51
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Coorens THH, Moore L, Robinson PS, Sanghvi R, Christopher J, Hewinson J, Przybilla MJ, Lawson ARJ, Spencer Chapman M, Cagan A, Oliver TRW, Neville MDC, Hooks Y, Noorani A, Mitchell TJ, Fitzgerald RC, Campbell PJ, Martincorena I, Rahbari R, Stratton MR. Extensive phylogenies of human development inferred from somatic mutations. Nature 2021; 597:387-392. [PMID: 34433963 DOI: 10.1038/s41586-021-03790-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.
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Affiliation(s)
| | - Luiza Moore
- Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Philip S Robinson
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Joseph Christopher
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
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52
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Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 2021; 597:393-397. [PMID: 34433967 DOI: 10.1038/s41586-021-03786-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/29/2021] [Indexed: 12/19/2022]
Abstract
Cellular dynamics and fate decision in early human embryogenesis remain largely unknown owing to the challenges of performing studies in human embryos1. Here, we explored whole-genomes of 334 single-cell colonies and targeted deep sequences of 379 bulk tissues obtained from various anatomical locations of seven recently deceased adult human donors. Using somatic mutations as an intrinsic barcode, we reconstructed early cellular phylogenies that demonstrate (1) an endogenous mutational rate that is higher in the first cell division but decreases to approximately one per cell per cell division later in life; (2) universal unequal contribution of early cells to embryo proper, resulting from early cellular bottlenecks that stochastically set aside epiblast cells within the embryo; (3) examples of varying degrees of early clonal imbalances between tissues on the left and right sides of the body, different germ layers and specific anatomical parts and organs; (4) emergence of a few ancestral cells that will substantially contribute to adult cell pools in blood and liver; and (5) presence of mitochondrial DNA heteroplasmy in the fertilized egg. Our approach also provides insights into the age-related mutational processes and loss of sex chromosomes in normal somatic cells. In sum, this study provides a foundation for future studies to complete cellular phylogenies in human embryogenesis.
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53
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Wangsanuwat C, Chialastri A, Aldeguer JF, Rivron NC, Dey SS. A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing. CELL REPORTS METHODS 2021; 1:100060. [PMID: 34590075 PMCID: PMC8478284 DOI: 10.1016/j.crmeth.2021.100060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 06/08/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022]
Abstract
Lineage reconstruction is central to understanding tissue development and maintenance. To overcome the limitations of current techniques that typically reconstruct clonal trees using genetically encoded reporters, we report scPECLR, a probabilistic algorithm to endogenously infer lineage trees at a single-cell-division resolution by using 5-hydroxymethylcytosine (5hmC). When applied to 8-cell pre-implantation mouse embryos, scPECLR predicts the full lineage tree with greater than 95% accuracy. In addition, we developed scH&G-seq to sequence both 5hmC and genomic DNA from the same cell. Given that genomic DNA sequencing yields information on both copy number variations and single-nucleotide polymorphisms, when combined with scPECLR it enables more accurate lineage reconstruction of larger trees. Finally, we show that scPECLR can also be used to map chromosome strand segregation patterns during cell division, thereby providing a strategy to test the "immortal strand" hypothesis. Thus, scPECLR provides a generalized method to endogenously reconstruct lineage trees at an individual-cell-division resolution.
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Affiliation(s)
- Chatarin Wangsanuwat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Alex Chialastri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Javier F. Aldeguer
- Hubrecht Institute – KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nicolas C. Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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54
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Yang J, Huang S, Cheng S, Jin Y, Zhang N, Wang Y. Application of Ovarian Cancer Organoids in Precision Medicine: Key Challenges and Current Opportunities. Front Cell Dev Biol 2021; 9:701429. [PMID: 34409036 PMCID: PMC8366314 DOI: 10.3389/fcell.2021.701429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/02/2021] [Indexed: 01/01/2023] Open
Abstract
Ovarian cancer (OC) is the leading cause of death among gynecologic malignances. Over the past decades, human-derived models have advanced from monolayer cell cultures to three-dimensional (3D) organoids that could faithfully recapitulate biological characteristics and tumor heterogeneity of primary tissues. As a complement of previous studies based on cell lines or xenografts, organoids provide a 3D platform for mutation–carcinogenesis modeling, high-throughput drug screening, genetic engineering, and biobanking, which might fulfill the gap between basic research and clinical practice. Stepwise, cutting-edge bioengineering techniques of organoid-on-a-chip and 3D bioprinting might converge current challenges and contribute to personalized therapy. We comprehensively reviewed the advantages, challenges, and translational potential of OC organoids. Undeniably, organoids represent an excellent near-physiological platform for OC, paving the way for precision medicine implementation. Future efforts will doubtlessly bring this innovative technique from bench to bedside.
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Affiliation(s)
- Jiani Yang
- Department of Obstetrics and Gynecology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
| | - Shan Huang
- Department of Obstetrics and Gynecology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shanshan Cheng
- Department of Obstetrics and Gynecology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Jin
- Department of Obstetrics and Gynecology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Nan Zhang
- Department of Obstetrics and Gynecology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Wang
- Department of Obstetrics and Gynecology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
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55
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Gong W, Granados AA, Hu J, Jones MG, Raz O, Salvador-Martínez I, Zhang H, Chow KHK, Kwak IY, Retkute R, Prusokiene A, Prusokas A, Khodaverdian A, Zhang R, Rao S, Wang R, Rennert P, Saipradeep VG, Sivadasan N, Rao A, Joseph T, Srinivasan R, Peng J, Han L, Shang X, Garry DJ, Yu T, Chung V, Mason M, Liu Z, Guan Y, Yosef N, Shendure J, Telford MJ, Shapiro E, Elowitz MB, Meyer P. Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees. Cell Syst 2021; 12:810-826.e4. [PMID: 34146472 DOI: 10.1016/j.cels.2021.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 12/20/2022]
Abstract
The recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve the ones of more complex organisms. To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells. To benchmark such methods, we decided to organize a DREAM challenge using in vitro experimental intMEMOIR recordings and in silico data for a C. elegans lineage tree of about 1,000 cells and a Mus musculus tree of 10,000 cells. Some of the 22 approaches submitted had excellent performance, but structural features of the trees prevented optimal reconstructions. Using smaller sub-trees as training sets proved to be a good approach for tuning algorithms to reconstruct larger trees. The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.
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Affiliation(s)
- Wuming Gong
- Lillehei Heart Institute, University of Minnesota, 2231 6th St S.E, 4-165 CCRB, Minneapolis, MN 55114, USA
| | | | - Jingyuan Hu
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew G Jones
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA; Integrative Program of Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Irepan Salvador-Martínez
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Hanrui Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ke-Huan K Chow
- California Institute of Technology, Pasadena, CA 91125, USA
| | - Il-Youp Kwak
- Department of Applied Statistics, College of Business & Economics, Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul, Republic of Korea
| | - Renata Retkute
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Alisa Prusokiene
- School of Natural and Environmental Sciences, Newcastle University, Newcastle NE1 7RU, UK
| | | | - Alex Khodaverdian
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Richard Zhang
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Suhas Rao
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Robert Wang
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Phil Rennert
- EC Wise Inc., 1299 4th St #505, San Rafael, CA 94901, USA
| | | | - Naveen Sivadasan
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Aditya Rao
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Thomas Joseph
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Rajgopal Srinivasan
- TCS Research and Innovation, Tata Consultancy Services, Hyderabad 500019, India
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Lu Han
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, 2231 6th St S.E, 4-165 CCRB, Minneapolis, MN 55114, USA
| | - Thomas Yu
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA
| | - Verena Chung
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA
| | - Michael Mason
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121, USA
| | - Zhandong Liu
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nir Yosef
- Department of Electrical Engineering & Computer Science, University of California, Berkeley, Berkeley, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | | | - Pablo Meyer
- T.J. Watson Research Center, IBM, Healthcare & Life Sciences, 1101 Kitchawan Rd 10598, Yorktown Heights, NY 10598, USA.
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56
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Somatic Mutations and Autoimmunity. Cells 2021; 10:cells10082056. [PMID: 34440825 PMCID: PMC8394445 DOI: 10.3390/cells10082056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
Autoimmune diseases are among the most common chronic illness caused by a dysregulated immune response against self-antigens. Close to 5% of the general population in Western countries develops some form of autoimmunity, yet its underlying causes, although intensively studied, are still not fully known, and no curative therapies exist. It is well established that autoimmune diseases have common mechanisms and are caused by both genetic and non-genetic risk factors. One novel risk factor that can contribute to autoimmunity is somatic mutations, in a role parallel to their role in cancer. Somatic mutations are stochastic, de novo, non-inherited mutations. In this hypothesis, the persistent proliferation of self-reactive lymphocytes (that is usually hindered by a series of checkpoints) is permitted, due to somatic mutations in these expanding cells, allowing them to bypass multiple regulatory checkpoints, causing autoimmunity. This novel concept of the contribution of these mutations in non-malignant diseases has recently started to be explored. It proposes a novel paradigm for autoimmunity etiology and could be the missing piece of the autoimmunity puzzle.
