101
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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102
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Lee-Six H, Kent DG. Tracking hematopoietic stem cells and their progeny using whole-genome sequencing. Exp Hematol 2020; 83:12-24. [PMID: 32007478 PMCID: PMC7118367 DOI: 10.1016/j.exphem.2020.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/07/2020] [Accepted: 01/13/2020] [Indexed: 12/20/2022]
Abstract
Despite decades of progress in our understanding of hematopoiesis through the study of animal models and transplantation in humans, investigating physiological human hematopoiesis directly has remained challenging. Questions on the clonal structure of the human hematopoietic stem cell (HSC) pool, such as "how many HSCs are there?" and "do all HSC clones actively produce all blood cell types in equal proportions?" remain open. These questions have inherent value for understanding normal human physiology, but also directly inform our comprehension of the process by which the system is subverted to drive diseases of the blood, in particular blood cancers and bone marrow failure syndromes. The critical link between normal and abnormal hematopoiesis is perhaps best illustrated by the recent discovery of clonal hematopoiesis in healthy people with no abnormal blood parameters. In such individuals, large clones derived from single cells are present and are dominant relative to their normal counterparts, but their presence does not necessitate abnormal blood cell production. Intriguingly, however, these individuals are also at a significantly greater risk of developing leukemias and of cardiovascular events, underscoring the importance of understanding how blood stem cell clones compete against each other.
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Affiliation(s)
- Henry Lee-Six
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - David G Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom; Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge, United Kingdom; Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
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103
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Georgakopoulos N, Prior N, Angres B, Mastrogiovanni G, Cagan A, Harrison D, Hindley CJ, Arnes-Benito R, Liau SS, Curd A, Ivory N, Simons BD, Martincorena I, Wurst H, Saeb-Parsy K, Huch M. Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids. BMC DEVELOPMENTAL BIOLOGY 2020; 20:4. [PMID: 32098630 PMCID: PMC7043048 DOI: 10.1186/s12861-020-0209-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/03/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Pancreatic organoid systems have recently been described for the in vitro culture of pancreatic ductal cells from mouse and human. Mouse pancreatic organoids exhibit unlimited expansion potential, while previously reported human pancreas organoid (hPO) cultures do not expand efficiently long-term in a chemically defined, serum-free medium. We sought to generate a 3D culture system for long-term expansion of human pancreas ductal cells as hPOs to serve as the basis for studies of human pancreas ductal epithelium, exocrine pancreatic diseases and the development of a genomically stable replacement cell therapy for diabetes mellitus. RESULTS Our chemically defined, serum-free, human pancreas organoid culture medium supports the generation and expansion of hPOs with high efficiency from both fresh and cryopreserved primary tissue. hPOs can be expanded from a single cell, enabling their genetic manipulation and generation of clonal cultures. hPOs expanded for months in vitro maintain their ductal morphology, biomarker expression and chromosomal integrity. Xenografts of hPOs survive long-term in vivo when transplanted into the pancreas of immunodeficient mice. Notably, mouse orthotopic transplants show no signs of tumorigenicity. Crucially, our medium also supports the establishment and expansion of hPOs in a chemically defined, modifiable and scalable, biomimetic hydrogel. CONCLUSIONS hPOs can be expanded long-term, from both fresh and cryopreserved human pancreas tissue in a chemically defined, serum-free medium with no detectable tumorigenicity. hPOs can be clonally expanded, genetically manipulated and are amenable to culture in a chemically defined hydrogel. hPOs therefore represent an abundant source of pancreas ductal cells that retain the characteristics of the tissue-of-origin, which opens up avenues for modelling diseases of the ductal epithelium and increasing understanding of human pancreas exocrine biology as well as for potentially producing insulin-secreting cells for the treatment of diabetes.
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Affiliation(s)
- Nikitas Georgakopoulos
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Cambridge Biorepository for Translational Medicine & Department of Surgery, University o.f Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Nicole Prior
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | | | - Gianmarco Mastrogiovanni
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Daisy Harrison
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Christopher J Hindley
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Physics, The Cavendish Laboratory, University of Cambridge, Thompson Avenue, Cambridge, JJ, CB3 0HE, UK
| | - Robert Arnes-Benito
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Siong-Seng Liau
- Hepatopancreatobiliary Surgical Unit, Addenbrooke's Hospital and MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Abbie Curd
- Cambridge Biorepository for Translational Medicine & Department of Surgery, University o.f Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Natasha Ivory
- Cambridge Biorepository for Translational Medicine & Department of Surgery, University o.f Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Benjamin D Simons
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Physics, The Cavendish Laboratory, University of Cambridge, Thompson Avenue, Cambridge, JJ, CB3 0HE, UK
| | | | | | - Kourosh Saeb-Parsy
- Cambridge Biorepository for Translational Medicine & Department of Surgery, University o.f Cambridge, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK.
| | - Meritxell Huch
- The Wellcome Trust/ Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany.
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104
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Nakamori M, Panigrahi GB, Lanni S, Gall-Duncan T, Hayakawa H, Tanaka H, Luo J, Otabe T, Li J, Sakata A, Caron MC, Joshi N, Prasolava T, Chiang K, Masson JY, Wold MS, Wang X, Lee MYWT, Huddleston J, Munson KM, Davidson S, Layeghifard M, Edward LM, Gallon R, Santibanez-Koref M, Murata A, Takahashi MP, Eichler EE, Shlien A, Nakatani K, Mochizuki H, Pearson CE. A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo. Nat Genet 2020; 52:146-159. [PMID: 32060489 PMCID: PMC7043212 DOI: 10.1038/s41588-019-0575-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/19/2019] [Indexed: 01/07/2023]
Abstract
In many repeat diseases, such as Huntington's disease (HD), ongoing repeat expansions in affected tissues contribute to disease onset, progression and severity. Inducing contractions of expanded repeats by exogenous agents is not yet possible. Traditional approaches would target proteins driving repeat mutations. Here we report a compound, naphthyridine-azaquinolone (NA), that specifically binds slipped-CAG DNA intermediates of expansion mutations, a previously unsuspected target. NA efficiently induces repeat contractions in HD patient cells as well as en masse contractions in medium spiny neurons of HD mouse striatum. Contractions are specific for the expanded allele, independently of DNA replication, require transcription across the coding CTG strand and arise by blocking repair of CAG slip-outs. NA-induced contractions depend on active expansions driven by MutSβ. NA injections in HD mouse striatum reduce mutant HTT protein aggregates, a biomarker of HD pathogenesis and severity. Repeat-structure-specific DNA ligands are a novel avenue to contract expanded repeats.
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Affiliation(s)
- Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Gagan B Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Terence Gall-Duncan
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hideki Hayakawa
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hana Tanaka
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jennifer Luo
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Takahiro Otabe
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Jinxing Li
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Akihiro Sakata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Quebec, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec, Quebec, Canada
| | - Niraj Joshi
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Quebec, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec, Quebec, Canada
| | - Tanya Prasolava
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Karen Chiang
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Quebec, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec, Quebec, Canada
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA
| | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Scott Davidson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Mehdi Layeghifard
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Lisa-Monique Edward
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Richard Gallon
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam Shlien
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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105
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Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis. Cell Rep 2019; 25:2308-2316.e4. [PMID: 30485801 PMCID: PMC6289083 DOI: 10.1016/j.celrep.2018.11.014] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/10/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022] Open
Abstract
Mutation accumulation during life can contribute to hematopoietic dysfunction; however, the underlying dynamics are unknown. Somatic mutations in blood progenitors can provide insight into the rate and processes underlying this accumulation, as well as the developmental lineage tree and stem cell division numbers. Here, we catalog mutations in the genomes of human-bone-marrow-derived and umbilical-cord-blood-derived hematopoietic stem and progenitor cells (HSPCs). We find that mutations accumulate gradually during life with approximately 14 base substitutions per year. The majority of mutations were acquired after birth and could be explained by the constant activity of various endogenous mutagenic processes, which also explains the mutation load in acute myeloid leukemia (AML). Using these mutations, we construct a developmental lineage tree of human hematopoiesis, revealing a polyclonal architecture and providing evidence that developmental clones exhibit multipotency. Our approach highlights features of human native hematopoiesis and its implications for leukemogenesis.
