of BioEngineering in Medicine, Department of Medicine, Center for Regenerative Therapeutics, Brigham and Women's Hospital, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Harvard - MIT Division of Health Sciences and Technology, Cambridge, MA, USA.,David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Benjamin E Mead
- Division of BioEngineering in Medicine, Department of Medicine, Center for Regenerative Therapeutics, Brigham and Women's Hospital, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Harvard - MIT Division of Health Sciences and Technology, Cambridge, MA, USA.,David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zhixiang Tong
- Division of BioEngineering in Medicine, Department of Medicine, Center for Regenerative Therapeutics, Brigham and Women's Hospital, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Harvard - MIT Division of Health Sciences and Technology, Cambridge, MA, USA
| | - Yuan Li
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Jeffrey M Karp
- Division of BioEngineering in Medicine, Department of Medicine, Center for Regenerative Therapeutics, Brigham and Women's Hospital, Cambridge, MA, USA .,Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Harvard - MIT Division of Health Sciences and Technology, Cambridge, MA, USA.,David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ole H Nielsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
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158
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Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures. Nat Protoc 2017; 13:59-78. [DOI: 10.1038/nprot.2017.111] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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159
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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160
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1235] [Impact Index Per Article: 176.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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161
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Schmid-Siegert E, Sarkar N, Iseli C, Calderon S, Gouhier-Darimont C, Chrast J, Cattaneo P, Schütz F, Farinelli L, Pagni M, Schneider M, Voumard J, Jaboyedoff M, Fankhauser C, Hardtke CS, Keller L, Pannell JR, Reymond A, Robinson-Rechavi M, Xenarios I, Reymond P. Low number of fixed somatic mutations in a long-lived oak tree. NATURE PLANTS 2017; 3:926-929. [PMID: 29209081 DOI: 10.1038/s41477-017-0066-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/27/2017] [Indexed: 05/06/2023]
Abstract
Because plants do not possess a defined germline, deleterious somatic mutations can be passed to gametes, and a large number of cell divisions separating zygote from gamete formation may lead to many mutations in long-lived plants. We sequenced the genome of two terminal branches of a 234-year-old oak tree and found several fixed somatic single-nucleotide variants whose sequential appearance in the tree could be traced along nested sectors of younger branches. Our data suggest that stem cells of shoot meristems in trees are robustly protected from the accumulation of mutations.
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Affiliation(s)
| | - Namrata Sarkar
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Evolutionary Bioinformatics Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian Iseli
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Calderon
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Pietro Cattaneo
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Marco Pagni
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michel Schneider
- Swiss-Prot group, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Jérémie Voumard
- Risk Analysis Group, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Michel Jaboyedoff
- Risk Analysis Group, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | | | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Evolutionary Bioinformatics Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ioannis Xenarios
- Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss-Prot group, Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.
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162
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Chen J, Rénia L, Ginhoux F. Constructing cell lineages from single-cell transcriptomes. Mol Aspects Med 2017; 59:95-113. [PMID: 29107741 DOI: 10.1016/j.mam.2017.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
Advances in single-cell RNA-sequencing have helped reveal the previously underappreciated level of cellular heterogeneity present during cellular differentiation. A static snapshot of single-cell transcriptomes provides a good representation of the various stages of differentiation as differentiation is rarely synchronized between cells. Data from numerous single-cell analyses has suggested that cellular differentiation and development can be conceptualized as continuous processes. Consequently, computational algorithms have been developed to infer lineage relationships between cell types and construct developmental trajectories along which cells are re-ordered such that similarity between successive cell pairs is maximized. Here, we compare and contrast the existing computational methods, and illustrate how they may be applied to build mouse myeloid progenitor lineages from massively parallel RNA single-cell sequencing data.
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Affiliation(s)
- Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
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163
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Spanjaard B, Junker JP. Methods for lineage tracing on the organism-wide level. Curr Opin Cell Biol 2017; 49:16-21. [PMID: 29175321 DOI: 10.1016/j.ceb.2017.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/22/2023]
Abstract
Determining the lineage origin of cell types is a major goal in developmental biology. Furthermore, lineage tracing is a powerful approach for understanding the origin of developmental defects as well as the origin of diseases such as cancer. There is now a variety of complementary approaches for identifying lineage relationships, ranging from direct observation of cell divisions by light microscopy to genetic labeling of cells using inducible recombinases and fluorescent reporters. A recent development, and the main topic of this review article, is the use of high-throughput sequencing data for lineage analysis. This emerging approach holds the promise of increased multiplexing capacity, allowing lineage analysis of large cell numbers up to the organism-wide level combined with simultaneous transcription profiling by single cell RNA sequencing.
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Affiliation(s)
- Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany.
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164
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The potential of liquid biopsies for the early detection of cancer. NPJ Precis Oncol 2017; 1:36. [PMID: 29872715 PMCID: PMC5871864 DOI: 10.1038/s41698-017-0039-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023] Open
Abstract
Precision medicine refers to the choosing of targeted therapies based on genetic data. Due to the increasing availability of data from large-scale tumor genome sequencing projects, genome-driven oncology may have enormous potential to change the clinical management of patients with cancer. To this end, components of tumors, which are shed into the circulation, i.e., circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or extracellular vesicles, are increasingly being used for monitoring tumor genomes. A growing number of publications have documented that these “liquid biopsies” are informative regarding response to given therapies, are capable of detecting relapse with lead time compared to standard measures, and reveal mechanisms of resistance. However, the majority of published studies relate to advanced tumor stages and the use of liquid biopsies for detection of very early malignant disease stages is less well documented. In early disease stages, strategies for analysis are in principle relatively similar to advanced stages. However, at these early stages, several factors pose particular difficulties and challenges, including the lower frequency and volume of aberrations, potentially confounding phenomena such as clonal expansions of non-tumorous tissues or the accumulation of cancer-associated mutations with age, and the incomplete insight into driver alterations. Here we discuss biology, technical complexities and clinical significance for early cancer detection and their impact on precision oncology.