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57
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Munisha M, Schimenti JC. Genome maintenance during embryogenesis. DNA Repair (Amst) 2021; 106:103195. [PMID: 34358805 DOI: 10.1016/j.dnarep.2021.103195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/25/2022]
Abstract
Genome maintenance during embryogenesis is critical, because defects during this period can be perpetuated and thus have a long-term impact on individual's health and longevity. Nevertheless, genome instability is normal during certain aspects of embryonic development, indicating that there is a balance between the exigencies of timely cell proliferation and mutation prevention. In particular, early embryos possess unique cellular and molecular features that underscore the challenge of having an appropriate balance. Here, we discuss genome instability during embryonic development, the mechanisms used in various cell compartments to manage genomic stress and address outstanding questions regarding the balance between genome maintenance mechanisms in key cell types that are important for adulthood and progeny.
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Affiliation(s)
- Mumingjiang Munisha
- Dept. of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, United States
| | - John C Schimenti
- Dept. of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, United States.
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58
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Latorre-Pellicer A, Gil-Salvador M, Parenti I, Lucia-Campos C, Trujillano L, Marcos-Alcalde I, Arnedo M, Ascaso Á, Ayerza-Casas A, Antoñanzas-Pérez R, Gervasini C, Piccione M, Mariani M, Weber A, Kanber D, Kuechler A, Munteanu M, Khuller K, Bueno-Lozano G, Puisac B, Gómez-Puertas P, Selicorni A, Kaiser FJ, Ramos FJ, Pié J. Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood. Sci Rep 2021; 11:15459. [PMID: 34326454 PMCID: PMC8322329 DOI: 10.1038/s41598-021-94958-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Postzygotic mosaicism (PZM) in NIPBL is a strong source of causality for Cornelia de Lange syndrome (CdLS) that can have major clinical implications. Here, we further delineate the role of somatic mosaicism in CdLS by describing a series of 11 unreported patients with mosaic disease-causing variants in NIPBL and performing a retrospective cohort study from a Spanish CdLS diagnostic center. By reviewing the literature and combining our findings with previously published data, we demonstrate a negative selection against somatic deleterious NIPBL variants in blood. Furthermore, the analysis of all reported cases indicates an unusual high prevalence of mosaicism in CdLS, occurring in 13.1% of patients with a positive molecular diagnosis. It is worth noting that most of the affected individuals with mosaicism have a clinical phenotype at least as severe as those with constitutive pathogenic variants. However, the type of genetic change does not vary between germline and somatic events and, even in the presence of mosaicism, missense substitutions are located preferentially within the HEAT repeat domain of NIPBL. In conclusion, the high prevalence of mosaicism in CdLS as well as the disparity in tissue distribution provide a novel orientation for the clinical management and genetic counselling of families.
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Affiliation(s)
- Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Marta Gil-Salvador
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Cristina Lucia-Campos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Laura Trujillano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
- Biosciences Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Arnedo
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ángela Ascaso
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ariadna Ayerza-Casas
- Unit of Paediatric Cardiology, Service of Paediatrics, Hospital Universitario Miguel Servet, 50009, Zaragoza, Spain
| | - Rebeca Antoñanzas-Pérez
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Cristina Gervasini
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Milena Mariani
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Axel Weber
- Institute of Human Genetics, Justus-Liebig-University, Giessen, Germany
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Katharina Khuller
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Gloria Bueno-Lozano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
| | - Angelo Selicorni
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsmedizin Essen, Universitätsklinikum Essen, Essen, Germany
| | - Feliciano J Ramos
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
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59
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Tao L, Raz O, Marx Z, Ghosh MS, Huber S, Greindl-Junghans J, Biezuner T, Amir S, Milo L, Adar R, Levy R, Onn A, Chapal-Ilani N, Berman V, Ben Arie A, Rom G, Oron B, Halaban R, Czyz ZT, Werner-Klein M, Klein CA, Shapiro E. Retrospective cell lineage reconstruction in humans by using short tandem repeats. CELL REPORTS METHODS 2021; 1:None. [PMID: 34341783 PMCID: PMC8313865 DOI: 10.1016/j.crmeth.2021.100054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/17/2021] [Accepted: 06/24/2021] [Indexed: 12/18/2022]
Abstract
Cell lineage analysis aims to uncover the developmental history of an organism back to its cell of origin. Recently, novel in vivo methods utilizing genome editing enabled important insights into the cell lineages of animals. In contrast, human cell lineage remains restricted to retrospective approaches, which still lack resolution and cost-efficient solutions. Here, we demonstrate a scalable platform based on short tandem repeats targeted by duplex molecular inversion probes. With this human cell lineage tracing method, we accurately reproduced a known lineage of DU145 cells and reconstructed lineages of healthy and metastatic single cells from a melanoma patient who matched the anatomical reference while adding further refinements. This platform allowed us to faithfully recapitulate lineages of developmental tissue formation in healthy cells. In summary, our lineage discovery platform can profile informative somatic mutations efficiently and provides solid lineage reconstructions even in challenging low-mutation-rate healthy single cells.
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Affiliation(s)
- Liming Tao
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Zipora Marx
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Manjusha S. Ghosh
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Sandra Huber
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Julia Greindl-Junghans
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Tamir Biezuner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Shiran Amir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Lilach Milo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Rivka Adar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ron Levy
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Amos Onn
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Veronika Berman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Asaf Ben Arie
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Guy Rom
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Barak Oron
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520-8059, USA
| | - Zbigniew T. Czyz
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Melanie Werner-Klein
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Christoph A. Klein
- Experimental Medicine and Therapy Research, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
- Division of Personalized Tumor Therapy, Fraunhofer Institute for Experimental Medicine and Toxicology Regensburg, Am Biopark 9, 93053 Regensburg, Germany
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
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Grossmann S, Hooks Y, Wilson L, Moore L, O'Neill L, Martincorena I, Voet T, Stratton MR, Heer R, Campbell PJ. Development, maturation, and maintenance of human prostate inferred from somatic mutations. Cell Stem Cell 2021; 28:1262-1274.e5. [PMID: 33657416 PMCID: PMC8260206 DOI: 10.1016/j.stem.2021.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/19/2020] [Accepted: 02/02/2021] [Indexed: 01/23/2023]
Abstract
Clonal dynamics and mutation burden in healthy human prostate epithelium are relevant to prostate cancer. We sequenced whole genomes from 409 microdissections of normal prostate epithelium across 8 donors, using phylogenetic reconstruction with spatial mapping in a 59-year-old man's prostate to reconstruct tissue dynamics across the lifespan. Somatic mutations accumulate steadily at ∼16 mutations/year/clone, with higher rates in peripheral than peri-urethral regions. The 24-30 independent glandular subunits are established as rudimentary ductal structures during fetal development by 5-10 embryonic cells each. Puberty induces formation of further side and terminal branches by local stem cells disseminated throughout the rudimentary ducts during development. During adult tissue maintenance, clonal expansions have limited geographic scope and minimal migration. Driver mutations are rare in aging prostate epithelium, but the one driver we did observe generated a sizable intraepithelial clonal expansion. Leveraging unbiased clock-like mutations, we define prostate stem cell dynamics through fetal development, puberty, and aging.
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Affiliation(s)
- Sebastian Grossmann
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Yvette Hooks
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Laura Wilson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Luiza Moore
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Laura O'Neill
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Thierry Voet
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
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61
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Revollo JR, McKinzie PB, Robison TW, Dobrovolsky VN. Mutational signatures in T-lymphocytes of rats treated with N-propyl-N-nitrosourea and procarbazine. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:350-363. [PMID: 34117657 DOI: 10.1002/em.22448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/12/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
We have used whole genome sequencing (WGS) to determine mutational signatures induced in the T-cells of rats treated in vivo with N-propyl-N-nitrosourea (PNU) or procarbazine (PCZ). The signatures from the treated rats were different from the signature of background mutations. The main component of the spontaneous T-cell mutational signature was C➔T transition with all other single base substitutions evenly distributed. The PNU-induced mutational signature showed relatively equal contributions from C➔T and T➔C transitions, and T➔A transversions. The PCZ-induced signature was characterized by T➔C transitions, T➔A and, to a smaller extent, T➔G transversions. C➔G transversions were infrequent in either the PNU or PCZ signatures. WGS not only allowed mutational signature detection, but also measured quantitative responses to mutagen treatment: 10-40× increases in the number of mutations per clone were detected in T-cell clones from treated rats. The overall strand specificity of induced mutations for annotated rat genes was comparable to the strand specificity of mutations determined previously for the endogenous X-linked Pig-a gene. Our results provide valuable reference data for future applications of WGS in safety research and risk assessment.