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106
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Coorens THH, Treger TD, Al-Saadi R, Moore L, Tran MGB, Mitchell TJ, Tugnait S, Thevanesan C, Young MD, Oliver TRW, Oostveen M, Collord G, Tarpey PS, Cagan A, Hooks Y, Brougham M, Reynolds BC, Barone G, Anderson J, Jorgensen M, Burke GAA, Visser J, Nicholson JC, Smeulders N, Mushtaq I, Stewart GD, Campbell PJ, Wedge DC, Martincorena I, Rampling D, Hook L, Warren AY, Coleman N, Chowdhury T, Sebire N, Drost J, Saeb-Parsy K, Stratton MR, Straathof K, Pritchard-Jones K, Behjati S. Embryonal precursors of Wilms tumor. Science 2019; 366:1247-1251. [PMID: 31806814 PMCID: PMC6914378 DOI: 10.1126/science.aax1323] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/04/2019] [Accepted: 11/06/2019] [Indexed: 12/27/2022]
Abstract
Adult cancers often arise from premalignant clonal expansions. Whether the same is true of childhood tumors has been unclear. To investigate whether Wilms tumor (nephroblastoma; a childhood kidney cancer) develops from a premalignant background, we examined the phylogenetic relationship between tumors and corresponding normal tissues. In 14 of 23 cases studied (61%), we found premalignant clonal expansions in morphologically normal kidney tissues that preceded tumor development. These clonal expansions were defined by somatic mutations shared between tumor and normal tissues but absent from blood cells. We also found hypermethylation of the H19 locus, a known driver of Wilms tumor development, in 58% of the expansions. Phylogenetic analyses of bilateral tumors indicated that clonal expansions can evolve before the divergence of left and right kidney primordia. These findings reveal embryonal precursors from which unilateral and multifocal cancers develop.
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Affiliation(s)
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Reem Al-Saadi
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Luiza Moore
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Suzanne Tugnait
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | | | | | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Minou Oostveen
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick S Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Mark Brougham
- Department of Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK
| | - Ben C Reynolds
- Department of Paediatric Nephrology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Giuseppe Barone
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - John Anderson
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Johannes Visser
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James C Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Naima Smeulders
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - David C Wedge
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | | | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Tanzina Chowdhury
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Neil Sebire
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, 3584 CS Utrecht, Netherlands
| | - Kourosh Saeb-Parsy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Karin Straathof
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Kathy Pritchard-Jones
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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107
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Innan H, Veitia R, Govindaraju DR. Genetic and epigenetic Muller's ratchet as a mechanism of frailty and morbidity during aging: a demographic genetic model. Hum Genet 2019; 139:409-420. [PMID: 31713020 DOI: 10.1007/s00439-019-02067-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022]
Abstract
Mutation accumulation has been proposed as a cause of senescence. During this process, age-related genetic and epigenetic mutations steadily accumulate. Cascading deleterious effects of mutations might initiate a steady "accumulation of deficits" in cells, despite the existence of repair mechanisms, leading to cellular senescence and functional decline of tissues and organs, which ultimately manifest as frailty and disease. Here, we investigate several of these aspects in differentiating cell populations through modeling and simulation using the Moran birth-death (demographic) process, under several scenarios of mutation accumulation. Deleterious mutations seem to rapidly accumulate particularly early in the course of life, during which the rate of cell division is high, thereby exerting a greater effect on subsequent cellular senescence. Our results are compatible with the principle of the Muller's ratchet taking place in asexually reproducing organisms. The ratchet speed in a given tissue depends on the size of the cell population, mutation rate and the impact of such mutations on cell phenotypes. It varies substantially among cells in different tissues and organs due to heterogeneity in relation to cell and organ-specific demographic features. Ratchet accelerates particularly after middle age, resulting in a synergistic fitness decay at the level of cell populations. We extend Fisher's average excess concept and rank order scale to interpret differential phenotypic effects of the increase of the mutation load among cell populations within a given tissue. We postulate that classical evolutionary genetic models can explain, at least in part, the origins of frailty, subclinical conditions, morbidity and the health consequences of senescence.
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Affiliation(s)
- Hideki Innan
- Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan.
| | - Reiner Veitia
- Institute Jacques Monod, Paris, France.,Universite Paris Diderot, Paris, France
| | - Diddahally R Govindaraju
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA. .,The Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY, 10460, USA.
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108
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Masuyama N, Mori H, Yachie N. DNA barcodes evolve for high-resolution cell lineage tracing. Curr Opin Chem Biol 2019; 52:63-71. [DOI: 10.1016/j.cbpa.2019.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/26/2019] [Accepted: 05/10/2019] [Indexed: 10/26/2022]
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109
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Lee-Six H, Olafsson S, Ellis P, Osborne RJ, Sanders MA, Moore L, Georgakopoulos N, Torrente F, Noorani A, Goddard M, Robinson P, Coorens THH, O'Neill L, Alder C, Wang J, Fitzgerald RC, Zilbauer M, Coleman N, Saeb-Parsy K, Martincorena I, Campbell PJ, Stratton MR. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 2019; 574:532-537. [PMID: 31645730 DOI: 10.1038/s41586-019-1672-7] [Citation(s) in RCA: 392] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 09/11/2019] [Indexed: 02/06/2023]
Abstract
The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer1. However, our understanding of the earliest phases of colorectal neoplastic changes-which may occur in morphologically normal tissue-is comparatively limited, as for most cancer types. Here we use whole-genome sequencing to analyse hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed; some of these were ubiquitous and continuous, whereas others were only found in some individuals, in some crypts or during certain periods of life. Probable driver mutations were present in around 1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. Colorectal cancers exhibit substantially increased mutational burdens relative to normal cells. Sequencing normal colorectal cells provides quantitative insights into the genomic and clonal evolution of cancer.
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Affiliation(s)
| | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
| | - Ayesha Noorani
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin Goddard
- Department of Pathology, Papworth Hospital NHS Trust, Cambridge, UK
| | | | | | | | | | | | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
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110
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Belderbos ME, Jacobs S, Koster TK, Ausema A, Weersing E, Zwart E, de Haan G, Bystrykh LV. Donor-to-Donor Heterogeneity in the Clonal Dynamics of Transplanted Human Cord Blood Stem Cells in Murine Xenografts. Biol Blood Marrow Transplant 2019; 26:16-25. [PMID: 31494231 DOI: 10.1016/j.bbmt.2019.08.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 08/26/2019] [Indexed: 01/12/2023]
Abstract
Umbilical cord blood (UCB) provides an alternative source of hematopoietic stem cells (HSCs) for allogeneic transplantation. Administration of sufficient donor HSCs is critical to restore recipient hematopoiesis and to maintain long-term polyclonal blood formation. However, due to lack of unique markers, the frequency of HSCs among UCB CD34+ cells is the subject of ongoing debate, urging for reproducible strategies for their counting. Here, we used cellular barcoding to determine the frequency and clonal dynamics of human UCB HSCs and to determine how data analysis methods affect these parameters. We transplanted lentivirally barcoded CD34+ cells from 20 UCB donors into Nod/Scid/IL2Ry-/- (NSG) mice (n = 30). Twelve recipients (of 8 UCB donors) engrafted with >1% GFP+ cells, allowing for clonal analysis by multiplexed barcode deep sequencing. Using multiple definitions of clonal diversity and strategies for data filtering, we demonstrate that differences in data analysis can change clonal counts by several orders of magnitude and propose methods to improve their consistency. Using these methods, we show that the frequency of NSG-repopulating cells was low (median ∼1 HSC/104 CD34+ UCB cells) and could vary up to 10-fold between donors. Clonal patterns in blood became increasingly consistent over time, likely reflecting initial output of transient progenitors, followed by long-term HSCs with stable hierarchies. The majority of long-term clones displayed multilineage output, yet clones with lymphoid- or myeloid-biased output were also observed. Altogether, this study uncovers substantial interdonor and analysis-induced variability in the frequency of UCB CD34+ clones that contribute to post-transplant hematopoiesis. As clone tracing is increasingly relevant, we urge for universal and transparent methods to count HSC clones during normal aging and upon transplantation.