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165
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Drost J, van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, de Ligt J, Behjati S, Grolleman JE, van Wezel T, Nik-Zainal S, Kuiper RP, Cuppen E, Clevers H. Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Science 2017; 358:234-238. [PMID: 28912133 PMCID: PMC6038908 DOI: 10.1126/science.aao3130] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/01/2017] [Indexed: 12/11/2022]
Abstract
Mutational processes underlie cancer initiation and progression. Signatures of these processes in cancer genomes may explain cancer etiology and could hold diagnostic and prognostic value. We developed a strategy that can be used to explore the origin of cancer-associated mutational signatures. We used CRISPR-Cas9 technology to delete key DNA repair genes in human colon organoids, followed by delayed subcloning and whole-genome sequencing. We found that mutation accumulation in organoids deficient in the mismatch repair gene MLH1 is driven by replication errors and accurately models the mutation profiles observed in mismatch repair-deficient colorectal cancers. Application of this strategy to the cancer predisposition gene NTHL1, which encodes a base excision repair protein, revealed a mutational footprint (signature 30) previously observed in a breast cancer cohort. We show that signature 30 can arise from germline NTHL1 mutations.
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Affiliation(s)
- Jarno Drost
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Ruben van Boxtel
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Francis Blokzijl
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Tomohiro Mizutani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Nobuo Sasaki
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Valentina Sasselli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Joep de Ligt
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tom van Wezel
- Departments of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584CT Utrecht, Netherlands
| | - Edwin Cuppen
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands.
- Center for Molecular Medicine, Department of Genetics, UMC Utrecht, 3584CX Utrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, 3584CT Utrecht, Netherlands.
- Cancer Genomics Netherlands, UMC Utrecht, 3584CX Utrecht, Netherlands
- Princess Máxima Center for Pediatric Oncology, 3584CT Utrecht, Netherlands
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166
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Abstract
The recent flood of single-cell data not only boosts our knowledge of cells and cell types, but also provides new insight into development and evolution from a cellular perspective. For example, assaying the genomes of multiple cells during development reveals developmental lineage trees-the kinship lineage-whereas cellular transcriptomes inform us about the regulatory state of cells and their gradual restriction in potency-the Waddington lineage. Beyond that, the comparison of single-cell data across species allows evolutionary changes to be tracked at all stages of development from the zygote, via different kinds of stem cells, to the differentiating cells. We discuss recent insights into the evolution of stem cells and initial attempts to reconstruct the evolutionary cell type tree of the mammalian forebrain, for example, by the comparative analysis of neuron types in the mesencephalic floor. These studies illustrate the immense potential of single-cell genomics to open up a new era in developmental and evolutionary research.
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Affiliation(s)
- John C Marioni
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom;
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Detlev Arendt
- Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany;
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
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167
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Stratz S, Verboket PE, Hasler K, Dittrich PS. Cultivation and quantitative single-cell analysis of Saccharomyces cerevisiae on a multifunctional microfluidic device. Electrophoresis 2017; 39:540-547. [PMID: 28880404 DOI: 10.1002/elps.201700253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 11/06/2022]
Abstract
Here, we present a multifunctional microfluidic device whose integrative design enables to combine cell culture studies and quantitative single cell biomolecule analysis. The platform consists of 32 analysis units providing two key features; first, a micrometer-sized trap for hydrodynamic capture of a single Saccharomyces cerevisiae (S. cerevisiae) yeast cell; second, a convenient double-valve configuration surrounding the trap. Actuating of the outer valve with integrated opening results in a partial isolation in a volume of 11.8 nL, i.e. the cell surrounding fluid can be exchanged diffusion-based without causing shear stress or cell loss. Actuation of the inner ring-shaped valve isolates the trapped cell completely in a small analysis volume of 230 pL. The device was used to determine the growth rate of yeast cells (S. cerevisiae) under under optimum and oxidative stress conditions. In addition, we successfully quantified the cofactor beta-nicotinamide adenine dinucleotide phosphate (NAD(P)H) in single and few cells exposed to the different microenvironments. In conclusion, the microdevice enables to analyze the influence of an external stress factor on the cellular fitness in a fast and more comprehensive way as cell growth and intracellular biomolecule levels can be investigated.
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Affiliation(s)
- Simone Stratz
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland.,ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Pascal Emilio Verboket
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland.,ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - Karina Hasler
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, Switzerland
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168
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169
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Sloma I, Mitjavila-Garcia MT, Feraud O, Griscelli F, Oudrhiri N, El Marsafy S, Gobbo E, Divers D, Proust A, Smadja DM, Desterke C, Carles A, Ma Y, Hirst M, Marra MA, Eaves CJ, Bennaceur-Griscelli A, Turhan AG. Whole-genome analysis reveals unexpected dynamics of mutant subclone development in a patient with JAK2-V617F-positive chronic myeloid leukemia. Exp Hematol 2017; 53:48-58. [DOI: 10.1016/j.exphem.2017.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 01/17/2023]
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170
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Chen C, Qi H, Shen Y, Pickrell J, Przeworski M. Contrasting Determinants of Mutation Rates in Germline and Soma. Genetics 2017; 207:255-267. [PMID: 28733365 PMCID: PMC5586376 DOI: 10.1534/genetics.117.1114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/01/2017] [Indexed: 12/13/2022] Open
Abstract
Recent studies of somatic and germline mutations have led to the identification of a number of factors that influence point mutation rates, including CpG methylation, expression levels, replication timing, and GC content. Intriguingly, some of the effects appear to differ between soma and germline: in particular, whereas mutation rates have been reported to decrease with expression levels in tumors, no clear effect has been detected in the germline. Distinct approaches were taken to analyze the data, however, so it is hard to know whether these apparent differences are real. To enable a cleaner comparison, we considered a statistical model in which the mutation rate of a coding region is predicted by GC content, expression levels, replication timing, and two histone repressive marks. We applied this model to both a set of germline mutations identified in exomes and to exonic somatic mutations in four types of tumors. Most determinants of mutations are shared: notably, we detected an effect of expression levels on both germline and somatic mutation rates. Moreover, in all tissues considered, higher expression levels are associated with greater strand asymmetry of mutations. However, mutation rates increase with expression levels in testis (and, more tentatively, in ovary), whereas they decrease with expression levels in somatic tissues. This contrast points to differences in damage or repair rates during transcription in soma and germline.