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Affiliation(s)
- Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Timothy W Robison
- Division of Pulmonary, Allergy and Critical Care Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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Jivanji S, Harland C, Cole S, Brophy B, Garrick D, Snell R, Littlejohn M, Laible G. The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis. BMC Genomics 2021; 22:457. [PMID: 34139989 PMCID: PMC8212539 DOI: 10.1186/s12864-021-07804-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Animal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes. In some cases, welfare-enhancing traits such as horn-status (i.e., polled) or diluted coat colour, which could enhance heat tolerance, may not segregate in breeds of primary interest, highlighting gene-editing tools such as the CRISPR-Cas9 technology as an approach to rapidly introduce variation into these populations. A major limitation preventing the acceptance of CRISPR-Cas9 mediated gene-editing, however, is the potential for off-target mutagenesis, which has raised concerns about the safety and ultimate applicability of this technology. Here, we present a clone-based study design that has allowed a detailed investigation of off-target and de novo mutagenesis in a cattle line bearing edits in the PMEL gene for diluted coat-colour. RESULTS No off-target events were detected from high depth whole genome sequencing performed in precursor cell-lines and resultant calves cloned from those edited and non-edited cell lines. Long molecule sequencing at the edited site and plasmid-specific PCRs did not reveal structural variations and/or plasmid integration events in edited samples. Furthermore, an in-depth analysis of de novo mutations across the edited and non-edited cloned calves revealed that the mutation frequency and spectra were unaffected by editing status. Cells in culture, however, appeared to have a distinct mutation signature where de novo mutations were predominantly C > A mutations, and in cloned calves they were predominantly T > G mutations, deviating from the expected excess of C > T mutations. CONCLUSIONS We found no detectable CRISPR-Cas9 associated off-target mutations in the gene-edited cells or calves derived from the gene-edited cell line. Comparison of de novo mutation in two gene-edited calves and three non-edited control calves did not reveal a higher mutation load in any one group, gene-edited or control, beyond those anticipated from spontaneous mutagenesis. Cell culture and somatic cell nuclear transfer cloning processes contributed the major source of contrast in mutational profile between samples.
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Affiliation(s)
- Swati Jivanji
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand.
| | - Chad Harland
- Livestock Improvement Corporation, Newstead, New Zealand
| | - Sally Cole
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Brigid Brophy
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Dorian Garrick
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Russell Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mathew Littlejohn
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Livestock Improvement Corporation, Newstead, New Zealand
| | - Götz Laible
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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63
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Organoids and Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112657. [PMID: 34071313 PMCID: PMC8197877 DOI: 10.3390/cancers13112657] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Organoids were first established as a three-dimensional cell culture system from mouse small intestine. Subsequent development has made organoids a key system to study many human physiological and pathological processes that affect a variety of tissues and organs. In particular, organoids are becoming very useful tools to dissect colorectal cancer (CRC) by allowing the circumvention of classical problems and limitations, such as the impossibility of long-term culture of normal intestinal epithelial cells and the lack of good animal models for CRC. In this review, we describe the features and current knowledge of intestinal organoids and how they are largely contributing to our better understanding of intestinal cell biology and CRC genetics. Moreover, recent data show that organoids are appropriate systems for antitumoral drug testing and for the personalized treatment of CRC patients.
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Bonis V, Rossell C, Gehart H. The Intestinal Epithelium - Fluid Fate and Rigid Structure From Crypt Bottom to Villus Tip. Front Cell Dev Biol 2021; 9:661931. [PMID: 34095127 PMCID: PMC8172987 DOI: 10.3389/fcell.2021.661931] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/21/2021] [Indexed: 12/19/2022] Open
Abstract
The single-layered, simple epithelium of the gastro-intestinal tract controls nutrient uptake, coordinates our metabolism and shields us from pathogens. Despite its seemingly simple architecture, the intestinal lining consists of highly distinct cell populations that are continuously renewed by the same stem cell population. The need to maintain balanced diversity of cell types in an unceasingly regenerating tissue demands intricate mechanisms of spatial or temporal cell fate control. Recent advances in single-cell sequencing, spatio-temporal profiling and organoid technology have shed new light on the intricate micro-structure of the intestinal epithelium and on the mechanisms that maintain it. This led to the discovery of unexpected plasticity, zonation along the crypt-villus axis and new mechanism of self-organization. However, not only the epithelium, but also the underlying mesenchyme is distinctly structured. Several new studies have explored the intestinal stroma with single cell resolution and unveiled important interactions with the epithelium that are crucial for intestinal function and regeneration. In this review, we will discuss these recent findings and highlight the technologies that lead to their discovery. We will examine strengths and limitations of each approach and consider the wider impact of these results on our understanding of the intestine in health and disease.
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Affiliation(s)
- Vangelis Bonis
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Carla Rossell
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Helmuth Gehart
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
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66
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Shukla V, Høffding MK, Hoffmann ER. Genome diversity and instability in human germ cells and preimplantation embryos. Semin Cell Dev Biol 2021; 113:132-147. [PMID: 33500205 PMCID: PMC8097364 DOI: 10.1016/j.semcdb.2020.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/18/2020] [Indexed: 12/26/2022]
Abstract
Genome diversity is essential for evolution and is of fundamental importance to human health. Generating genome diversity requires phases of DNA damage and repair that can cause genome instability. Humans have a high incidence of de novo congenital disorders compared to other organisms. Recent access to eggs, sperm and preimplantation embryos is revealing unprecedented rates of genome instability that may result in infertility and de novo mutations that cause genomic imbalance in at least 70% of conceptions. The error type and incidence of de novo mutations differ during developmental stages and are influenced by differences in male and female meiosis. In females, DNA repair is a critical factor that determines fertility and reproductive lifespan. In males, aberrant meiotic recombination causes infertility, embryonic failure and pregnancy loss. Evidence suggest germ cells are remarkably diverse in the type of genome instability that they display and the DNA damage responses they deploy. Additionally, the initial embryonic cell cycles are characterized by a high degree of genome instability that cause congenital disorders and may limit the use of CRISPR-Cas9 for heritable genome editing.
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Affiliation(s)
- Vallari Shukla
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Miya Kudo Høffding
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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Abstract
Tissue-resident macrophages are present in most tissues with developmental, self-renewal, or functional attributes that do not easily fit into a textbook picture of a plastic and multifunctional macrophage originating from hematopoietic stem cells; nor does it fit a pro- versus anti-inflammatory paradigm. This review presents and discusses current knowledge on the developmental biology of macrophages from an evolutionary perspective focused on the function of macrophages, which may aid in study of developmental, inflammatory, tumoral, and degenerative diseases. We also propose a framework to investigate the functions of macrophages in vivo and discuss how inherited germline and somatic mutations may contribute to the roles of macrophages in diseases.
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Affiliation(s)
- Nehemiah Cox
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Maria Pokrovskii
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Rocio Vicario
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
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68
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Wang M, Zhang C, Wang X, Yu H, Zhang H, Xu J, Zhao J, Jiang X. Tumor-treating fields (TTFields)-based cocktail therapy: a novel blueprint for glioblastoma treatment. Am J Cancer Res 2021; 11:1069-1086. [PMID: 33948346 PMCID: PMC8085847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023] Open
Abstract
Glioblastoma is one of the most common malignant tumors in the central nervous system. Due to the high plasticity, heterogeneity and complexity of the tumor microenvironment, these tumors are resistant to almost all therapeutic strategies when they reach an advanced stage. Along with being a unique and effective way to kill cancer cells, tumor-treating fields (TTFields) has emerged as a breakthrough among glioblastoma therapies since the advent of temozolomide (TMZ), and the combination of these treatments has gradually been promoted and applied in the clinic. The combination of TTFields with other therapies is particularly suitable for this type of "cold" tumors and has attracted a large amount of attention from clinicians and researchers in the era of cancer cocktail therapy. Here, we introduced the current treatment regimen for glioblastoma, highlighting the unique advantages of TTFields in the treatment of glioblastoma. Then, we summarized current glioblastoma clinical trials that combine TTFields and other therapies. In addition, the main and potential mechanisms of TTFields were introduced to further understand the rationale for each combination therapy. Finally, we focused on the most advanced technologies applied in glioblastoma research and treatment and the prospect of their combination with TTFields. This review provides a unique overview of glioblastoma treatment.