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Affiliation(s)
- Mirjam E Belderbos
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands; Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands.
| | - Sabrina Jacobs
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Taco K Koster
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Albertina Ausema
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Ellen Weersing
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Erik Zwart
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Gerald de Haan
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Leonid V Bystrykh
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
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111
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FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue. G3-GENES GENOMES GENETICS 2019; 9:2977-2987. [PMID: 31352405 PMCID: PMC6723130 DOI: 10.1534/g3.119.400438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With growing interest in monitoring mutational processes in normal tissues, tumor heterogeneity, and cancer evolution under therapy, the ability to accurately and economically detect ultra-rare mutations is becoming increasingly important. However, this capability has often been compromised by significant sequencing, PCR and DNA preparation error rates. Here, we describe FERMI (Fast Extremely Rare Mutation Identification) - a novel method designed to eliminate the majority of these sequencing and library-preparation errors in order to significantly improve rare somatic mutation detection. This method leverages barcoded targeting probes to capture and sequence DNA of interest with single copy resolution. The variant calls from the barcoded sequencing data are then further filtered in a position-dependent fashion against an adaptive, context-aware null model in order to distinguish true variants. As a proof of principle, we employ FERMI to probe bone marrow biopsies from leukemia patients, and show that rare mutations and clonal evolution can be tracked throughout cancer treatment, including during historically intractable periods like minimum residual disease. Importantly, FERMI is able to accurately detect nascent clonal expansions within leukemias in a manner that may facilitate the early detection and characterization of cancer relapse.
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112
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Yoo JH, Donowitz M. Intestinal enteroids/organoids: A novel platform for drug discovery in inflammatory bowel diseases. World J Gastroenterol 2019; 25:4125-4147. [PMID: 31435168 PMCID: PMC6700704 DOI: 10.3748/wjg.v25.i30.4125] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/14/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
The introduction of biologics such as anti-tumor necrosis factor (TNF) monoclonal antibodies followed by anti-integrins has dramatically changed the therapeutic paradigm of inflammatory bowel diseases (IBD). Furthermore, a newly developed anti-p40 subunit of interleukin (IL)-12 and IL-23 (ustekinumab) has been recently approved in the United States for patients with moderate to severe Crohn’s disease who have failed treatment with anti-TNFs. However, these immunosuppressive therapeutics which focus on anti-inflammatory mechanisms or immune cells still fail to achieve long-term remission in a significant percentage of patients. This strongly underlines the need to identify novel treatment targets beyond immune suppression to treat IBD. Recent studies have revealed the critical role of intestinal epithelial cells (IECs) in the pathogenesis of IBD. Physical, biochemical and immunologic driven barrier dysfunctions of epithelial cells contribute to the development of IBD. In addition, the recent establishment of adult stem cell-derived intestinal enteroid/organoid culture technology has allowed an exciting opportunity to study human IECs comprising all normal epithelial cells. This long-term epithelial culture model can be generated from endoscopic biopsies or surgical resections and recapitulates the tissue of origin, representing a promising platform for novel drug discovery in IBD. This review describes the advantages of intestinal enteroids/organoids as a research tool for intestinal diseases, introduces studies with these models in IBD, and gives a description of the current status of therapeutic approaches in IBD. Finally, we provide an overview of the current endeavors to identify a novel drug target for IBD therapy based on studies with human enteroids/organoids and describe the challenges in using enteroids/organoids as an IBD model.
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Affiliation(s)
- Jun-Hwan Yoo
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
- Digestive Disease Center, CHA Bundang Medical Center, CHA University, Seongnam 13496, South Korea
| | - Mark Donowitz
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
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113
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Schultze JL, Mass E, Schlitzer A. Emerging Principles in Myelopoiesis at Homeostasis and during Infection and Inflammation. Immunity 2019; 50:288-301. [PMID: 30784577 DOI: 10.1016/j.immuni.2019.01.019] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
Abstract
Myelopoiesis ensures the steady state of the myeloid cell compartment. Technological advances in fate mapping and genetic engineering, as well as the advent of single cell RNA-sequencing, have highlighted the heterogeneity of the hematopoietic system and revealed new concepts in myeloid cell ontogeny. These technologies are also shedding light on mechanisms of myelopoiesis at homeostasis and at different phases of infection and inflammation, illustrating important feedback loops between affected tissues and the bone marrow. We review these findings here and revisit principles in myelopoiesis in light of the evolving understanding of myeloid cell ontogeny and heterogeneity. We argue for the importance of system-wide evaluation of changes in myelopoiesis and discuss how even after the resolution of inflammation, long-lasting alterations in myelopoiesis may play a role in innate immune memory or trained immunity.
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Affiliation(s)
- Joachim L Schultze
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany; Genomics & Immunoregulation, LIMES Institute, University of Bonn, 53115 Bonn, Germany.
| | - Elvira Mass
- Developmental Biology of the Innate Immune System, LIMES Institute, University of Bonn, 53115 Bonn, Germany.
| | - Andreas Schlitzer
- Myeloid Cell Biology, LIMES Institute, University of Bonn, 53115 Bonn, Germany.
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114
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Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet 2019; 20:71-88. [PMID: 30410101 DOI: 10.1038/s41576-018-0071-5] [Citation(s) in RCA: 803] [Impact Index Per Article: 160.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | | | | | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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115
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Buczacki S. Fate plasticity in the intestine: The devil is in the detail. World J Gastroenterol 2019; 25:3116-3122. [PMID: 31333305 PMCID: PMC6626720 DOI: 10.3748/wjg.v25.i25.3116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023] Open
Abstract
The intestinal epithelium possesses a remarkable ability for both proliferation and regeneration. The last two decades have generated major advances in our understanding of the stem cell populations responsible for its maintenance during homeostasis and more recently the events that occur during injury induced regeneration. These fundamental discoveries have capitalised on the use of transgenic mouse models and in vivo lineage tracing to make their conclusions. It is evident that maintenance is driven by rapidly proliferating crypt base stem cells, but complexities associated with the technicality of mouse modelling have led to several overlapping populations being held responsible for the same behaviour. Similarly, it has been shown that essentially any population in the intestinal crypt can revert to a stem cell state given the correct stimulus during epithelial regeneration. Whilst these observations are profound it is uncertain how relevant they are to human intestinal homeostasis and pathology. Here, these recent studies are presented, in context with technical considerations of the models used, to argue that their conclusions may indeed not be applicable in understanding "homeostatic regeneration" and experimental suggestions presented for validating their results in human tissue.
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Affiliation(s)
- Simon Buczacki
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Addenbrooke’s Biomedical Campus, Cambridge CB2 0AF, United Kingdom
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116
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Bowling S, Lawlor K, Rodríguez TA. Cell competition: the winners and losers of fitness selection. Development 2019; 146:146/13/dev167486. [PMID: 31278123 DOI: 10.1242/dev.167486] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The process of cell competition results in the 'elimination of cells that are viable but less fit than surrounding cells'. Given the highly heterogeneous nature of our tissues, it seems increasingly likely that cells are engaged in a 'survival of the fittest' battle throughout life. The process has a myriad of positive roles in the organism: it selects against mutant cells in developing tissues, prevents the propagation of oncogenic cells and eliminates damaged cells during ageing. However, 'super-fit' cancer cells can exploit cell competition mechanisms to expand and spread. Here, we review the regulation, roles and risks of cell competition in organism development, ageing and disease.
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Affiliation(s)
- Sarah Bowling
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Katerina Lawlor
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Tristan A Rodríguez
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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117
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Abstract
Every animal grows from a single fertilized egg into an intricate network of cell types and organ systems. This process is captured in a lineage tree: a diagram of every cell's ancestry back to the founding zygote. Biologists have long sought to trace this cell lineage tree in individual organisms and have developed a variety of technologies to map the progeny of specific cells. However, there are billions to trillions of cells in complex organisms, and conventional approaches can only map a limited number of clonal populations per experiment. A new generation of tools that use molecular recording methods integrated with single cell profiling technologies may provide a solution. Here, we summarize recent breakthroughs in these technologies, outline experimental and computational challenges, and discuss biological questions that can be addressed using single cell dynamic lineage tracing.