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Affiliation(s)
- Chen Chen
- Department of Biological Sciences, Columbia University, New York, New York 10025
- New York Genome Center, New York, New York 10013
| | - Hongjian Qi
- Department of Systems Biology, Columbia University Medical Center, New York, New York 10032
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10025
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, New York 10032
- Department of Biomedical Informatics, Columbia University, New York, New York 10025
| | - Joseph Pickrell
- Department of Biological Sciences, Columbia University, New York, New York 10025
- New York Genome Center, New York, New York 10013
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York 10025
- Department of Systems Biology, Columbia University Medical Center, New York, New York 10032
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171
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A somatic mutation in erythro-myeloid progenitors causes neurodegenerative disease. Nature 2017; 549:389-393. [PMID: 28854169 PMCID: PMC6047345 DOI: 10.1038/nature23672] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/26/2017] [Indexed: 12/23/2022]
Abstract
The pathophysiology of neurodegenerative diseases is poorly understood, and therapeutic options are few. Neurodegenerative diseases are hallmarked by progressive neuronal dysfunction and loss, associated with chronic glial activation1. Whether microglial activation, which is viewed in general as a secondary process, is detrimental or protective in neurodegeneration remains unclear1–8. Late-onset neurodegenerative disease observed in patients with histiocytoses9–12, which are clonal myeloid diseases associated with somatic mutations in the RAS/MEK/ERK pathway such as BRAFV600E 13–17, suggests a possible role of somatic mutations in myeloid cells in neurodegeneration. Yet expression of BRAFV600E in the hematopoietic stem cell (HSC) lineage causes leukemic and tumoral diseases but not neurodegenerative disease18,19. Microglia belong to a lineage of adult tissue-resident myeloid cells that develop during organogenesis from yolk sac erythro-myeloid progenitors (EMP) distinct from HSC20–23. We thus hypothesized that a somatic BRAFV600E mutation in the EMP lineage may cause neurodegeneration. Here we show that mosaic expression of BRAFV600E in EMP results in clonal expansion of tissue-resident macrophages and a severe late-onset neurodegenerative disorder, associated with accumulation of ERK-activated amoeboid microglia in mice, also observed in human histiocytoses patients. In the murine model, neurobehavioral signs, astrogliosis, amyloid precursor protein deposition, synaptic loss and neuronal death were driven by ERK-activated microglia and were preventable by BRAF inhibition. These results identify the fetal precursors of tissue-resident macrophages as a potential cell-of-origin for histiocytoses, and demonstrate in mice that a somatic mutation in the EMP lineage can drive late-onset neurodegeneration. Moreover, these data identify activation of the MAP kinase pathway in microglia as a cause of neurodegeneration, and provide opportunities for therapeutic intervention aimed at preventing neuronal death in neurodegenerative diseases.
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172
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Affiliation(s)
- Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK. .,Department of Pediatrics, University of Cambridge, Cambridge CB2 1TN, UK
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173
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DeGregori J. Connecting Cancer to Its Causes Requires Incorporation of Effects on Tissue Microenvironments. Cancer Res 2017; 77:6065-6068. [PMID: 28754675 DOI: 10.1158/0008-5472.can-17-1207] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/29/2017] [Accepted: 07/13/2017] [Indexed: 11/16/2022]
Abstract
In a recent article in Science, Tomasetti and colleagues present an expanded model for cancer risk, which they claim demonstrates the relative contribution of mutations caused by replication errors, environment, and heredity. The foundation of this model is the theory that the overwhelming driver of cancer risk is mutations. This perspective will present experimental evidence and evolutionary theory to challenge the basis of this underlying theory. An argument will be presented that the mutation-centric model of cancer suggests unrealistic solutions to cancer and distracts the research community from more promising approaches that consider tissue context. Cancer Res; 77(22); 6065-8. ©2017 AACR.
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Affiliation(s)
- James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado.
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174
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Weeber F, Ooft SN, Dijkstra KK, Voest EE. Tumor Organoids as a Pre-clinical Cancer Model for Drug Discovery. Cell Chem Biol 2017; 24:1092-1100. [PMID: 28757181 DOI: 10.1016/j.chembiol.2017.06.012] [Citation(s) in RCA: 330] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/24/2017] [Accepted: 06/20/2017] [Indexed: 01/21/2023]
Abstract
Tumor organoids are 3D cultures of cancer cells that can be derived on an individual patient basis with a high success rate. This creates opportunities to build large biobanks with relevant patient material that can be used to perform drug screens and facilitate drug development. The high take rate will also allow side-by-side comparison to evaluate the translational potential of this model system to the patient. These tumors-in-a-dish can be established for a variety of tumor types including colorectal, pancreas, stomach, prostate, and breast cancers. In this review, we highlight what is currently known about tumor organoid culture, the advantages and challenges of the model system, compare it with other pre-clinical cancer models, and evaluate its value for drug development.