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Affiliation(s)
- Minjie Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Chaocai Zhang
- Department of Neurosurgery, Hainan General Hospital/Hainan Affiliated Hospital of Hainan Medical UniversityHaikou 570311, China
| | - Xuan Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Hao Yu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
| | - Hemei Zhang
- Department of Neurosurgery, Hainan General Hospital/Hainan Affiliated Hospital of Hainan Medical UniversityHaikou 570311, China
| | - Junnv Xu
- Department of Medical Oncology, The Second Affiliated Hospital of Hainan Medical UniversityHaikou 570311, China
| | - Jiannong Zhao
- Department of Neurosurgery, Hainan General Hospital/Hainan Affiliated Hospital of Hainan Medical UniversityHaikou 570311, China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430022, China
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Chow KHK, Budde MW, Granados AA, Cabrera M, Yoon S, Cho S, Huang TH, Koulena N, Frieda KL, Cai L, Lois C, Elowitz MB. Imaging cell lineage with a synthetic digital recording system. Science 2021; 372:eabb3099. [PMID: 33833095 DOI: 10.1126/science.abb3099] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
During multicellular development, spatial position and lineage history play powerful roles in controlling cell fate decisions. Using a serine integrase-based recording system, we engineered cells to record lineage information in a format that can be read out in situ. The system, termed integrase-editable memory by engineered mutagenesis with optical in situ readout (intMEMOIR), allowed in situ reconstruction of lineage relationships in cultured mouse cells and flies. intMEMOIR uses an array of independent three-state genetic memory elements that can recombine stochastically and irreversibly, allowing up to 59,049 distinct digital states. It reconstructed lineage trees in stem cells and enabled simultaneous analysis of single-cell clonal history, spatial position, and gene expression in Drosophila brain sections. These results establish a foundation for microscopy-readable lineage recording and analysis in diverse systems.
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Affiliation(s)
- Ke-Huan K Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark W Budde
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alejandro A Granados
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Maria Cabrera
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shinae Yoon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Soomin Cho
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ting-Hao Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Noushin Koulena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Kretzschmar K. Cancer research using organoid technology. J Mol Med (Berl) 2021; 99:501-515. [PMID: 33057820 PMCID: PMC8026469 DOI: 10.1007/s00109-020-01990-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/14/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
Organoid technology has rapidly transformed basic biomedical research and contributed to significant discoveries in the last decade. With the application of protocols to generate organoids from cancer tissue, organoid technology has opened up new opportunities for cancer research and therapy. Using organoid cultures derived from healthy tissues, different aspects of tumour initiation and progression are widely studied including the role of pathogens or specific cancer genes. Cancer organoid cultures, on the other hand, are applied to generate biobanks, perform drug screens, and study mutational signatures. With the incorporation of cellular components of the tumour microenvironment such as immune cells into the organoid cultures, the technology is now also exploited in the rapidly advancing field of immuno-oncology. In this review, I discuss how organoid technology is currently being utilised in cancer research and what obstacles are still to be overcome for its broader use in anti-cancer therapy.
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Affiliation(s)
- Kai Kretzschmar
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research Würzburg, University Hospital Würzburg, MSNZ/IZKF, Josef-Schneider-Str. 2, 97080, Würzburg, Germany.
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71
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Leeper K, Kalhor K, Vernet A, Graveline A, Church GM, Mali P, Kalhor R. Lineage barcoding in mice with homing CRISPR. Nat Protoc 2021; 16:2088-2108. [PMID: 33692551 PMCID: PMC8049957 DOI: 10.1038/s41596-020-00485-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Classic approaches to mapping the developmental history of cells in vivo have relied on techniques that require complex interventions and often capture only a single trajectory or moment in time. We have previously described a developmental barcoding system to address these issues using synthetically induced mutations to record information about each cell's lineage in its genome. This system uses MARC1 mouse lines, which have multiple homing guide RNAs that each generate hundreds of mutant alleles and combine to produce an exponential diversity of barcodes. Here, we detail two MARC1 lines that are available from a public repository. We describe strategies for using MARC1 mice and experimental design considerations. We provide a protocol for barcode retrieval and sequencing as well as the analysis of the sequencing data. This protocol generates barcodes based on synthetically induced mutations in mice to enable lineage analysis.
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Affiliation(s)
- Kathleen Leeper
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Andyna Vernet
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Amanda Graveline
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Reza Kalhor
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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72
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Coorens THH, Oliver TRW, Sanghvi R, Sovio U, Cook E, Vento-Tormo R, Haniffa M, Young MD, Rahbari R, Sebire N, Campbell PJ, Charnock-Jones DS, Smith GCS, Behjati S. Inherent mosaicism and extensive mutation of human placentas. Nature 2021; 592:80-85. [PMID: 33692543 PMCID: PMC7611644 DOI: 10.1038/s41586-021-03345-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Placentas can exhibit chromosomal aberrations that are absent from the fetus1. The basis of this genetic segregation, which is known as confined placental mosaicism, remains unknown. Here we investigated the phylogeny of human placental cells as reconstructed from somatic mutations, using whole-genome sequencing of 86 bulk placental samples (with a median weight of 28 mg) and of 106 microdissections of placental tissue. We found that every bulk placental sample represents a clonal expansion that is genetically distinct, and exhibits a genomic landscape akin to that of childhood cancer in terms of mutation burden and mutational imprints. To our knowledge, unlike any other healthy human tissue studied so far, the placental genomes often contained changes in copy number. We reconstructed phylogenetic relationships between tissues from the same pregnancy, which revealed that developmental bottlenecks genetically isolate placental tissues by separating trophectodermal lineages from lineages derived from the inner cell mass. Notably, there were some cases with full segregation-within a few cell divisions of the zygote-of placental lineages and lineages derived from the inner cell mass. Such early embryonic bottlenecks may enable the normalization of zygotic aneuploidy. We observed direct evidence for this in a case of mosaic trisomic rescue. Our findings reveal extensive mutagenesis in placental tissues and suggest that mosaicism is a typical feature of placental development.
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Affiliation(s)
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Gordon C S Smith
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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73
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Abstract
Cancer is a clonal disorder derived from a single ancestor cell and its progenies that are positively selected by acquisition of 'driver mutations'. However, the evolution of positively selected clones does not necessarily imply the presence of cancer. On the contrary, it has become clear that expansion of these clones in phenotypically normal or non-cancer tissues is commonly seen in association with ageing and/or in response to environmental insults and chronic inflammation. Recent studies have reported expansion of clones harbouring mutations in cancer driver genes in the blood, skin, oesophagus, bronchus, liver, endometrium and bladder, where the expansion could be so extensive that tissues undergo remodelling of an almost entire tissue. The presence of common cancer driver mutations in normal tissues suggests a strong link to cancer development, providing an opportunity to understand early carcinogenic processes. Nevertheless, some driver mutations are unique to normal tissues or have a mutation frequency that is much higher in normal tissue than in cancer, indicating that the respective clones may not necessarily be destined for evolution to cancer but even negatively selected for carcinogenesis depending on the mutated gene. Moreover, tissues that are remodelled by genetically altered clones might define functionalities of aged tissues or modified inflammatory processes. In this Review, we provide an overview of major findings on clonal expansion in phenotypically normal or non-cancer tissues and discuss their biological significance not only in cancer development but also in ageing and inflammatory diseases.
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Affiliation(s)
- Nobuyuki Kakiuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan.
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.
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74
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Zubareva EV, Nadezhdin SV, Nadezhdina NA, Belyaeva VS, Burda YE, Avtina TV, Gudyrev OS, Kolesnik IM, Kulikova SY, Mishenin MO. 3D organotypic cell structures for drug development and Microorganism-Host interaction research. RESEARCH RESULTS IN PHARMACOLOGY 2021. [DOI: 10.3897/rrpharmacology.7.62118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: The article describes a new method of tissue engineering, which is based on the use of three-dimensional multicellular constructs consisting of stem cells that mimic the native tissue in vivo – organoids.
3D cell cultures: The currently existing model systems of three-dimensional cultures are described.
Characteristics of organoids and strategies for their culturing: The main approaches to the fabrication of 3D cell constructs using pluripotent (embryonic and induced) stem cells or adult stem cells are described.
Brain organoids (Cerebral organoids): Organoids of the brain, which are used to study the development of the human brain, are characterized, with the description of biology of generating region-specific cerebral organoids.
Lung organoids: Approaches to the generation of lung organoids are described, by means of pluripotent stem cells and lung tissue cell lines.
Liver organoids: The features of differentiation of stem cells into hepatocyte-like cells and the creation of 3D hepatic organoids are characterized.