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Affiliation(s)
- Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - James A Gagnon
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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118
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Jager M, Blokzijl F, Kuijk E, Bertl J, Vougioukalaki M, Janssen R, Besselink N, Boymans S, de Ligt J, Pedersen JS, Hoeijmakers J, Pothof J, van Boxtel R, Cuppen E. Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer. Genome Res 2019; 29:1067-1077. [PMID: 31221724 PMCID: PMC6633256 DOI: 10.1101/gr.246223.118] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 06/07/2019] [Indexed: 12/24/2022]
Abstract
Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of NER-deficiency may reveal important diagnostic opportunities, as tumors deficient in NER are more sensitive to certain treatments. Here, we analyzed the genome-wide somatic mutational profiles of adult stem cells (ASCs) from NER-deficient Ercc1 -/Δ mice. Our results indicate that NER-deficiency increases the base substitution load twofold in liver but not in small intestinal ASCs, which coincides with the tissue-specific aging pathology observed in these mice. Moreover, NER-deficient ASCs of both tissues show an increased contribution of Signature 8 mutations, which is a mutational pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the base substitutions indicates that deficiency of global-genome NER (GG-NER) underlies the observed mutational consequences. In line with this, we observe increased Signature 8 mutations in a GG-NER-deficient human organoid culture, in which XPC was deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations could therefore contribute to a predictor of NER-deficiency based on a patient's mutational profile.
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Affiliation(s)
- Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Francis Blokzijl
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Johanna Bertl
- Department of Molecular Medicine, Aarhus University, 8200 Aarhus N, Denmark
| | | | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | | | | | - Joris Pothof
- Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
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119
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Niedernhofer LJ, Gurkar AU, Wang Y, Vijg J, Hoeijmakers JHJ, Robbins PD. Nuclear Genomic Instability and Aging. Annu Rev Biochem 2019; 87:295-322. [PMID: 29925262 DOI: 10.1146/annurev-biochem-062917-012239] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nuclear genome decays as organisms age. Numerous studies demonstrate that the burden of several classes of DNA lesions is greater in older mammals than in young mammals. More challenging is proving this is a cause rather than a consequence of aging. The DNA damage theory of aging, which argues that genomic instability plays a causal role in aging, has recently gained momentum. Support for this theory stems partly from progeroid syndromes in which inherited defects in DNA repair increase the burden of DNA damage leading to accelerated aging of one or more organs. Additionally, growing evidence shows that DNA damage accrual triggers cellular senescence and metabolic changes that promote a decline in tissue function and increased susceptibility to age-related diseases. Here, we examine multiple lines of evidence correlating nuclear DNA damage with aging. We then consider how, mechanistically, nuclear genotoxic stress could promote aging. We conclude that the evidence, in toto, supports a role for DNA damage as a nidus of aging.
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Affiliation(s)
- Laura J Niedernhofer
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute Florida, Jupiter, Florida 33458, USA;
| | - Aditi U Gurkar
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute Florida, Jupiter, Florida 33458, USA; .,Department of Medicine, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Michael F. Price Center, Bronx, New York 10461, USA
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 CE Rotterdam, The Netherlands
| | - Paul D Robbins
- Department of Molecular Medicine and the Center on Aging, The Scripps Research Institute Florida, Jupiter, Florida 33458, USA;
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120
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Pei W, Wang X, Rössler J, Feyerabend TB, Höfer T, Rodewald HR. Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nat Protoc 2019; 14:1820-1840. [PMID: 31110297 DOI: 10.1038/s41596-019-0163-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/12/2019] [Indexed: 01/02/2023]
Abstract
Fate mapping is a powerful genetic tool for linking stem or progenitor cells with their progeny, and hence for defining cell lineages in vivo. The resolution of fate mapping depends on the numbers of distinct markers that are introduced in the beginning into stem or progenitor cells; ideally, numbers should be sufficiently large to allow the tracing of output from individual cells. Highly diverse genetic barcodes can serve this purpose. We recently developed an endogenous genetic barcoding system, termed Polylox. In Polylox, random DNA recombination can be induced by transient activity of Cre recombinase in a 2.1-kb-long artificial recombination substrate that has been introduced into a defined locus in mice (Rosa26Polylox reporter mice). Here, we provide a step-by-step protocol for the use of Polylox, including barcode induction and estimation of induction efficiency, barcode retrieval with single-molecule real-time (SMRT) DNA sequencing followed by computational barcode identification, and the calculation of barcode-generation probabilities, which is key for estimations of single-cell labeling for a given number of stem cells. Thus, Polylox barcoding enables high-resolution fate mapping in essentially all tissues in mice for which inducible Cre driver lines are available. Alternative methods include ex vivo cell barcoding, inducible transposon insertion and CRISPR-Cas9-based barcoding; Polylox currently allows combining non-invasive and cell-type-specific labeling with high label diversity. The execution time of this protocol is ~2-3 weeks for experimental data generation and typically <2 d for computational Polylox decoding and downstream analysis.
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Affiliation(s)
- Weike Pei
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Xi Wang
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Jens Rössler
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany. .,Bioquant Center, University of Heidelberg, Heidelberg, Germany.
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
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121
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Kucab JE, Zou X, Morganella S, Joel M, Nanda AS, Nagy E, Gomez C, Degasperi A, Harris R, Jackson SP, Arlt VM, Phillips DH, Nik-Zainal S. A Compendium of Mutational Signatures of Environmental Agents. Cell 2019; 177:821-836.e16. [PMID: 30982602 PMCID: PMC6506336 DOI: 10.1016/j.cell.2019.03.001] [Citation(s) in RCA: 349] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/21/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
Abstract
Whole-genome-sequencing (WGS) of human tumors has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational signatures in 324 WGS human-induced pluripotent stem cells exposed to 79 known or suspected environmental carcinogens. Forty-one yielded characteristic substitution mutational signatures. Some were similar to signatures found in human tumors. Additionally, six agents produced double-substitution signatures and eight produced indel signatures. Investigating mutation asymmetries across genome topography revealed fully functional mismatch and transcription-coupled repair pathways. DNA damage induced by environmental mutagens can be resolved by disparate repair and/or replicative pathways, resulting in an assortment of signature outcomes even for a single agent. This compendium of experimentally induced mutational signatures permits further exploration of roles of environmental agents in cancer etiology and underscores how human stem cell DNA is directly vulnerable to environmental agents. VIDEO ABSTRACT.
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Affiliation(s)
- Jill E Kucab
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Madeleine Joel
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - A Scott Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
| | - Eszter Nagy
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Celine Gomez
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Rebecca Harris
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK.
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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122
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Yang L, Yang S, Li X, Li B, Li Y, Zhang X, Ma Y, Peng X, Jin H, Fan Q, Wei S, Liu J, Li H. Tumor organoids: From inception to future in cancer research. Cancer Lett 2019; 454:120-133. [PMID: 30981763 DOI: 10.1016/j.canlet.2019.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 12/18/2022]
Abstract
Tumor models have created new avenues for personalized medicine and drug development. A new culture model derived from a three-dimensional system, the tumor organoid, is gradually being used in many fields. An organoid can simulate the physiological structure and function of tissue in situ and maintain the characteristics of tumor cells in vivo, overcoming the disadvantages of traditional experimental tumor models. Organoids can mimic pathological features of tumors and maintain genetic stability, making them suitable for both molecular mechanism studies and pharmacological experiments of clinical transformation. In addition, the application of tumor organoids combined with other technologies, such as liquid biopsy technology, microraft array (MRA), and high-content screening (HCS), for the development of personalized diagnosis and cancer treatment has a promising future. In this review, we introduce the evolution of organoids and discuss their specific application and advantages. We also summarize the characteristics of several tumor organoids culture systems.
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Affiliation(s)
- Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Bowen Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Yan Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Xiaodong Zhang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Yingbo Ma
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Hongyuan Jin
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Qing Fan
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Jingang Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110000, PR China.