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Affiliation(s)
- Fleur Weeber
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, Noord-Holland 1066CX, the Netherlands
| | - Salo N Ooft
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, Noord-Holland 1066CX, the Netherlands
| | - Krijn K Dijkstra
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, Noord-Holland 1066CX, the Netherlands
| | - Emile E Voest
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, Noord-Holland 1066CX, the Netherlands; Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, Noord-Holland 1066CX, the Netherlands; Foundation Hubrecht Organoid Technology (HUB), Utrecht, Utrecht 3584CM, the Netherlands; Cancer Genomics.nl, Utrecht, Utrecht 3584 CG, the Netherlands.
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175
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Zurkirchen L, Sommer L. Quo vadis: tracing the fate of neural crest cells. Curr Opin Neurobiol 2017; 47:16-23. [PMID: 28753439 DOI: 10.1016/j.conb.2017.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/16/2022]
Abstract
The neural crest is a transient structure in vertebrate embryos that produces migratory cells with an astonishing developmental potential. While neural crest fate maps have originally been established through interspecies transplantation assays, dye labeling, and retroviral infection, more recent methods rely on approaches involving transgenesis and genome editing. These technologies allowed the identification of minor neural crest-derived cell populations in tissues of non-neural crest origin. Furthermore, in vivo multipotency at the single cell level and stage-dependent fate acquisitions were demonstrated using genetic technologies. Finally, recent reports indicate that neural crest-derived cells become activated in response to injury to secrete factors supporting tissue repair. Thus, neural crest-derived cells apparently contribute to tissue formation and regeneration by cell autonomous and non-autonomous mechanisms.
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Affiliation(s)
- Luis Zurkirchen
- Stem Cell Biology, Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lukas Sommer
- Stem Cell Biology, Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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176
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Genome instability: a conserved mechanism of ageing? Essays Biochem 2017; 61:305-315. [PMID: 28550046 DOI: 10.1042/ebc20160082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/18/2017] [Accepted: 05/02/2017] [Indexed: 01/09/2023]
Abstract
DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals. More recently, next-generation sequencing-based methods have been developed to accurately determine the complete landscape of base substitution mutations in single cells. The first results show that the somatic mutation rate is much higher than the germline mutation rate and that base substitution loads in somatic cells are high enough to potentially affect cellular function.
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177
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Lozada JR, Burke KA, Maguire A, Pareja F, Lim RS, Kim J, Gularte-Merida R, Murray MP, Brogi E, Weigelt B, Reis-Filho JS, Geyer FC. Myxoid fibroadenomas differ from conventional fibroadenomas: a hypothesis-generating study. Histopathology 2017; 71:626-634. [PMID: 28513873 DOI: 10.1111/his.13258] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/14/2017] [Indexed: 12/13/2022]
Abstract
AIMS Breast myxoid fibroadenomas (MFAs) are characterized by a distinctive hypocellular myxoid stroma, and occur sporadically or in the context of Carney complex, an inheritable condition caused by PRKAR1A-inactivating germline mutations. Conventional fibroadenomas (FAs) are underpinned by recurrent MED12 mutations in the stromal components of the lesions. The aim of this study was to investigate the genomic landscape of MFAs and compare it with that of conventional FAs. METHODS AND RESULTS Eleven MFAs from patients without clinical and/or genetic evidence of Carney complex were retrieved. DNA samples of tumour and matching normal tissue were subjected to massively parallel sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay, an assay targeting 410 cancer genes. Genetic alterations detected by MSK-IMPACT were tested in samples in which the stromal and epithelial components were separately laser capture-microdissected. Sequencing revealed no germline PRKAR1A mutations and non-synonymous mutations in six MFAs. Interestingly, in three of the MFAs in which the stromal and epithelial components were separately microdissected, the mutations were found to be restricted to the epithelial rather than the stromal component. The sole exception was a lesion harbouring a somatic truncating PRKAR1A mutation. Upon histological re-review, this case was reclassified as a breast myxoma, consistent with the spectrum of tumous observed in Carney complex patients. In this case, the PRKAR1A somatic mutation was restricted to the stromal component. CONCLUSION MFAs lack MED12 mutations, and their stromal components seem not to harbour mutations in the 410 cancer genes tested. Whole-exome and/or whole-genome analyses of MFAs are required to elucidate their genetic drivers.
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Affiliation(s)
- John R Lozada
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aoife Maguire
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jisun Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Melissa P Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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178
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Poulin JF, Tasic B, Hjerling-Leffler J, Trimarchi JM, Awatramani R. Disentangling neural cell diversity using single-cell transcriptomics. Nat Neurosci 2017; 19:1131-41. [PMID: 27571192 DOI: 10.1038/nn.4366] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/22/2016] [Indexed: 12/12/2022]
Abstract
Cellular specialization is particularly prominent in mammalian nervous systems, which are composed of millions to billions of neurons that appear in thousands of different 'flavors' and contribute to a variety of functions. Even in a single brain region, individual neurons differ greatly in their morphology, connectivity and electrophysiological properties. Systematic classification of all mammalian neurons is a key goal towards deconstructing the nervous system into its basic components. With the recent advances in single-cell gene expression profiling technologies, it is now possible to undertake the enormous task of disentangling neuronal heterogeneity. High-throughput single-cell RNA sequencing and multiplexed quantitative RT-PCR have become more accessible, and these technologies enable systematic categorization of individual neurons into groups with similar molecular properties. Here we provide a conceptual and practical guide to classification of neural cell types using single-cell gene expression profiling technologies.