Intestinal organoids: The formation of small intestine organoids from stem cells is described.
Osteochondral organoids: Fabrication of osteochondral organoids is characterised.
Use of organoids as test systems for drugs screening: The information on drug screening using organoids is provided.
Using organoids to model infectious diseases and study adaptive responses of microorganisms when interacting with the host: The use of organoids for modeling infectious diseases and studying the adaptive responses of microorganisms when interacting with the host organism is described.
Conclusion: The creation of three-dimensional cell structures that reproduce the structural and functional characteristics of tissue in vivo, makes it possible to study the biology of the body’s development, the features of intercellular interactions, screening drugs and co-cultivating with viruses, bacteria and parasites.
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75
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Jia X, Zhang Q, Jiang M, Huang J, Yu L, Traw MB, Tian D, Hurst LD, Yang S. Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation. PLoS Biol 2021; 19:e3001164. [PMID: 33750968 PMCID: PMC8016264 DOI: 10.1371/journal.pbio.3001164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/01/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
In contrast to common meiotic gene conversion, mitotic gene conversion, because it is so rare, is often ignored as a process influencing allelic diversity. We show that if there is a large enough number of premeiotic cell divisions, as seen in many organisms without early germline sequestration, such as plants, this is an unsafe position. From examination of 1.1 million rice plants, we determined that the rate of mitotic gene conversion events, per mitosis, is 2 orders of magnitude lower than the meiotic rate. However, owing to the large number of mitoses between zygote and gamete and because of long mitotic tract lengths, meiotic and mitotic gene conversion can be of approximately equivalent importance in terms of numbers of markers converted from zygote to gamete. This holds even if we assume a low number of premeiotic cell divisions (approximately 40) as witnessed in Arabidopsis. A low mitotic rate associated with long tracts is also seen in yeast, suggesting generality of results. For species with many mitoses between each meiotic event, mitotic gene conversion should not be overlooked. Gene conversion associated with meiosis has long been a focus of attention in population genomics, but mitotic conversion has been relatively overlooked as it was thought to be rare. Analysis in plants suggests that this could be a mistake; long tract lengths and multiple mitoses in species lacking germline sequestration suggest that mitotic conversion, although rare per mitosis, should not be ignored.
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Affiliation(s)
- Xianqing Jia
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Qijun Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Milton Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Dacheng Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,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
| | - Sihai Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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76
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Rauth S, Karmakar S, Batra SK, Ponnusamy MP. Recent advances in organoid development and applications in disease modeling. Biochim Biophys Acta Rev Cancer 2021; 1875:188527. [PMID: 33640383 DOI: 10.1016/j.bbcan.2021.188527] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
An improved understanding of stem cell niches, organogenesis, and disease models has paved the way for developing a three-dimensional (3D) organoid culture system. Organoid cultures can be derived from primary tissues (single cells or tissue subunits), adult stem cells (ASCs), induced pluripotent stem cells (iPSCs), or embryonic stem cells (ESCs). As a significant technological breakthrough, 3D organoid models offer a promising approach for understanding the complexities of human diseases ranging from the mechanistic investigation of disease pathogenesis to therapy. Here, we discuss the recent applications, advantages, and limitations of organoids as in vitro models for studying metabolomics, drug development, infectious diseases, and the gut microbiome. We further discuss the use of organoids in cancer modeling using high throughput sequencing approaches.
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Affiliation(s)
- Sanchita Rauth
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Saswati Karmakar
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA; Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA; Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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77
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Hwang SH, Lee S, Park JY, Jeon JS, Cho YJ, Kim S. Potential of Drug Efficacy Evaluation in Lung and Kidney Cancer Models Using Organ-on-a-Chip Technology. MICROMACHINES 2021; 12:215. [PMID: 33669950 PMCID: PMC7924856 DOI: 10.3390/mi12020215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/13/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Organ-on-a-chip (OoC) is an exponential technology with the potential to revolutionize disease, toxicology research, and drug discovery. Recent advances in OoC could be utilized for drug screening in disease models to evaluate the efficacy of new therapies and support new tools for the understanding of disease mechanisms. Rigorous validation of this technology is required to determine whether OoC models may represent human-relevant physiology and predict clinical outcomes in target disease models. Achievements in the OoC field could reveal exciting new avenues for drug development and discovery. This review attempts to highlight the benefits of OoC as per our understanding of the cellular and molecular pathways in lung and kidney cancer models, and discusses the challenges in evaluating drug efficacy.
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Affiliation(s)
- Seong-Hye Hwang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.-H.H.); (Y.-J.C.)
| | - Sangchul Lee
- Department of Urology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | - Jee Yoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 03080, Korea;
| | | | - Young-Jae Cho
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.-H.H.); (Y.-J.C.)
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sejoong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam 13620, Korea; (S.-H.H.); (Y.-J.C.)
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
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78
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O'Connell L, Winter DC, Aherne CM. The Role of Organoids as a Novel Platform for Modeling of Inflammatory Bowel Disease. Front Pediatr 2021; 9:624045. [PMID: 33681101 PMCID: PMC7925404 DOI: 10.3389/fped.2021.624045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2021] [Indexed: 12/03/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing-remitting immune-mediated disorder affecting the gut. It is common in Westernized regions and is increasing in incidence in developing countries. At a molecular level, intrinsic deficiencies in epithelial integrity, mucosal barrier function, and mechanisms of immune response and resolution contribute to the development of IBD. Traditionally two platforms have been utilized for disease modeling of IBD; in-vitro monolayer cell culture and in-vivo animal models. Both models have limitations, including cost, lack of representative cell types, lack of complexity of cellular interactions in a living organism, and xenogeneity. Organoids, three-dimensional cellular structures which recapitulate the basic architecture and functional processes of the organ of origin, hold potential as a third platform with which to investigate the pathogenesis and molecular defects which give rise to IBD. Organoids retain the genetic and transcriptomic profile of the tissue of origin over time and unlike monolayer cell culture can be induced to differentiate into most adult intestinal cell types. They may be used to model intestinal host-microbe interactions occurring at the mucosal barrier, are amenable to genetic manipulation and can be co-cultured with other cell lines of interest. Bioengineering approaches may be applied to render a more faithful representation of the intestinal epithelial niche. In this review, we outline the concept of intestinal organoids, discuss the advantages and disadvantages of the platform comparative to alternative models, and describe the translational applications of organoids in IBD.
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Affiliation(s)
- Lauren O'Connell
- Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Colorectal Disease, St. Vincents' University Hospital, Dublin, Ireland
| | - Des C Winter
- Centre for Colorectal Disease, St. Vincents' University Hospital, Dublin, Ireland
| | - Carol M Aherne
- Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
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79
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Gottlieb B, Trifiro M, Batist G. Why Tumor Genetic Heterogeneity May Require Rethinking Cancer Genesis and Treatment. Trends Cancer 2020; 7:400-409. [PMID: 33243702 DOI: 10.1016/j.trecan.2020.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022]
Abstract
Tumor genetic heterogeneity, in which individual tumors contain both multiple variant cancer-associated and normal genes, has been widely reported, although its significance has yet to be fully understood. We propose a genetic heterogeneity-based selection-centric hypothesis in which genetic heterogeneity, caused by the temporary reduction of DNA repair efficiency, occurs very early in human development, resulting in a small minority of cells in normal tissues acquiring cancer-associated genes that remain dormant. Cancer develops when precancer cells are selected for by altered tissue microenvironments; similar scenarios occur with development of metastases and therapeutic resistance in established cancer. This suggests that a normal cell selection treatment approach based on preferentially selecting normal cells within tumors may be effective in treating cancer.
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Affiliation(s)
- Bruce Gottlieb
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Department of Nursing, McGill University, Montreal, Quebec, Canada.
| | - Mark Trifiro
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Gerald Batist
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Segal Cancer Center, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada; McGill Centre for Translational Research in Cancer, McGill University, Montreal, Quebec, Canada
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80
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Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G. Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. HGG ADVANCES 2020; 1:100008. [PMID: 33263113 PMCID: PMC7703690 DOI: 10.1016/j.xhgg.2020.100008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
The diaphragm is critical for respiration and separation of the thoracic and abdominal cavities, and defects in diaphragm development are the cause of congenital diaphragmatic hernias (CDH), a common and often lethal birth defect. The genetic etiology of CDH is complex. Single-nucleotide variants (SNVs), insertions/deletions (indels), and structural variants (SVs) in more than 150 genes have been associated with CDH, although few genes are recurrently mutated in multiple individuals and mutated genes are incompletely penetrant. This suggests that multiple genetic variants in combination, other not-yet-investigated classes of variants, and/or nongenetic factors contribute to CDH etiology. However, no studies have comprehensively investigated in affected individuals the contribution of all possible classes of variants throughout the genome to CDH etiology. In our study, we used a unique cohort of four individuals with isolated CDH with samples from blood, skin, and diaphragm connective tissue and parental blood and deep whole-genome sequencing to assess germline and somatic de novo and inherited SNVs, indels, and SVs. In each individual we found a different mutational landscape that included germline de novo and inherited SNVs and indels in multiple genes. We also found in two individuals a 343 bp deletion interrupting an annotated enhancer of the CDH-associated gene GATA4, and we hypothesize that this common SV (found in 1%-2% of the population) acts as a sensitizing allele for CDH. Overall, our comprehensive reconstruction of the genetic architecture of four CDH individuals demonstrates that the etiology of CDH is heterogeneous and multifactorial.