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Zhivagui M, Ng AWT, Ardin M, Churchwell MI, Pandey M, Renard C, Villar S, Cahais V, Robitaille A, Bouaoun L, Heguy A, Guyton KZ, Stampfer MR, McKay J, Hollstein M, Olivier M, Rozen SG, Beland FA, Korenjak M, Zavadil J. Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans. Genome Res 2019; 29:521-531. [PMID: 30846532 PMCID: PMC6442384 DOI: 10.1101/gr.242453.118] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/01/2019] [Indexed: 02/06/2023]
Abstract
Humans are frequently exposed to acrylamide, a probable human carcinogen found in commonplace sources such as most heated starchy foods or tobacco smoke. Prior evidence has shown that acrylamide causes cancer in rodents, yet epidemiological studies conducted to date are limited and, thus far, have yielded inconclusive data on association of human cancers with acrylamide exposure. In this study, we experimentally identify a novel and unique mutational signature imprinted by acrylamide through the effects of its reactive metabolite glycidamide. We next show that the glycidamide mutational signature is found in a full one-third of approximately 1600 tumor genomes corresponding to 19 human tumor types from 14 organs. The highest enrichment of the glycidamide signature was observed in the cancers of the lung (88% of the interrogated tumors), liver (73%), kidney (>70%), bile duct (57%), cervix (50%), and, to a lesser extent, additional cancer types. Overall, our study reveals an unexpectedly extensive contribution of acrylamide-associated mutagenesis to human cancers.
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Affiliation(s)
- Maria Zhivagui
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Alvin W T Ng
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Maude Ardin
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Mona I Churchwell
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
| | - Manuraj Pandey
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Claire Renard
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Stephanie Villar
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Alexis Robitaille
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Liacine Bouaoun
- Environment and Radiation Section, International Agency for Research on Cancer, Lyon 69008, France
| | - Adriana Heguy
- Department of Pathology and Genome Technology Center, New York University, Langone Medical Center, New York, New York 10016, USA
| | - Kathryn Z Guyton
- IARC Monographs Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Martha R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - James McKay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Monica Hollstein
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
- Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany
- Faculty of Medicine and Health, University of Leeds, LIGHT Laboratories, Leeds LS2 9JT, United Kingdom
| | - Magali Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Steven G Rozen
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456, Singapore
| | - Frederick A Beland
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon 69008, France
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124
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Wang L, Ji Y, Hu Y, Hu H, Jia X, Jiang M, Zhang X, Zhao L, Zhang Y, Jia Y, Qin C, Yu L, Huang J, Yang S, Hurst LD, Tian D. The architecture of intra-organism mutation rate variation in plants. PLoS Biol 2019; 17:e3000191. [PMID: 30964866 PMCID: PMC6456163 DOI: 10.1371/journal.pbio.3000191] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/06/2019] [Indexed: 12/30/2022] Open
Abstract
Given the disposability of somatic tissue, selection can favor a higher mutation rate in the early segregating soma than in germline, as seen in some animals. Although in plants intra-organismic mutation rate heterogeneity is poorly resolved, the same selectionist logic can predict a lower rate in shoot than in root and in longer-lived terminal tissues (e.g., leaves) than in ontogenetically similar short-lived ones (e.g., petals), and that mutation rate heterogeneity should be deterministic with no significant differences between biological replicates. To address these expectations, we sequenced 754 genomes from various tissues of eight plant species. Consistent with a selectionist model, the rate of mutation accumulation per unit time in shoot apical meristem is lower than that in root apical tissues in perennials, in which a high proportion of mutations in shoots are themselves transmissible, but not in annuals, in which somatic mutations tend not to be transmissible. Similarly, the number of mutations accumulated in leaves is commonly lower than that within a petal of the same plant, and there is no more heterogeneity in accumulation rates between replicate branches than expected by chance. High mutation accumulation in runners of strawberry is, we argue, the exception that proves the rule, as mutation transmission patterns indicate that runner has a restricted germline. However, we also find that in vitro callus tissue has a higher mutation rate (per unit time) than the wild-grown comparator, suggesting nonadaptive mutational "fragility". As mutational fragility does not obviously explain why the shoot-root difference varies with plant longevity, we conclude that some mutation rate variation between tissues is consistent with selectionist theory but that a mechanistic null of mutational fragility should be considered.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yilun Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yingwen Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Huaying Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xianqin Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Lina Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanchun Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanxiao Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chao Qin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Laurence D. Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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125
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Abstract
Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Amanda Finck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
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126
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Affiliation(s)
- Mo Li
- From the King Abdullah University of Science and Technology, Thuwal, Saudi Arabia (M.L.); and the Salk Institute for Biological Studies, La Jolla, CA (J.C.I.B.)
| | - Juan C Izpisua Belmonte
- From the King Abdullah University of Science and Technology, Thuwal, Saudi Arabia (M.L.); and the Salk Institute for Biological Studies, La Jolla, CA (J.C.I.B.)
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127
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Fujii M, Clevers H, Sato T. Modeling Human Digestive Diseases With CRISPR-Cas9-Modified Organoids. Gastroenterology 2019; 156:562-576. [PMID: 30476497 DOI: 10.1053/j.gastro.2018.11.048] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
Abstract
Insights into the stem cell niche have allowed researchers to cultivate adult tissue stem cells as organoids that display structural and phenotypic features of healthy and diseased epithelial tissues. Organoids derived from patients' tissues are used as models of disease and to test drugs. CRISPR-Cas9 technology can be used to genetically engineer organoids for studies of monogenic diseases and cancer. We review the derivation of organoids from human gastrointestinal tissues and how CRISPR-Cas9 technology can be used to study these organoids. We discuss burgeoning technologies that are broadening our understanding of diseases of the digestive system.
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Affiliation(s)
- Masayuki Fujii
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Hans Clevers
- Hubrecht Institute, University Medical Center Utrecht and Princess Maxima Center, Utrecht, The Netherlands
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan.
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128
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Namekawa T, Ikeda K, Horie-Inoue K, Inoue S. Application of Prostate Cancer Models for Preclinical Study: Advantages and Limitations of Cell Lines, Patient-Derived Xenografts, and Three-Dimensional Culture of Patient-Derived Cells. Cells 2019; 8:cells8010074. [PMID: 30669516 PMCID: PMC6357050 DOI: 10.3390/cells8010074] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Various preclinical models have been developed to clarify the pathophysiology of prostate cancer (PCa). Traditional PCa cell lines from clinical metastatic lesions, as exemplified by DU-145, PC-3, and LNCaP cells, are useful tools to define mechanisms underlying tumorigenesis and drug resistance. Cell line-based experiments, however, have limitations for preclinical studies because those cells are basically adapted to 2-dimensional monolayer culture conditions, in which the majority of primary PCa cells cannot survive. Recent tissue engineering enables generation of PCa patient-derived xenografts (PDXs) from both primary and metastatic lesions. Compared with fresh PCa tissue transplantation in athymic mice, co-injection of PCa tissues with extracellular matrix in highly immunodeficient mice has remarkably improved the success rate of PDX generation. PDX models have advantages to appropriately recapitulate the molecular diversity, cellular heterogeneity, and histology of original patient tumors. In contrast to PDX models, patient-derived organoid and spheroid PCa models in 3-dimensional culture are more feasible tools for in vitro studies for retaining the characteristics of patient tumors. In this article, we review PCa preclinical model cell lines and their sublines, PDXs, and patient-derived organoid and spheroid models. These PCa models will be applied to the development of new strategies for cancer precision medicine.
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Affiliation(s)
- Takeshi Namekawa
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
- Department of Urology, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8677, Japan.
| | - Kazuhiro Ikeda
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1241, Japan.
- Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan.
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129
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Miao X, Li X, Wang L, Zheng C, Cai J. DSMNC: a database of somatic mutations in normal cells. Nucleic Acids Res 2019; 47:D971-D975. [PMID: 30380071 PMCID: PMC6323907 DOI: 10.1093/nar/gky1045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/25/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022] Open
Abstract
Numerous non-inherited somatic mutations, distinct from those of germ-line origin, occur in somatic cells during DNA replication per cell-division. The somatic mutations, recording the unique genetic cell-lineage 'history' of each proliferating normal cell, are important but remain to be investigated because of their ultra-low frequency hidden in the genetic background of heterogeneous cells. Luckily, the recent development of single-cell genomics biotechnologies enables the screening and collection of the somatic mutations, especial single nucleotide variations (SNVs), occurring in normal cells. Here, we established DSMNC: a database of somatic mutations in normal cells (http://dsmnc.big.ac.cn/), which provides most comprehensive catalogue of somatic SNVs in single cells from various normal tissues. In the current version, the database collected ∼0.8 million SNVs accumulated in ∼600 single normal cells (579 human cells and 39 mouse cells). The database interface supports the user-friendly capability of browsing and searching the SNVs and their annotation information. DSMNC, which serves as a timely and valuable collection of somatic mutations in individual normal cells, has made it possible to analyze the burdens and signatures of somatic mutations in various types of heterogeneous normal cells. Therefore, DSMNC will significantly improve our understanding of the characteristics of somatic mutations in normal cells.