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Affiliation(s)
| | - Bosiljka Tasic
- Department of Molecular Genetics, Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jens Hjerling-Leffler
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
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179
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Vijg J, Dong X, Zhang L. A high-fidelity method for genomic sequencing of single somatic cells reveals a very high mutational burden. Exp Biol Med (Maywood) 2017; 242:1318-1324. [PMID: 28737476 PMCID: PMC5529006 DOI: 10.1177/1535370217717696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Postzygotic mutations in somatic cells lead to genome mosaicism and can be the cause of cancer, possibly other human diseases and aging. Somatic mutations are difficult to detect in bulk tissue samples. Here, we review the available assays for measuring somatic mutations, with a focus on recent single-cell, whole genome sequencing methods. Impact statement Somatic mutations cause cancer, possibly other diseases and aging. Yet, very little is known about the frequency of such mutations in vivo, their distribution across the genome, and their possible functional consequences other than cancer. Even in cancer, we do not know the heterogeneity of mutations within a tumor and if seemingly normal cells in its surroundings already have elevated mutation frequencies. Here, we review a new, whole genome amplification system that allows accurate quantification and characterization of single-cell mutational landscapes in human cells and tissues in relation to disease.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, NY 10461, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, NY 10461, USA
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, NY 10461, USA
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180
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Mendez P, Fang LT, Jablons DM, Kim IJ. Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues. Sci Rep 2017; 7:4055. [PMID: 28642587 PMCID: PMC5481435 DOI: 10.1038/s41598-017-04419-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
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Affiliation(s)
- Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Li Tai Fang
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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181
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Huang AY, Zhang Z, Ye AY, Dou Y, Yan L, Yang X, Zhang Y, Wei L. MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples. Nucleic Acids Res 2017; 45:e76. [PMID: 28132024 PMCID: PMC5449543 DOI: 10.1093/nar/gkx024] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/24/2016] [Accepted: 01/26/2017] [Indexed: 02/07/2023] Open
Abstract
Genomic mosaicism arising from postzygotic mutations has long been associated with cancer and more recently with non-cancer diseases. It has also been detected in healthy individuals including healthy parents of children affected with genetic disorders, highlighting its critical role in the origin of genetic mutations. However, most existing software for the genome-wide identification of single-nucleotide mosaicisms (SNMs) requires a paired control tissue obtained from the same individual which is often unavailable for non-cancer individuals and sometimes missing in cancer studies. Here, we present MosaicHunter (http://mosaichunter.cbi.pku.edu.cn), a bioinformatics tool that can identify SNMs in whole-genome and whole-exome sequencing data of unpaired samples without matched controls using Bayesian genotypers. We evaluate the accuracy of MosaicHunter on both simulated and real data and demonstrate that it has improved performance compared with other somatic mutation callers. We further demonstrate that incorporating sequencing data of the parents can be an effective approach to significantly improve the accuracy of detecting SNMs in an individual when a matched control sample is unavailable. Finally, MosaicHunter also has a paired mode that can take advantage of matched control samples when available, making it a useful tool for detecting SNMs in both non-cancer and cancer studies.
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Affiliation(s)
- August Yue Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Zheng Zhang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- Peking-Tsinghua Center for Life Sciences, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Yanmei Dou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Linlin Yan
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yuehua Zhang
- Peking University First Hospital, Peking University, Beijing 100034, People's Republic of China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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182
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Enhanced Rate of Acquisition of Point Mutations in Mouse Intestinal Adenomas Compared to Normal Tissue. Cell Rep 2017; 19:2185-2192. [DOI: 10.1016/j.celrep.2017.05.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/11/2017] [Accepted: 05/14/2017] [Indexed: 10/19/2022] Open
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183
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Lynch M, Ackerman MS, Gout JF, Long H, Sung W, Thomas WK, Foster PL. Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet 2017; 17:704-714. [PMID: 27739533 DOI: 10.1038/nrg.2016.104] [Citation(s) in RCA: 438] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Matthew S Ackerman
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Jean-Francois Gout
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Hongan Long
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Patricia L Foster
- Department of Biology, Indiana University, Bloomington, Indiana 47401, USA
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184
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Dong X, Zhang L, Milholland B, Lee M, Maslov AY, Wang T, Vijg J. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nat Methods 2017; 14:491-493. [PMID: 28319112 PMCID: PMC5408311 DOI: 10.1038/nmeth.4227] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/22/2017] [Indexed: 01/22/2023]
Abstract
Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.
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Affiliation(s)
- Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Alexander Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
- Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
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185
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Veitia RA, Govindaraju DR, Bottani S, Birchler JA. Aging: Somatic Mutations, Epigenetic Drift and Gene Dosage Imbalance. Trends Cell Biol 2017; 27:299-310. [DOI: 10.1016/j.tcb.2016.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
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186
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Woodworth MB, Girskis KM, Walsh CA. Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat Rev Genet 2017; 18:230-244. [PMID: 28111472 PMCID: PMC5459401 DOI: 10.1038/nrg.2016.159] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Resolving lineage relationships between cells in an organism is a fundamental interest of developmental biology. Furthermore, investigating lineage can drive understanding of pathological states, including cancer, as well as understanding of developmental pathways that are amenable to manipulation by directed differentiation. Although lineage tracking through the injection of retroviral libraries has long been the state of the art, a recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible. In this Review, we discuss these techniques for cell lineage tracking, with attention both to those that trace lineage forwards from experimental labelling, and those that trace backwards across the life history of an organism.
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Affiliation(s)
- Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Kelly M Girskis
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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187
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Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin S, Alder C, Patel N, Gamble S, O’Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg Å, Stunnenberg H, van de Vijver M, Tan BK, Caldas C, Tutt A, Ueno NT, van’t Veer LJ, Martens JWM, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjörd JE, Børresen-Dale AL, Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature 2017; 543:714-718. [PMID: 28329761 PMCID: PMC6169740 DOI: 10.1038/nature21703] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/08/2017] [Indexed: 01/05/2023]
Abstract
Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos, our understanding of early embryonic somatic mutations is very limited. Here we use whole-genome sequences of normal blood from 241 adults to identify 163 early embryonic mutations. We estimate that approximately three base substitution mutations occur per cell per cell-doubling event in early human embryogenesis and these are mainly attributable to two known mutational signatures. We used the mutations to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell-doubling events contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study therefore provides insights into the mutation rates, mutational processes and developmental outcomes of cell dynamics that operate during early human embryogenesis.