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Affiliation(s)
- Eric L. Bogenschutz
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Zac D. Fox
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Andrew Farrell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Barry Moore
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lan Yu
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gudrun Aspelund
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gabor Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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81
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Tang J, Fewings E, Chang D, Zeng H, Liu S, Jorapur A, Belote RL, McNeal AS, Tan TM, Yeh I, Arron ST, Judson-Torres RL, Bastian BC, Shain AH. The genomic landscapes of individual melanocytes from human skin. Nature 2020; 586:600-605. [PMID: 33029006 PMCID: PMC7581540 DOI: 10.1038/s41586-020-2785-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/03/2020] [Indexed: 01/13/2023]
Abstract
Every cell in the human body has a unique set of somatic mutations, yet it remains difficult to comprehensively genotype an individual cell1. Here, we developed solutions to overcome this obstacle in the context of normal human skin, thus offering the first glimpse into the genomic landscapes of individual melanocytes from human skin. As expected, sun-shielded melanocytes had fewer mutations than sun-exposed melanocytes. However, within sun-exposed sites, melanocytes on chronically sun-exposed skin (e.g. the face) displayed a lower mutation burden than melanocytes on intermittently sun-exposed skin (e.g. the back). Melanocytes located adjacent to a skin cancer had higher mutation burdens than melanocytes from donors without skin cancer, implying that the mutation burden of normal skin can be harnessed to measure cumulative sun damage and skin cancer risk. Moreover, melanocytes from healthy skin commonly harbor pathogenic mutations, though these mutations tended to be weakly oncogenic, likely explaining why they did not give rise to discernible lesions. Phylogenetic analyses identified groups of related melanocytes, suggesting that melanocytes spread throughout skin as fields of clonally related cells, invisible to the naked eye. Overall, our study offers an unprecedented view into the genomic landscapes of individual melanocytes, revealing key insights into the causes and origins of melanoma.
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Affiliation(s)
- Jessica Tang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Eleanor Fewings
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Darwin Chang
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Hanlin Zeng
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Shanshan Liu
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Aparna Jorapur
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rachel L Belote
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Andrew S McNeal
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tuyet M Tan
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Iwei Yeh
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Sarah T Arron
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert L Judson-Torres
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Boris C Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - A Hunter Shain
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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82
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Al Zouabi L, Bardin AJ. Stem Cell DNA Damage and Genome Mutation in the Context of Aging and Cancer Initiation. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036210. [PMID: 31932318 DOI: 10.1101/cshperspect.a036210] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Adult stem cells fuel tissue homeostasis and regeneration through their unique ability to self-renew and differentiate into specialized cells. Thus, their DNA provides instructions that impact the tissue as a whole. Since DNA is not an inert molecule, but rather dynamic, interacting with a myriad of chemical and physical factors, it encounters damage from both endogenous and exogenous sources. Damage to DNA introduces deviations from its normal intact structure and, if left unrepaired, may result in a genetic mutation. In turn, mutant genomes of stem and progenitor cells are inherited in cells of the lineage, thus eroding the genetic information that maintains homeostasis of the somatic cell population. Errors arising in stem and progenitor cells will have a substantially larger impact on the tissue in which they reside than errors occurring in postmitotic differentiated cells. Therefore, maintaining the integrity of genomic DNA within our stem cells is essential to protect the instructions necessary for rebuilding healthy tissues during homeostatic renewal. In this review, we will first discuss DNA damage arising in stem cells and cell- and tissue-intrinsic mechanisms that protect against harmful effects of this damage. Secondly, we will examine how erroneous DNA repair and persistent DNA damage in stem and progenitor cells impact stem cells and tissues in the context of cancer initiation and aging. Finally, we will discuss the use of invertebrate and vertebrate model systems to address unanswered questions on the role that DNA damage and mutation may play in aging and precancerous conditions.
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Affiliation(s)
- Lara Al Zouabi
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
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83
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Liggett LA, Sankaran VG. Unraveling Hematopoiesis through the Lens of Genomics. Cell 2020; 182:1384-1400. [PMID: 32946781 PMCID: PMC7508400 DOI: 10.1016/j.cell.2020.08.030] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/14/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023]
Abstract
Hematopoiesis has long served as a paradigm of stem cell biology and tissue homeostasis. In the past decade, the genomics revolution has ushered in powerful new methods for investigating the hematopoietic system that have provided transformative insights into its biology. As part of the advances in genomics, increasingly accurate deep sequencing and novel methods of cell tracking have revealed hematopoiesis to be more of a continuous and less of a discrete and punctuated process than originally envisioned. In part, this continuous nature of hematopoiesis is made possible by the emergent outcomes of vast, interconnected regulatory networks that influence cell fates and lineage commitment. It is also becoming clear how these mechanisms are modulated by genetic variation present throughout the population. This review describes how these recently uncovered complexities are reshaping our concept of tissue development and homeostasis while opening up a more comprehensive future understanding of hematopoiesis.
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Affiliation(s)
- L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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84
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Miao X, Li Y, Zheng C, Wang L, Jin C, Chen L, Mi S, Zhai W, Wang QF, Cai J. A promising iPS-based single-cell cloning strategy revealing signatures of somatic mutations in heterogeneous normal cells. Comput Struct Biotechnol J 2020; 18:2326-2335. [PMID: 32994891 PMCID: PMC7493045 DOI: 10.1016/j.csbj.2020.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/15/2020] [Accepted: 08/26/2020] [Indexed: 11/24/2022] Open
Abstract
Single-cell genomics has advanced rapidly as trace-DNA amplification technologies evolved. However, current technologies are subject to a variety of pitfalls such as contamination, uneven genomic coverage, and amplification errors. Even for the "golden" strategy of single stem cell-derived clonal formation, high-fidelity amplification is applicable merely to single stem cells. It's still challenging to accurately define somatic mutations of a single cell in various cell types. Herein, we provided evidence, for the first time, to prove that induced pluripotent stem cells (iPS cells or iPSC), being a single somatic cell-derived clone, are recording almost identical (>90%) mutational profile of the initial cell progenitor. This finding demonstrates iPS technique, applicable to any cell type, can be utilized as a cell cloning strategy favorable for single-cell genomic amplification. This novel strategy is not limited by cell-type constraints or amplification artifacts, and thus enables our detailed investigation on the characteristics of somatic mutations in heterogeneous 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, China National Center for Bioinformation, Beijing 100101, China
| | - Yueying Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, 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, China National Center for Bioinformation, Beijing 100101, China
| | - Lifei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Jin
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangli Mi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiwei Zhai
- Department of Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qian-Fei Wang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Cai
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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85
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Jia Z, Wang Y, Cao L, Wang Y, Song Y, Yang X, Bing Z, Cao Z, Liu P, Zhang S, Chen Z, Huang M, Yu Y, Han-Zhang H, Song J, Christoph DC, Passaro A, Gridelli C, Hishida T, Liang N, Li S. First-line treatment selection with organoids of an EGFRm + TP53m stage IA1 patient with early metastatic recurrence after radical surgery and follow-up. J Thorac Dis 2020; 12:3764-3773. [PMID: 32802455 PMCID: PMC7399434 DOI: 10.21037/jtd-20-1882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ziqi Jia
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Eight-Year MD Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanyu Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Cao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoying Yang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Eight-Year MD Program, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhongxing Bing
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhili Cao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Peng Liu
- Medical Research Center, Central Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuyang Zhang
- Medical Research Center, Central Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zexin Chen
- Accurate International Biotechnology Co. Ltd., Guangzhou, China
| | - Min Huang
- Accurate International Biotechnology Co. Ltd., Guangzhou, China
| | - Yan Yu
- Accurate International Biotechnology Co. Ltd., Guangzhou, China
| | - Han Han-Zhang
- Burning Rock Biotechnology Co. Ltd., Guangzhou, China
| | - Jinlei Song
- Burning Rock Biotechnology Co. Ltd., Guangzhou, China
| | - Daniel C Christoph
- Department of Medical Oncology/Haematology, Evang. Kliniken Essen-Mitte, Essen, Germany
| | - Antonio Passaro
- Division of Thoracic Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Cesare Gridelli
- Division of Medical Oncology, "S.G. Moscati" Hospital, Contrada Amoretta, 83100, Avellino, Italy
| | - Tomoyuki Hishida
- Division of Thoracic Surgery, Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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86
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Abstract
Organoid technologies enable the creation of in vitro physiologic systems that model tissues of origin more accurately than classical culture approaches. Seminal characteristics, including three-dimensional structure and recapitulation of self-renewal, differentiation, and disease pathology, render organoids eminently suited as hybrids that combine the experimental tractability of traditional 2D cell lines with cellular attributes of in vivo model systems. Here, we describe recent advances in this rapidly evolving field and their applications in cancer biology, clinical translation and precision medicine.