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Affiliation(s)
- Xuexia Miao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caihong Zheng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Cai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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130
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Hormoz S, Singer ZS, Linton JM, Antebi YE, Shraiman BI, Elowitz MB. Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements. Cell Syst 2019; 3:419-433.e8. [PMID: 27883889 DOI: 10.1016/j.cels.2016.10.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 06/01/2016] [Accepted: 10/18/2016] [Indexed: 12/28/2022]
Abstract
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees). Combining KCA with pedigrees obtained from time-lapse imaging and endpoint single-molecule RNA-fluorescence in situ hybridization (RNA-FISH) measurements of gene expression, we determined the cell-state transition network of mouse embryonic stem (ES) cells. This analysis revealed that mouse ES cells exhibit stochastic and reversible transitions along a linear chain of states ranging from 2C-like to epiblast-like. Our approach is broadly applicable and may be applied to systems with irreversible transitions and non-stationary dynamics, such as in cancer and development.
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Affiliation(s)
- Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Zakary S Singer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yaron E Antebi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Boris I Shraiman
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute (HHMI) and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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131
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Song Y, Xu X, Wang W, Tian T, Zhu Z, Yang C. Single cell transcriptomics: moving towards multi-omics. Analyst 2019; 144:3172-3189. [DOI: 10.1039/c8an01852a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Single-cell multi-omics analysis helps characterize multiple layers of molecular features at a single-cell scale to provide insights into cellular processes and functions.
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Affiliation(s)
- Yanling Song
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
| | - Xing Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Wei Wang
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
| | - Tian Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Chaoyong Yang
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
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132
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Approaches and Methods for Variant Analysis in the Genome of a Single Cell. HEALTHY AGEING AND LONGEVITY 2019. [DOI: 10.1007/978-3-030-24970-0_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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133
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Franco I, Fernandez-Gonzalo R, Vrtačnik P, Lundberg TR, Eriksson M, Gustafsson T. Healthy skeletal muscle aging: The role of satellite cells, somatic mutations and exercise. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 346:157-200. [DOI: 10.1016/bs.ircmb.2019.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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134
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Dotti I, Salas A. Potential Use of Human Stem Cell-Derived Intestinal Organoids to Study Inflammatory Bowel Diseases. Inflamm Bowel Dis 2018; 24:2501-2509. [PMID: 30169820 PMCID: PMC6262197 DOI: 10.1093/ibd/izy275] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic remitting disorder with increasing incidence worldwide. The intestinal epithelial barrier plays a major role in IBD, contributing to its pathogenesis, evolution, and perpetuation over time. Until recently, studies focused on exploring the role of the intestinal epithelium in IBD were hampered by the lack of techniques for the long-term culturing of human primary epithelial cells ex vivo. Recently, however, a methodology for generating stable human 3D epithelial cultures directly from adult intestinal stem cells was established. These long-term cultures, called organoids, mimic the tissue of origin and can be generated from small-size intestinal tissue samples, making it a promising tool for modeling the course of IBD.In this review, we provide an overview of the versatility of human organoid cultures in IBD modeling. We discuss recent advances and current limitations in the application of this tool for modeling the contribution of the intestinal epithelium alone and in combination with other key cellular and molecular players in the context of IBD pathophysiology. Finally, we outline the pressing need for technically standardizing the laboratory manipulation of human epithelial organoids for their broader implementation in clinically oriented IBD studies.
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Affiliation(s)
- Isabella Dotti
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBERehd, Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBERehd, Barcelona, Spain
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135
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Saini N, Gordenin DA. Somatic mutation load and spectra: A record of DNA damage and repair in healthy human cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:672-686. [PMID: 30152078 PMCID: PMC6188803 DOI: 10.1002/em.22215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 05/31/2023]
Abstract
Somatic genome instability is a hallmark of cancer genomes and has been linked to aging and a variety of other pathologies. Large-scale cancer genome and exome sequencing have revealed that mutation load and spectra in cancers can be influenced by environmental exposures, the anatomical site of exposures, and tissue type. There is now an abundance of data favoring the hypothesis that a substantial portion of the mutations in cancers originate prior to carcinogenesis in stem cells of the healthy individual. Rapid advances in sequencing of noncancer cells from healthy humans have shown that their mutation loads and spectra resemble cancer data. Similar to cancer genomes, mutation profiles of healthy cells show marked intra-individual variation, thus providing a metric of the various factors-environmental and endogenous-involved in mutagenesis in these individuals. This review focuses on the current methodologies to measure mutation loads and to determine mutation signatures for evaluating the environmental and endogenous sources of DNA damage in human somatic cells. We anticipate that in future, such large-scale studies aimed at exploring the landscapes of somatic mutations across different cell types in healthy people would provide a valuable resource for designing personalized preventative strategies against diseases associated with somatic genome instability. Environ. Mol. Mutagen. 59:672-686, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
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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, USA
| | - 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, USA
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136
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A Bioinformatic Profile of Gene Expression of Colorectal Carcinoma Derived Organoids. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2594076. [PMID: 30363662 PMCID: PMC6180985 DOI: 10.1155/2018/2594076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/29/2018] [Accepted: 08/15/2018] [Indexed: 02/05/2023]
Abstract
Colorectal carcinoma is one of the common cancers in human. It has been intensely debated whether the in vitro cancer cell lines are closely enough for recapitulating the original tumor in understanding the molecular characteristic of CRC. Organoid as a new in vitro 3D culture system has sprang out in CRC study for the capability in reviving the original tissue. The aim of this study is to profile the gene expression of CRC organoid. The gene expression GSE64392 was from GEO database contained 20-patients-derived 37 organoid samples, including 22 colorectal tumor organoid samples and 15 paired healthy samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied for classifying differentially expressed genes (DEGs). Protein interaction among DEGs was analyzed by Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. In total, 853 gene sequences were identified. GO analysis revealed that DEGs were extensively involved in various biological process (BP), like proliferation, cell cycle, and biosynthesis. KEEG pathway analysis showed that WNT, MAPK, TGF-β, SHH, ECM-receptor interaction, and FGF pathways were altered. DEGs which were identified with protein interactions were major response for extracellular matrix organization and the GPCR pathway. In conclusion, our study profiled the DEGs in CRC organoids and promotes our understanding of the CRC organoids as a new model for colorectal cancer research.
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137
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Abstract
DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences.
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Affiliation(s)
- Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA;
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138
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Lee-Six H, Øbro NF, Shepherd MS, Grossmann S, Dawson K, Belmonte M, Osborne RJ, Huntly BJP, Martincorena I, Anderson E, O'Neill L, Stratton MR, Laurenti E, Green AR, Kent DG, Campbell PJ. Population dynamics of normal human blood inferred from somatic mutations. Nature 2018; 561:473-478. [PMID: 30185910 PMCID: PMC6163040 DOI: 10.1038/s41586-018-0497-0] [Citation(s) in RCA: 355] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/01/2018] [Indexed: 01/25/2023]
Abstract
Haematopoietic stem cells drive blood production, but their population size and lifetime dynamics have not been quantified directly in humans. Here we identified 129,582 spontaneous, genome-wide somatic mutations in 140 single-cell-derived haematopoietic stem and progenitor colonies from a healthy 59-year-old man and applied population-genetics approaches to reconstruct clonal dynamics. Cell divisions from early embryogenesis were evident in the phylogenetic tree; all blood cells were derived from a common ancestor that preceded gastrulation. The size of the stem cell population grew steadily in early life, reaching a stable plateau by adolescence. We estimate the numbers of haematopoietic stem cells that are actively making white blood cells at any one time to be in the range of 50,000-200,000. We observed adult haematopoietic stem cell clones that generate multilineage outputs, including granulocytes and B lymphocytes. Harnessing naturally occurring mutations to report the clonal architecture of an organ enables the high-resolution reconstruction of somatic cell dynamics in humans.