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Affiliation(s)
- Young Seok Ju
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | | | - Moritz Gerstung
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mia Petljak
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Raheleh Rahbari
- Genomic Mutation and Genetic Disease, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Oxford Big Data Institute and Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Helen R Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Anthony Fullam
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Nikita Patel
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steve Gamble
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sarah O’Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Dilip D Giri
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Torril Sauer
- Institute of Clinical Medicine, Campus at Akershus University Hospital, University of Oslo, Lørenskog, Norway
| | - Sarah E Pinder
- King’s Health Partners Cancer Biobank, Guy’s Hospital, King’s College London School of Medicine, London, UK
| | - Colin A Purdie
- Department of Pathology, Ninewells Hospital and Medical School, Dundee, UK
| | - Åke Borg
- BioCare, Strategic Cancer Research Program, Lund, Sweden
- CREATE Health, Strategic Centre for Translational Cancer Research, Lund, Sweden
- Department of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden
| | | | - Marc van de Vijver
- Department of Pathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Benita K.T. Tan
- SingHealth Duke-NUS Breast Centre, Division of Surgical Oncology, National Cancer Centre Singapore, Department of General Surgery, Singapore General Hospital, Singapore
| | - Carlos Caldas
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Andrew Tutt
- Breast Cancer Now Research Unit, King’s College London, London SE1 9RT, UK
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London SW3 6JB, UK
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura J van’t Veer
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, USA
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Paul N. Span
- Department of Radiation Oncology and Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sunil R. Lakhani
- University of Queensland, School of Medicine, Brisbane, Australia
- Pathology Queensland, Royal Brisbane and Women's s Hospital, Brisbane, Australia
- University of Queensland, UQ Centre for Clinical Research, Brisbane, Australia
| | | | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
- The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Andrea Richardson
- Sibley Pathology Department, Johns Hopkins Medicine, Washington DC 20016, USA
| | - Alastair M. Thompson
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alain Viari
- Plateforme Gilles Thomas - Synergie Lyon Cancer, Centre Léon Bérard, Lyon Cedex 08, FRANCE
| | - Matthew E Hurles
- Genomic Mutation and Genetic Disease, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
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188
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Drost J, Clevers H. Translational applications of adult stem cell-derived organoids. Development 2017; 144:968-975. [DOI: 10.1242/dev.140566] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
Adult stem cells from a variety of organs can be expanded long-term in vitro as three-dimensional organotypic structures termed organoids. These adult stem cell-derived organoids retain their organ identity and remain genetically stable over long periods of time. The ability to grow organoids from patient-derived healthy and diseased tissue allows for the study of organ development, tissue homeostasis and disease. In this Review, we discuss the generation of adult stem cell-derived organoid cultures and their applications in in vitro disease modeling, personalized cancer therapy and regenerative medicine.
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Affiliation(s)
- Jarno Drost
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht 3584CT, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, Utrecht 3584CG, The Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht 3584CT, The Netherlands
- Cancer Genomics Netherlands, UMC Utrecht, Utrecht 3584CG, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584CT, The Netherlands
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189
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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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190
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One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. Genome Res 2017; 27:512-523. [PMID: 28235832 PMCID: PMC5378170 DOI: 10.1101/gr.215517.116] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/24/2017] [Indexed: 01/01/2023]
Abstract
Few studies have been conducted to understand post-zygotic accumulation of mutations in cells of the healthy human body. We reprogrammed 32 skin fibroblast cells from families of donors into human induced pluripotent stem cell (hiPSC) lines. The clonal nature of hiPSC lines allows a high-resolution analysis of the genomes of the founder fibroblast cells without being confounded by the artifacts of single-cell whole-genome amplification. We estimate that on average a fibroblast cell in children has 1035 mostly benign mosaic SNVs. On average, 235 SNVs could be directly confirmed in the original fibroblast population by ultradeep sequencing, down to an allele frequency (AF) of 0.1%. More sensitive droplet digital PCR experiments confirmed more SNVs as mosaic with AF as low as 0.01%, suggesting that 1035 mosaic SNVs per fibroblast cell is the true average. Similar analyses in adults revealed no significant increase in the number of SNVs per cell, suggesting that a major fraction of mosaic SNVs in fibroblasts arises during development. Mosaic SNVs were distributed uniformly across the genome and were enriched in a mutational signature previously observed in cancers and in de novo variants and which, we hypothesize, is a hallmark of normal cell proliferation. Finally, AF distribution of mosaic SNVs had distinct narrow peaks, which could be a characteristic of clonal cell selection, clonal expansion, or both. These findings reveal a large degree of somatic mosaicism in healthy human tissues, link de novo and cancer mutations to somatic mosaicism, and couple somatic mosaicism with cell proliferation.