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87
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Zhang C, Jin M, Zhao J, Chen J, Jin W. Organoid models of glioblastoma: advances, applications and challenges. Am J Cancer Res 2020; 10:2242-2257. [PMID: 32905502 PMCID: PMC7471358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023] Open
Abstract
The high mortality and poor clinical prognosis of glioblastoma multiforme (GBM) are concerns for many GBM patients as well as clinicians and researchers. The lack of a preclinical model that can easily be established and accurately recapitulate tumour biology and the tumour microenvironment further complicates GBM research and its clinical translation. GBM organoids (GBOs) are promising high-fidelity models that can be applied to model the disease, develop drugs, establish a living biobank, mimic therapeutic responses and explore personalized therapy. However, GBO models face some challenges, including deficient immune responses, absent vascular system and controversial reliability. In recent years, considerable progress has been achieved in the improvement of brain tumour organoid models and research based on such models. In addition to the traditional cultivation method, these models can be cultivated via genetic engineering and co-culture of cerebral organoids and GBM. In this review, we summarize the applications of GBM organoids and related advances and provide our opinions on associated limitations and challenges.
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Affiliation(s)
- Chaocai Zhang
- Department of Neurosurgery, Hainan General Hospital/Hainan Affiliated Hospital of Hainan Medical UniversityHaikou, PR China
| | - Mingzhu Jin
- Shanghai Jiao Tong University School of MedicineShanghai, PR China
| | - Jiannong Zhao
- Department of Neurosurgery, Hainan General Hospital/Hainan Affiliated Hospital of Hainan Medical UniversityHaikou, PR China
| | - Juxiang Chen
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Changzheng Hospital, Second Military Medical UniversityShanghai, PR China
| | - Weilin Jin
- Key Laboratory for Thin Film and Microfabrication Technology of Ministry of Education, Department of Instrument Science and Engineering, Institute of Nano Biomedicine and Engineering, School of Electronic Information and Electronic Engineering, Shanghai Jiao Tong UniversityShanghai, PR China
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88
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Hasaart KAL, Manders F, van der Hoorn ML, Verheul M, Poplonski T, Kuijk E, de Sousa Lopes SMC, van Boxtel R. Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis. Sci Rep 2020; 10:12991. [PMID: 32737409 PMCID: PMC7395765 DOI: 10.1038/s41598-020-69822-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/17/2020] [Indexed: 11/30/2022] Open
Abstract
Children show a higher incidence of leukemia compared to young adolescents, yet their cells have less age-related (oncogenic) somatic mutations. Newborns with Down syndrome have an even higher risk of developing leukemia, which is thought to be driven by mutations that accumulate during fetal development. To characterize mutation accumulation in individual stem and progenitor cells of Down syndrome and karyotypically normal fetuses, we clonally expanded single cells and performed whole-genome sequencing. We found a higher mutation rate in haematopoietic stem and progenitor cells during fetal development compared to the post-infant rate. In fetal trisomy 21 cells the number of somatic mutations is even further increased, which was already apparent during the first cell divisions of embryogenesis before gastrulation. The number and types of mutations in fetal trisomy 21 haematopoietic stem and progenitor cells were similar to those in Down syndrome-associated myeloid preleukemia and could be attributed to mutational processes that were active during normal fetal haematopoiesis. Finally, we found that the contribution of early embryonic cells to human fetal tissues can vary considerably between individuals. The increased mutation rates found in this study, may contribute to the increased risk of leukemia early during life and the higher incidence of leukemia in Down syndrome.
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Affiliation(s)
- Karlijn A L Hasaart
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | | | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Tomasz Poplonski
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine, University Medical Center Utrecht and Oncode Institute, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.
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89
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You X, Thiruppathi S, Liu W, Cao Y, Naito M, Furihata C, Honma M, Luan Y, Suzuki T. Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair-derived artifacts as residual errors. Arch Toxicol 2020; 94:3475-3485. [PMID: 32737516 DOI: 10.1007/s00204-020-02832-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/24/2020] [Indexed: 02/06/2023]
Abstract
To improve the accuracy and the cost-efficiency of next-generation sequencing in ultralow-frequency mutation detection, we developed the Paired-End and Complementary Consensus Sequencing (PECC-Seq), a PCR-free duplex consensus sequencing approach. PECC-Seq employed shear points as endogenous barcodes to identify consensus sequences from the overlap in the shortened, complementary DNA strand-derived paired-end reads for sequencing error correction. With the high accuracy of PECC-Seq, we identified the characteristic base substitution errors introduced by the end-repair process of mechanical fragmentation-based library preparations, which were prominent at the terminal 7 bp of the library fragments in the 5'-NpCpA-3' and 5'-NpCpT-3' trinucleotide context. As demonstrated at the human genome scale (TK6 cells), after removing these potential end-repair artifacts from the terminal 7 bp, PECC-Seq could reduce the sequencing error frequency to mid-10-7 with a relatively low sequencing depth. For TA base pairs, the background error rate could be suppressed to mid-10-8. In mutagen-treated (6 μg/mL methyl methanesulfonate or 12 μg/mL N-nitroso-N-ethylurea) TK6, increases in mutagen treatment-related mutant frequencies could be detected, indicating the potential of PECC-Seq in detecting genome-wide ultra-rare mutations. In addition, our finding on the patterns of end-repair artifacts may provide new insights into further reducing technical errors not only for PECC-Seq, but also for other next-generation sequencing techniques.
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Affiliation(s)
- Xinyue You
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, 200025, China.,Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan
| | - Suresh Thiruppathi
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan
| | - Weiying Liu
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, 200025, China
| | - Yiyi Cao
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, 200025, China.,Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan
| | - Chie Furihata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan
| | - Yang Luan
- School of Public Health, Hongqiao International Institute of Medicine, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, Shanghai, 200025, China.
| | - Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, 210-9501, Japan.
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90
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Vogel I, Blanshard RC, Hoffmann ER. SureTypeSC-a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data. Bioinformatics 2020; 35:5055-5062. [PMID: 31116387 DOI: 10.1093/bioinformatics/btz412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 04/08/2019] [Accepted: 05/21/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Accurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single-cell environment is challenging due to the errors caused by whole-genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single-cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole-genome amplification step. Algorithms designed for bulk DNA genotyping cause significant data loss when used for single-cell applications. RESULTS In this study, we have created a resource of 28.7 million SNPs, typed at high confidence from whole-genome amplified DNA from single cells using the Illumina SNP bead array technology. The resource is generated from 104 single cells from two cell lines that are available from the Coriell repository. We used mother-father-proband (trio) information from multiple technical replicates of bulk DNA to establish a high quality reference genotype for the two cell lines on the SNP array. This enabled us to develop SureTypeSC-a two-stage machine learning algorithm that filters a substantial part of the noise, thereby retaining the majority of the high quality SNPs. SureTypeSC also provides a simple statistical output to show the confidence of a particular single-cell genotype using Bayesian statistics. AVAILABILITY AND IMPLEMENTATION The implementation of SureTypeSC in Python and sample data are available in the GitHub repository: https://github.com/puko818/SureTypeSC. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ivan Vogel
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.,Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Robert C Blanshard
- Illumina Cambridge Ltd., Fulbourn, UK.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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91
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Guenat OT, Geiser T, Berthiaume F. Clinically Relevant Tissue Scale Responses as New Readouts from Organs-on-a-Chip for Precision Medicine. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:111-133. [PMID: 31961712 DOI: 10.1146/annurev-anchem-061318-114919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organs-on-chips (OOC) are widely seen as being the next generation in vitro models able to accurately recreate the biochemical-physical cues of the cellular microenvironment found in vivo. In addition, they make it possible to examine tissue-scale functional properties of multicellular systems dynamically and in a highly controlled manner. Here we summarize some of the most remarkable examples of OOC technology's ability to extract clinically relevant tissue-level information. The review is organized around the types of OOC outputs that can be measured from the cultured tissues and transferred to clinically meaningful information. First, the creation of functional tissues-on-chip is discussed, followed by the presentation of tissue-level readouts specific to OOC, such as morphological changes, vessel formation and function, tissue properties, and metabolic functions. In each case, the clinical relevance of the extracted information is highlighted.