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Affiliation(s)
- Henry Lee-Six
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Nina Friesgaard Øbro
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mairi S Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Kevin Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Miriam Belmonte
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Robert J Osborne
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J P Huntly
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - Laura O'Neill
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Elisa Laurenti
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK.
| | - David G Kent
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
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139
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Autologous reference types can confound the detection of somatic mutation in solid cancers. DNA Repair (Amst) 2018; 69:6-13. [PMID: 30029072 DOI: 10.1016/j.dnarep.2018.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/17/2018] [Accepted: 07/03/2018] [Indexed: 11/22/2022]
Abstract
Vast number of somatic mutations has been proved to be affected by the factors of sequencing methods, analysis pipelines and validation methods. We here showed the effect of autologous reference types on the detection of cancer-associated somatic mutations with the somatic single nucleotide variations (SNVs) and clinical data of solid tumors from the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). The distribution of somatic SNVs was significantly different among groups of autologous references in 6 cancers detected by whole genome sequencing (WGS) and 5 cancers detected by the random sequencing of exonic regions selected from the genome (WXS), especially in protein coding region of 5 cancers with age, gender and TNM adjusted. In addition, only 60.24% (95% CI: 49.65%-70.83%) of the somatic SNVs called from normal blood by WXS were found in those called from normal solid tissue tested by WXS / WGS, while 31.78% (95%CI: 4.14%-59.42%) of the somatic SNVs called from normal tissue adjacent to primary by WXS were found in those from normal blood tested by WXS / WGS. These findings suggested that more representative types of normal tissues should be included in detection of cancer-associated somatic mutations.
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140
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Abstract
The recent advances in in vitro 3D culture technologies, such as organoids, have opened new avenues for the development of novel, more physiological human cancer models. Such preclinical models are essential for more efficient translation of basic cancer research into novel treatment regimens for patients with cancer. Wild-type organoids can be grown from embryonic and adult stem cells and display self-organizing capacities, phenocopying essential aspects of the organs they are derived from. Genetic modification of organoids allows disease modelling in a setting that approaches the physiological environment. Additionally, organoids can be grown with high efficiency from patient-derived healthy and tumour tissues, potentially enabling patient-specific drug testing and the development of individualized treatment regimens. In this Review, we evaluate tumour organoid protocols and how they can be utilized as an alternative model for cancer research.
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Affiliation(s)
- Jarno Drost
- Princess Máxima Centre for Paediatric Oncology, Utrecht, Netherlands.
| | - Hans Clevers
- Princess Máxima Centre for Paediatric Oncology, Utrecht, Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
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141
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Dou Y, Gold HD, Luquette LJ, Park PJ. Detecting Somatic Mutations in Normal Cells. Trends Genet 2018; 34:545-557. [PMID: 29731376 PMCID: PMC6029698 DOI: 10.1016/j.tig.2018.04.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/12/2023]
Abstract
Somatic mutations have been studied extensively in the context of cancer. Recent studies have demonstrated that high-throughput sequencing data can be used to detect somatic mutations in non-tumor cells. Analysis of such mutations allows us to better understand the mutational processes in normal cells, explore cell lineages in development, and examine potential associations with age-related disease. We describe here approaches for characterizing somatic mutations in normal and non-tumor disease tissues. We discuss several experimental designs and common pitfalls in somatic mutation detection, as well as more recent developments such as phasing and linked-read technology. With the dramatically increasing numbers of samples undergoing genome sequencing, bioinformatic analysis will enable the characterization of somatic mutations and their impact on non-cancer tissues.
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Affiliation(s)
- Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Heather D Gold
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
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142
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Wang Y, Masaki T, Khan SG, Tamura D, Kuschal C, Rogers M, DiGiovanna JJ, Kraemer KH. Four-dimensional, dynamic mosaicism is a hallmark of normal human skin that permits mapping of the organization and patterning of human epidermis during terminal differentiation. PLoS One 2018; 13:e0198011. [PMID: 29897937 PMCID: PMC5999106 DOI: 10.1371/journal.pone.0198011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 05/11/2018] [Indexed: 01/12/2023] Open
Abstract
Recent findings of mosaicism (DNA sequence variation) challenge the dogma that each person has a stable genetic constitution. Copy number variations, point mutations and chromosome abnormalities in normal or diseased tissues have been described. We studied normal skin mosaicism of a single nucleotide polymorphism (SNP) [rs1426654, p.Thr111Ala] in SLC24A5, an ion transporter gene. This SNP is unusual in that more than 90% of people of European descent have homozygous germline A/A alleles, while more than 90% of East Asians and Blacks have homozygous germline G/G alleles. We found mosaicism in neonatal foreskins as well as in 69% of nearly 600 skin surface scraping samples from 114 donors of different ages. Strikingly, donors with germline (buccal or blood) A/A, A/G or G/G genotypes had all three sequences (A/A, A/G or G/G) in the skin surface scrapings. SNP sequence differences extended within the epidermis in the vertical dimension from basal cell layer to the stratum corneum at the surface, as well as across the two-dimensions of the skin surface. Furthermore, repeated scrapings in the same location revealed variation in the sequences in the same individuals over time, adding a fourth dimension to this variation. We then used this mosaicism to track the movement of epidermal cells during normal differentiation and characterize the patterning of epidermal cells during terminal differentiation. In this coordinated proliferation model of epidermal differentiation, the skin surface is alternatively populated by synchronous, cycling of waves of cells, with each group having a different DNA sequence. These groups of cells abruptly flatten into large sheets at the surface providing patches of uniform SNP sequence. This four-dimensional mosaicism is a normal, previously unrecognized form of dynamic mosaicism in human skin.
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Affiliation(s)
- Yun Wang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
- Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Taro Masaki
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
- Department of Dermatology, Kobe University School of Medicine, Kobe, Japan
| | - Sikandar G. Khan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Deborah Tamura
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Christiane Kuschal
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Megan Rogers
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - John J. DiGiovanna
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Kenneth H. Kraemer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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143
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Huang AY, Yang X, Wang S, Zheng X, Wu Q, Ye AY, Wei L. Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs. PLoS Genet 2018; 14:e1007395. [PMID: 29763432 PMCID: PMC5969758 DOI: 10.1371/journal.pgen.1007395] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 05/25/2018] [Accepted: 05/04/2018] [Indexed: 12/26/2022] Open
Abstract
Postzygotic single-nucleotide mosaicisms (pSNMs) have been extensively studied in tumors and are known to play critical roles in tumorigenesis. However, the patterns and origin of pSNMs in normal organs of healthy humans remain largely unknown. Using whole-genome sequencing and ultra-deep amplicon re-sequencing, we identified and validated 164 pSNMs from 27 postmortem organ samples obtained from five healthy donors. The mutant allele fractions ranged from 1.0% to 29.7%. Inter- and intra-organ comparison revealed two distinctive types of pSNMs, with about half originating during early embryogenesis (embryonic pSNMs) and the remaining more likely to result from clonal expansion events that had occurred more recently (clonal expansion pSNMs). Compared to clonal expansion pSNMs, embryonic pSNMs had higher proportion of C>T mutations with elevated mutation rate at CpG sites. We observed differences in replication timing between these two types of pSNMs, with embryonic and clonal expansion pSNMs enriched in early- and late-replicating regions, respectively. An increased number of embryonic pSNMs were located in open chromatin states and topologically associating domains that transcribed embryonically. Our findings provide new insights into the origin and spatial distribution of postzygotic mosaicism during normal human development. Genomic mosaicism led by postzygotic mutation is the major cause of cancers and many non-cancer developmental disorders. Theoretically, postzygotic mutations should be accumulated during the developmental process of healthy individuals, but the genome-wide characterization of postzygotic mosaicisms across many organ types of the same individual remained limited. In this study, we identified and validated two types of postzygotic mosaicism from the whole-genomes of 27 organs obtained from five healthy donors. We further found that the postzygotic mosaicisms arising during early embryogenesis and later clonal expansion events show distinct genomic patterns in mutation spectrum, replication timing, and chromatin status.