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191
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192
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Liggett LA, DeGregori J. Changing mutational and adaptive landscapes and the genesis of cancer. Biochim Biophys Acta Rev Cancer 2017; 1867:84-94. [PMID: 28167050 DOI: 10.1016/j.bbcan.2017.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/27/2017] [Accepted: 01/28/2017] [Indexed: 12/31/2022]
Abstract
By the time the process of oncogenesis has produced an advanced cancer, tumor cells have undergone extensive evolution. The cellular phenotypes resulting from this evolution have been well studied, and include accelerated growth rates, apoptosis resistance, immortality, invasiveness, and immune evasion. Yet with all of our current knowledge of tumor biology, the details of early oncogenesis have been difficult to observe and understand. Where different oncogenic mutations may work together to enhance the survival of a tumor cell, in isolation they are often pro-apoptotic, pro-differentiative or pro-senescent, and therefore often, somewhat paradoxically, disadvantageous to a cell. It is also becoming clear that somatic mutations, including those in known oncogenic drivers, are common in tissues starting at a young age. These observations raise the question: how do we largely avoid cancer for most of our lives? Here we propose that evolutionary forces can help explain this paradox. As humans and other organisms age or experience external insults such as radiation or smoking, the structure and function of tissues progressively degrade, resulting in altered stem cell niche microenvironments. As tissue integrity declines, it becomes less capable of supporting and maintaining resident stem cells. These stem cells then find themselves in a microenvironment to which they are poorly adapted, providing a competitive advantage to those cells that can restore their functionality and fitness through mutations or epigenetic changes. The resulting oncogenic clonal expansions then increase the odds of further cancer progression. Understanding how the causes of cancer, such as aging or smoking, affect tissue microenvironments to control the impact of mutations on somatic cell fitness can help reconcile the discrepancy between marked mutation accumulation starting early in life and the somatic evolution that leads to cancer at advanced ages or following carcinogenic insults. 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)
- L Alexander Liggett
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, United States
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, United States; Integrated Department of Immunology, University of Colorado School of Medicine, Aurora, CO 80045, United States; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, United States; Department of Medicine, Section of Hematology, University of Colorado School of Medicine, Aurora, CO 80045, United States.
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193
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Mathieson I, Reich D. Differences in the rare variant spectrum among human populations. PLoS Genet 2017; 13:e1006581. [PMID: 28146552 PMCID: PMC5310914 DOI: 10.1371/journal.pgen.1006581] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 02/15/2017] [Accepted: 01/12/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations occur at vastly different rates across the genome, and populations, leading to differences in the spectrum of segregating polymorphisms. Here, we investigate variation in the rare variant spectrum in a sample of human genomes representing all major world populations. We find at least two distinct signatures of variation. One, consistent with a previously reported signature is characterized by an increased rate of TCC>TTC mutations in people from Western Eurasia and South Asia, likely related to differences in the rate, or efficiency of repair, of damage due to deamination of methylated guanine. We describe the geographic extent of this signature and show that it is detectable in the genomes of ancient, but not archaic humans. The second signature is private to certain Native American populations, and is concentrated at CpG sites. We show that this signature is not driven by differences in the CpG mutation rate, but is a result of the fact that highly mutable CpG sites are more likely to undergo multiple independent mutations across human populations, and the spectrum of such mutations is highly sensitive to recent demography. Both of these effects dramatically affect the spectrum of rare variants across human populations, and should be taken into account when using mutational clocks to make inference about demography.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
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194
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Frieda KL, Linton JM, Hormoz S, Choi J, Chow KHK, Singer ZS, Budde MW, Elowitz MB, Cai L. Synthetic recording and in situ readout of lineage information in single cells. Nature 2017; 541:107-111. [PMID: 27869821 PMCID: PMC6487260 DOI: 10.1038/nature20777] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022]
Abstract
Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here we describe a synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out of single cells in situ. This system, termed memory by engineered mutagenesis with optical in situ readout (MEMOIR), is based on a set of barcoded recording elements termed scratchpads. The state of a given scratchpad can be irreversibly altered by CRISPR/Cas9-based targeted mutagenesis, and later read out in single cells through multiplexed single-molecule RNA fluorescence hybridization (smFISH). Using MEMOIR as a proof of principle, we engineered mouse embryonic stem cells to contain multiple scratchpads and other recording components. In these cells, scratchpads were altered in a progressive and stochastic fashion as the cells proliferated. Analysis of the final states of scratchpads in single cells in situ enabled reconstruction of lineage information from cell colonies. Combining analysis of endogenous gene expression with lineage reconstruction in the same cells further allowed inference of the dynamic rates at which embryonic stem cells switch between two gene expression states. Finally, using simulations, we show how parallel MEMOIR systems operating in the same cell could enable recording and readout of dynamic cellular event histories. MEMOIR thus provides a versatile platform for information recording and in situ, single-cell readout across diverse biological systems.
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Affiliation(s)
- Kirsten L Frieda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Joonhyuk Choi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Ke-Huan K Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Zakary S Singer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mark W Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
| | - Long Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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195
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Dempsey PW. CTCs and ctDNA: Two Tales of a Complex Biology. LIQUID BIOPSIES IN SOLID TUMORS 2017. [DOI: 10.1007/978-3-319-50956-3_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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196
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Abstract
This review is a summary of a talk presented at the 2015 American Epilepsy Society Annual Meeting. Its purposes are 1) to review developments in epilepsy genetics, 2) to discuss which groups of patients with epilepsy might benefit from genetic testing, and 3) to present a rational approach to genetic testing in epilepsy in the rapidly evolving era of genomic medicine.
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197
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Cai S, Kalisky T, Sahoo D, Dalerba P, Feng W, Lin Y, Qian D, Kong A, Yu J, Wang F, Chen EY, Scheeren FA, Kuo AH, Sikandar SS, Hisamori S, van Weele LJ, Heiser D, Sim S, Lam J, Quake S, Clarke MF. A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell 2016; 20:247-260.e5. [PMID: 28041896 DOI: 10.1016/j.stem.2016.11.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/12/2016] [Accepted: 11/04/2016] [Indexed: 12/31/2022]
Abstract
Stem cells in many tissues sustain themselves by entering a quiescent state to avoid genomic insults and to prevent exhaustion caused by excessive proliferation. In the mammary gland, the identity and characteristics of quiescent epithelial stem cells are not clear. Here, we identify a quiescent mammary epithelial cell population expressing high levels of Bcl11b and located at the interface between luminal and basal cells. Bcl11bhigh cells are enriched for cells that can regenerate mammary glands in secondary transplants. Loss of Bcl11b leads to a Cdkn2a-dependent exhaustion of ductal epithelium and loss of epithelial cell regenerative capacity. Gain- and loss-of-function studies show that Bcl11b induces cells to enter the G0 phase of the cell cycle and become quiescent. Taken together, these results suggest that Bcl11b acts as a central intrinsic regulator of mammary epithelial stem cell quiescence and exhaustion and is necessary for long-term maintenance of the mammary gland.