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Affiliation(s)
- Olivier T Guenat
- ARTORG Center for Biomedical Engineering Research, Medical Faculty, University of Bern, CH-3008 Bern, Switzerland;
- Department of Pulmonary Medicine, University Hospital and University of Bern, CH-3008 Bern, Switzerland
- Thoracic Surgery Department, University Hospital of Bern, Switzerland
| | - Thomas Geiser
- Department of Pulmonary Medicine, University Hospital and University of Bern, CH-3008 Bern, Switzerland
| | - François Berthiaume
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA
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92
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Ultra-High-Frequency Reprogramming of Individual Long-Term Hematopoietic Stem Cells Yields Low Somatic Variant Induced Pluripotent Stem Cells. Cell Rep 2020; 26:2580-2592.e7. [PMID: 30840883 PMCID: PMC6754097 DOI: 10.1016/j.celrep.2019.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/18/2018] [Accepted: 02/06/2019] [Indexed: 02/07/2023] Open
Abstract
Efficiency of reprogramming of human cells into induced pluripotent stem cells (iPSCs) has remained low. We report that individual adult human CD49f+ long-term hematopoietic stem cells (LT-HSCs) can be reprogrammed into iPSCs at close to 50% efficiency using Sendai virus transduction. This exquisite sensitivity to reprogramming is specific to LT-HSCs, since it progressively decreases in committed progenitors. LT-HSC reprogramming can follow multiple paths and is most efficient when transduction is performed after the cells have exited G0. Sequencing of 75 paired skin fibroblasts/LT-HSC samples collected from nine individuals revealed that LT-HSCs contain a lower load of somatic single-nucleotide variants (SNVs) and indels than skin fibroblasts and accumulate about 12 SNVs/year. Mutation analysis revealed that LT-HSCs and fibroblasts have very different somatic mutation signatures and that somatic mutations in iPSCs generally exist prior to reprogramming. LT-HSCs may become the preferred cell source for the production of clinical-grade iPSCs. Wang et al. show that single adult human long-term hematopoietic stem cells can be reprogrammed into induced pluripotent stem cells at close to 50% efficiency and contain fewer somatic single-nucleotide variants and indels than skin fibroblasts. They may become the preferred source for the production of clinical-grade iPSCs.
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93
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Lodato MA, Walsh CA. Genome aging: somatic mutation in the brain links age-related decline with disease and nominates pathogenic mechanisms. Hum Mol Genet 2020; 28:R197-R206. [PMID: 31578549 DOI: 10.1093/hmg/ddz191] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 12/19/2022] Open
Abstract
Aging is a mysterious process, not only controlled genetically but also subject to random damage that can accumulate over time. While DNA damage and subsequent mutation in somatic cells were first proposed as drivers of aging more than 60 years ago, whether and to what degree these processes shape the neuronal genome in the human brain could not be tested until recent technological breakthroughs related to single-cell whole-genome sequencing. Indeed, somatic single-nucleotide variants (SNVs) increase with age in the human brain, in a somewhat stochastic process that may nonetheless be controlled by underlying genetic programs. Evidence from the literature suggests that in addition to demonstrated increases in somatic SNVs during aging in normal brains, somatic mutation may also play a role in late-onset, sporadic neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. In this review, we will discuss somatic mutation in the human brain, mechanisms by which somatic mutations occur and can be controlled, and how this process can impact human health.
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Affiliation(s)
- Michael A Lodato
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA.,Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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94
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Abstract
Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial DNA as well as variations in DNA methylation status. It is also apparent that the scientific community is on the verge of being able to make a comprehensive and detailed cell lineage map of human embryonic and fetal development. In this review, we discuss the advantages and disadvantages of different approaches and markers for lineage tracing. We also describe the general conceptual design for how to derive a lineage map for humans.
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Affiliation(s)
- Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA;
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, Connecticut 06520, USA;
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95
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Yu L, Boström C, Franzenburg S, Bayer T, Dagan T, Reusch TBH. Somatic genetic drift and multilevel selection in a clonal seagrass. Nat Ecol Evol 2020; 4:952-962. [PMID: 32393866 DOI: 10.1038/s41559-020-1196-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 04/02/2020] [Indexed: 11/09/2022]
Abstract
All multicellular organisms are genetic mosaics owing to somatic mutations. The accumulation of somatic genetic variation in clonal species undergoing asexual (or clonal) reproduction may lead to phenotypic heterogeneity among autonomous modules (termed ramets). However, the abundance and dynamics of somatic genetic variation under clonal reproduction remain poorly understood. Here we show that branching events in a seagrass (Zostera marina) clone or genet lead to population bottlenecks of tissue that result in the evolution of genetically differentiated ramets in a process of somatic genetic drift. By studying inter-ramet somatic genetic variation, we uncovered thousands of single nucleotide polymorphisms that segregated among ramets. Ultra-deep resequencing of single ramets revealed that the strength of purifying selection on mosaic genetic variation was greater within than among ramets. Our study provides evidence for multiple levels of selection during the evolution of seagrass genets. Somatic genetic drift during clonal propagation leads to the emergence of genetically unique modules that constitute an elementary level of selection and individuality in long-lived clonal species.
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Affiliation(s)
- Lei Yu
- GEOMAR Helmholtz-Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | | | - Sören Franzenburg
- Institute for Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Till Bayer
- GEOMAR Helmholtz-Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany
| | - Tal Dagan
- Institute of Microbiology, University of Kiel, Kiel, Germany
| | - Thorsten B H Reusch
- GEOMAR Helmholtz-Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Kiel, Germany.
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96
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McKinley KL, Castillo-Azofeifa D, Klein OD. Tools and Concepts for Interrogating and Defining Cellular Identity. Cell Stem Cell 2020; 26:632-656. [PMID: 32386555 PMCID: PMC7250495 DOI: 10.1016/j.stem.2020.03.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Defining the mechanisms that generate specialized cell types and coordinate their functions is critical for understanding organ development and renewal. New tools and discoveries are challenging and refining our definitions of a cell type. A rapidly growing toolkit for single-cell analyses has expanded the number of markers that can be assigned to a cell simultaneously, revealing heterogeneity within cell types that were previously regarded as homogeneous populations. Additionally, cell types defined by specific molecular markers can exhibit distinct, context-dependent functions; for example, between tissues in homeostasis and those responding to damage. Here we review the current technologies used to identify and characterize cells, and we discuss how experimental and pathological perturbations are adding increasing complexity to our definitions of cell identity.
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Affiliation(s)
- Kara L McKinley
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - David Castillo-Azofeifa
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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97
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Melki PN, Korenjak M, Zavadil J. Experimental investigations of carcinogen-induced mutation spectra: Innovation, challenges and future directions. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 853:503195. [PMID: 32522347 DOI: 10.1016/j.mrgentox.2020.503195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 11/18/2022]
Abstract
Recent years have witnessed an expansion of mutagenesis research focusing on experimentally modeled genome-scale mutational signatures of carcinogens and of endogenous processes. Experimental mutational signatures can explain etiologic links to patterns found in human tumors that may be linked to same exposures, and can serve as biomarkers of exposure history and may even provide insights on causality. A number of innovative exposure models have been employed and reported, based on cells cultured in monolayers or in 3-D, on organoids, induced pluripotent stem cells, non-mammalian organisms, microorganisms and rodent bioassays. Here we discuss some of the latest developments and pros and cons of these experimental systems used in mutational signature analysis. Integrative designs that bring together multiple exposure systems (in vitro, in vivo and in silico pan-cancer data mining) started emerging as powerful tools to identify robust mutational signatures of the tested cancer risk agents. We further propose that devising a new generation of cell-based models is warranted to streamline systematic testing of carcinogen effects on the cell genomes, while seeking to increasingly supplant animal with non-animal systems to address relevant ethical issues and accentuate the 3R principles. We conclude that the knowledge accumulating from the growing body of signature modelling investigations has considerable power to advance cancer etiology studies and to support cancer prevention efforts through streamlined characterization of cancer-causing agents and the recognition of their specific effects.
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Affiliation(s)
- Pamela N Melki
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France.
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98
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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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99
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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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100
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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: 62] [Impact Index Per Article: 15.5] [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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