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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, China
- * E-mail: (LW); (AYH)
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Wang
- National Institute of Biological Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xianing Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Qixi Wu
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- Human Genetics Resources Core Facility, School of Life Sciences, Peking University, Beijing, China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- * E-mail: (LW); (AYH)
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144
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Chen Q, Shi J, Tao Y, Zernicka-Goetz M. Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo. Nat Commun 2018; 9:1819. [PMID: 29739935 PMCID: PMC5940674 DOI: 10.1038/s41467-018-04155-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 04/06/2018] [Indexed: 01/02/2023] Open
Abstract
A fundamental question in developmental and stem cell biology concerns the origin and nature of signals that initiate asymmetry leading to pattern formation and self-organization. Instead of having prominent pre-patterning determinants as present in model organisms (worms, sea urchin, frog), we propose that the mammalian embryo takes advantage of more subtle cues such as compartmentalized intracellular reactions that generate micro-scale inhomogeneity, which is gradually amplified over several cellular generations to drive pattern formation while keeping developmental plasticity. It is therefore possible that by making use of compartmentalized information followed by its amplification, mammalian embryos would follow general principle of development found in other organisms in which the spatial cue is more robustly presented.
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Affiliation(s)
- Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Yi Tao
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Magdalena Zernicka-Goetz
- Mammalian Development and Stem Cell Group, Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
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145
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Zou X, Owusu M, Harris R, Jackson SP, Loizou JI, Nik-Zainal S. Validating the concept of mutational signatures with isogenic cell models. Nat Commun 2018; 9:1744. [PMID: 29717121 PMCID: PMC5931590 DOI: 10.1038/s41467-018-04052-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/29/2018] [Indexed: 12/23/2022] Open
Abstract
The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems-the exposures to different mutational processes in a patient's lifetime are uncontrolled and any relationships observed can only be described as an association. Here, we demonstrate the proof-of-principle that it is possible to recreate cancer mutational signatures in vitro using CRISPR-Cas9-based gene-editing experiments in an isogenic human-cell system. We provide experimental and algorithmic methods to discover mutational signatures generated under highly experimentally-controlled conditions. Our in vitro findings strikingly recapitulate in vivo observations of cancer data, fundamentally validating the concept of (particularly) endogenously-arising mutational signatures.
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Affiliation(s)
- Xueqing Zou
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Michel Owusu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Rebecca Harris
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephen P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK.
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146
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Roerink SF, Sasaki N, Lee-Six H, Young MD, Alexandrov LB, Behjati S, Mitchell TJ, Grossmann S, Lightfoot H, Egan DA, Pronk A, Smakman N, van Gorp J, Anderson E, Gamble SJ, Alder C, van de Wetering M, Campbell PJ, Stratton MR, Clevers H. Intra-tumour diversification in colorectal cancer at the single-cell level. Nature 2018; 556:457-462. [DOI: 10.1038/s41586-018-0024-3] [Citation(s) in RCA: 346] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/05/2018] [Indexed: 01/08/2023]
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147
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Nishioka M, Bundo M, Ueda J, Katsuoka F, Sato Y, Kuroki Y, Ishii T, Ukai W, Murayama S, Hashimoto E, Nagasaki M, Yasuda J, Kasai K, Kato T, Iwamoto K. Identification of somatic mutations in postmortem human brains by whole genome sequencing and their implications for psychiatric disorders. Psychiatry Clin Neurosci 2018; 72:280-294. [PMID: 29283202 DOI: 10.1111/pcn.12632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/07/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022]
Abstract
AIM Somatic mutations in the human brain are hypothesized to contribute to the functional diversity of brain cells as well as the pathophysiology of neuropsychiatric diseases. However, there are still few reports on somatic mutations in non-neoplastic human brain tissues. This study attempted to unveil the landscape of somatic mutations in the human brain. METHODS We explored the landscape of somatic mutations in human brain tissues derived from three individuals with no neuropsychiatric diseases by whole-genome deep sequencing at a depth of around 100. The candidate mutations underwent multi-layered filtering, and were validated by ultra-deep target amplicon sequencing at a depth of around 200 000. RESULTS Thirty-one somatic mutations were identified in the human brain, demonstrating the utility of whole-genome sequencing of bulk brain tissue. The mutations were enriched in neuron-expressed genes, and two-thirds of the identified somatic single nucleotide variants in the brain tissues were cytosine-to-thymine transitions, half of which were in CpG dinucleotides. CONCLUSION Our developed filtering and validation approaches will be useful to identify somatic mutations in the human brain. The vulnerability of neuron-expressed genes to mutational events suggests their potential relevance to neuropsychiatric diseases.
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Affiliation(s)
- Masaki Nishioka
- Department of Molecular Psychiatry, The University of Tokyo, Tokyo, Japan.,Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Psychiatry, The University of Tokyo, Tokyo, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan.,Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junko Ueda
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yukuto Sato
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoko Kuroki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takao Ishii
- Department of Neuropsychiatry, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Wataru Ukai
- Department of Neuropsychiatry, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Shigeo Murayama
- Department of Neuropathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Eri Hashimoto
- Department of Neuropsychiatry, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Saitama, Japan
| | - Kazuya Iwamoto
- Department of Molecular Psychiatry, The University of Tokyo, Tokyo, Japan.,Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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148
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Mebarki M, Bennaceur A, Bonhomme-Faivre L. Human-cell-derived organoids as a new ex vivo model for drug assays in oncology. Drug Discov Today 2018; 23:857-863. [DOI: 10.1016/j.drudis.2018.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/19/2018] [Accepted: 02/04/2018] [Indexed: 12/13/2022]
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149
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Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A. Whole-organism clone tracing using single-cell sequencing. Nature 2018; 556:108-112. [PMID: 29590089 DOI: 10.1038/nature25969] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 02/02/2018] [Indexed: 12/31/2022]
Abstract
Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.
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Affiliation(s)
- Anna Alemany
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Maria Florescu
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Chloé S Baron
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josi Peterson-Maduro
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
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150
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Franco I, Johansson A, Olsson K, Vrtačnik P, Lundin P, Helgadottir HT, Larsson M, Revêchon G, Bosia C, Pagnani A, Provero P, Gustafsson T, Fischer H, Eriksson M. Somatic mutagenesis in satellite cells associates with human skeletal muscle aging. Nat Commun 2018; 9:800. [PMID: 29476074 PMCID: PMC5824957 DOI: 10.1038/s41467-018-03244-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/26/2018] [Indexed: 01/06/2023] Open
Abstract
Human aging is associated with a decline in skeletal muscle (SkM) function and a reduction in the number and activity of satellite cells (SCs), the resident stem cells. To study the connection between SC aging and muscle impairment, we analyze the whole genome of single SC clones of the leg muscle vastus lateralis from healthy individuals of different ages (21–78 years). We find an accumulation rate of 13 somatic mutations per genome per year, consistent with proliferation of SCs in the healthy adult muscle. SkM-expressed genes are protected from mutations, but aging results in an increase in mutations in exons and promoters, targeting genes involved in SC activity and muscle function. In agreement with SC mutations affecting the whole tissue, we detect a missense mutation in a SC propagating to the muscle. Our results suggest somatic mutagenesis in SCs as a driving force in the age-related decline of SkM function. Aging skeletal muscle shows declining numbers and activity of satellite cells. Here, Franco et al. show that in satellite cells of the human leg muscle vastus lateralis, somatic mutations accumulate with age and that these mutations become enriched in exons and promoters of genes involved in muscle function.
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Affiliation(s)
- Irene Franco
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, 14157, Huddinge, Sweden.
| | - Anna Johansson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75237, Uppsala, Sweden
| | - Karl Olsson
- Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, 14186, Huddinge, Sweden
| | - Peter Vrtačnik
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, 14157, Huddinge, Sweden
| | - Pär Lundin
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, 14157, Huddinge, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics (DBB), Stockholm University, 10691, Stockholm, Sweden
| | - Hafdis T Helgadottir
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, 14157, Huddinge, Sweden
| | - Malin Larsson
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - Gwladys Revêchon
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, 14157, Huddinge, Sweden
| | - Carla Bosia
- Italian Institute for Genomic Medicine (IIGM), 10126, Turin, Italy.,Department of Applied Science and Technology, Politecnico di Torino, 10129, Turin, Italy
| | - Andrea Pagnani
- Italian Institute for Genomic Medicine (IIGM), 10126, Turin, Italy.,Department of Applied Science and Technology, Politecnico di Torino, 10129, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, 10126, Turin, Italy.,Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Thomas Gustafsson
- Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, 14186, Huddinge, Sweden
| | - Helene Fischer
- Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, 14186, Huddinge, Sweden
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, 14157, Huddinge, Sweden.
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