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Affiliation(s)
- Shang Cai
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tomer Kalisky
- Department of Bioengineering, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Debashis Sahoo
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Department of Computer Science and Engineering, University of California San Diego, San Diego, CA 92123-0984, USA
| | - Piero Dalerba
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Weiguo Feng
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuan Lin
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA; Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dalong Qian
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela Kong
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey Yu
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Flora Wang
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth Y Chen
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ferenc A Scheeren
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angera H Kuo
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shaheen S Sikandar
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shigeo Hisamori
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Linda J van Weele
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Diane Heiser
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sopheak Sim
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jessica Lam
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Stephen Quake
- Department of Bioengineering, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael F Clarke
- Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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198
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Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T, Campbell PJ, Vineis P, Phillips DH, Stratton MR. Mutational signatures associated with tobacco smoking in human cancer. Science 2016; 354:618-622. [PMID: 27811275 PMCID: PMC6141049 DOI: 10.1126/science.aag0299] [Citation(s) in RCA: 689] [Impact Index Per Article: 86.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Tobacco smoking increases the risk of at least 17 classes of human cancer. We analyzed somatic mutations and DNA methylation in 5243 cancers of types for which tobacco smoking confers an elevated risk. Smoking is associated with increased mutation burdens of multiple distinct mutational signatures, which contribute to different extents in different cancers. One of these signatures, mainly found in cancers derived from tissues directly exposed to tobacco smoke, is attributable to misreplication of DNA damage caused by tobacco carcinogens. Others likely reflect indirect activation of DNA editing by APOBEC cytidine deaminases and of an endogenous clocklike mutational process. Smoking is associated with limited differences in methylation. The results are consistent with the proposition that smoking increases cancer risk by increasing the somatic mutation load, although direct evidence for this mechanism is lacking in some smoking-related cancer types.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87102, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Iñigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Medical Genetics, Addenbrooke's Hospital National Health Service Trust, Cambridge, UK
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Paolo Vineis
- Human Genetics Foundation, 10126 Torino, Italy
- Department of Epidemiology and Biostatistics, Medical Research Council (MRC)-Public Health England (PHE) Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - David H Phillips
- King's College London, MRC-PHE Centre for Environment and Health, Analytical and Environmental Sciences Division, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK.
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Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet 2016; 12:e1006385. [PMID: 27788131 PMCID: PMC5082821 DOI: 10.1371/journal.pgen.1006385] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/23/2016] [Indexed: 12/24/2022] Open
Abstract
Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology, and improving the prognosis and prevention of cancers and other genetic diseases. Previous methods relying on either the generation of induced pluripotent stem cells, or sequencing of single-cell genomes were inherently error-prone and did not allow independent validation of the mutations. In the current study we eliminated these potential sources of error by high coverage genome sequencing of single-cell derived clonal fibroblast lineages, obtained after minimal propagation in culture, prepared from skin biopsies of two healthy adult humans. We report here accurate measurement of genome-wide magnitude and spectra of mutations accrued in skin fibroblasts of healthy adult humans. We found that every cell contains at least one chromosomal rearrangement and 600–13,000 base substitutions. The spectra and correlation of base substitutions with epigenomic features resemble many cancers. Moreover, because biopsies were taken from body parts differing by sun exposure, we can delineate the precise contributions of environmental and endogenous factors to the accrual of genetic changes within the same individual. We show here that UV-induced and endogenous DNA damage can have a comparable impact on the somatic mutation loads in skin fibroblasts. Somatic genomes are constantly accumulating changes caused by endogenous lesions, errors in DNA replication and repair, as well as environmental insults. Despite the importance of somatic genome instability in aging and age-related pathologies, including cancers, accurate measurements of mutation loads in healthy cells is still missing. In this study, we developed an experimental approach to accurately determine the somatic genome changes accrued in cell lineages over the lifetime of healthy humans. We show that the amounts and types of mutations in skin cells resemble many cancers, thus indicating that the mechanisms that lead to carcinogenesis are also functional in healthy cells. Moreover, sun-exposed skin cells have a higher mutation load attributable to ultraviolet radiation (UV) unlike cells from hips that were protected by clothing. Our work provides precise measurements of the mutation loads in single cells in human skin. Furthermore our data allowed defining the mutagenic impacts of environmental and endogenous processes within the same individual and led to conclusion that these processes have a comparable impact on the somatic mutation load.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Steven A. Roberts
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States Of America
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Kin Chan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Sara A. Grimm
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Shuangshuang Dai
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - David C. Fargo
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Jayne C. Boyer
- Department of Environmental Science and Engineering, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - William K. Kaufmann
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Eunjung Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States Of America
| | - Isidro Cortes-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States Of America
| | - Shepherd H. Schurman
- Clinical Research Unit, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Ewa P. Malc
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Piotr A. Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
- * E-mail:
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Abstract
Our understanding of the chronology of human evolution relies on the “molecular clock” provided by the steady accumulation of substitutions on an evolutionary lineage. Recent analyses of human pedigrees have called this understanding into question by revealing unexpectedly low germline mutation rates, which imply that substitutions accrue more slowly than previously believed. Translating mutation rates estimated from pedigrees into substitution rates is not as straightforward as it may seem, however. We dissect the steps involved, emphasizing that dating evolutionary events requires not “a mutation rate” but a precise characterization of how mutations accumulate in development in males and females—knowledge that remains elusive.
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Affiliation(s)
- Priya Moorjani
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Ziyue Gao
- Howard Hughes Medical Institute & Dept. of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail: (PM); (ZG); (MP)
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail: (PM); (ZG); (MP)
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