1
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Aalam SMM, Nguyen LV, Ritting ML, Kannan N. Clonal tracking in cancer and metastasis. Cancer Metastasis Rev 2024; 43:639-656. [PMID: 37910295 DOI: 10.1007/s10555-023-10149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
The eradication of many cancers has proven challenging due to the presence of functionally and genetically heterogeneous clones maintained by rare cancer stem cells (CSCs), which contribute to disease progression, treatment refractoriness, and late relapse. The characterization of functional CSC activity has necessitated the development of modern clonal tracking strategies. This review describes viral-based and CRISPR-Cas9-based cellular barcoding, lineage tracing, and imaging-based approaches. DNA-based cellular barcoding technology is emerging as a powerful and robust strategy that has been widely applied to in vitro and in vivo model systems, including patient-derived xenograft models. This review also highlights the potential of these methods for use in the clinical and drug discovery contexts and discusses the important insights gained from such approaches.
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Affiliation(s)
| | - Long Viet Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Megan L Ritting
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
- Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA.
- Center for Regenerative Biotherapeutics, Mayo Clinic, Rochester, MN, USA.
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2
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Kumamoto T, Ohtaka-Maruyama C. Visualizing Cortical Development and Evolution: A Toolkit Update. Front Neurosci 2022; 16:876406. [PMID: 35495046 PMCID: PMC9039325 DOI: 10.3389/fnins.2022.876406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Visualizing the process of neural circuit formation during neurogenesis, using genetically modified animals or somatic transgenesis of exogenous plasmids, has become a key to decipher cortical development and evolution. In contrast to the establishment of transgenic animals, the designing and preparation of genes of interest into plasmids are simple and easy, dispensing with time-consuming germline modifications. These advantages have led to neuron labeling based on somatic transgenesis. In particular, mammalian expression plasmid, CRISPR-Cas9, and DNA transposon systems, have become widely used for neuronal visualization and functional analysis related to lineage labeling during cortical development. In this review, we discuss the advantages and limitations of these recently developed techniques.
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3
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Single-cell delineation of lineage and genetic identity in the mouse brain. Nature 2022; 601:404-409. [PMID: 34912118 PMCID: PMC8770128 DOI: 10.1038/s41586-021-04237-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 11/12/2021] [Indexed: 01/25/2023]
Abstract
During neurogenesis, mitotic progenitor cells lining the ventricles of the embryonic mouse brain undergo their final rounds of cell division, giving rise to a wide spectrum of postmitotic neurons and glia1,2. The link between developmental lineage and cell-type diversity remains an open question. Here we used massively parallel tagging of progenitors to track clonal relationships and transcriptomic signatures during mouse forebrain development. We quantified clonal divergence and convergence across all major cell classes postnatally, and found diverse types of GABAergic neuron that share a common lineage. Divergence of GABAergic clones occurred during embryogenesis upon cell-cycle exit, suggesting that differentiation into subtypes is initiated as a lineage-dependent process at the progenitor cell level.
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4
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Wang MY, Zhou Y, Lai GS, Huang Q, Cai WQ, Han ZW, Wang Y, Ma Z, Wang XW, Xiang Y, Fang SX, Peng XC, Xin HW. DNA barcode to trace the development and differentiation of cord blood stem cells (Review). Mol Med Rep 2021; 24:849. [PMID: 34643250 PMCID: PMC8524429 DOI: 10.3892/mmr.2021.12489] [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: 07/02/2021] [Accepted: 09/15/2021] [Indexed: 12/05/2022] Open
Abstract
Umbilical cord blood transplantation was first reported in 1980. Since then, additional research has indicated that umbilical cord blood stem cells (UCBSCs) have various advantages, such as multi-lineage differentiation potential and potent renewal activity, which may be induced to promote their differentiation into a variety of seed cells for tissue engineering and the treatment of clinical and metabolic diseases. Recent studies suggested that UCBSCs are able to differentiate into nerve cells, chondrocytes, hepatocyte-like cells, fat cells and osteoblasts. The culture of UCBSCs has developed from feeder-layer to feeder-free culture systems. The classical techniques of cell labeling and tracing by gene transfection and fluorescent dye and nucleic acid analogs have evolved to DNA barcode technology mediated by transposon/retrovirus, cyclization recombination-recombinase and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 strategies. DNA barcoding for cell development tracing has advanced to include single cells and single nucleic acid mutations. In the present study, the latest research findings on the development and differentiation, culture techniques and labeling and tracing of UCBSCs are reviewed. The present study may increase the current understanding of UCBSC biology and its clinical applications.
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Affiliation(s)
- Mo-Yu Wang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Yang Zhou
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Guang-Shun Lai
- Department of Digestive Medicine, People's Hospital of Lianjiang, Lianjiang, Guangdong 524400, P.R. China
| | - Qi Huang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Wen-Qi Cai
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Zi-Wen Han
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Yingying Wang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Zhaowu Ma
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Xian-Wang Wang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Ying Xiang
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Shu-Xian Fang
- State Key Laboratory of Respiratory Disease, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Xiao-Chun Peng
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
| | - Hong-Wu Xin
- Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, P.R. China
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5
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In Vivo Tracking of Hematopoietic Stem and Progenitor Cell Ontogeny by Cellular Barcoding. Methods Mol Biol 2021. [PMID: 34057730 DOI: 10.1007/978-1-0716-1425-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cellular barcoding is a powerful technique that allows for high-throughput mapping of the fate of single cells, notably hematopoietic stem and progenitor cells (HSPCs) after transplantation. Unique artificial DNA fragments, termed barcodes, are stably inserted into HSPCs using lentiviral transduction, making sure that each individual cell receives a single unique barcode. Barcoded HSPCs are transplanted into sublethally irradiated mice where they reconstitute the hematopoietic system through proliferation and differentiation. During this process, the barcode of each HSPC is inherited by all of its daughter cells and their subsequent mature hematopoietic cell progeny. After sorting mature hematopoietic cell subsets, their barcodes can be retrieved from genomic DNA through nested PCR and sequencing. Analysis of barcode sequencing results allows for determination of clonal relationships between the mature cells, that is, which cell types were produced by a single barcoded HSPC, as well as the heterogeneity of the initial HSPC population. Here, we give a detailed protocol of a complete HSPC cellular barcoding experiment, starting with barcode lentivirus production, isolation, transduction, and transplantation of HSPCs, isolation of target cells followed by PCR amplification and sequencing of DNA barcodes. Finally, we describe the basic filtering and analysis steps of barcode sequencing data to ensure high-quality results.
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6
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Figueres-Oñate M, Sánchez-González R, López-Mascaraque L. Deciphering neural heterogeneity through cell lineage tracing. Cell Mol Life Sci 2021; 78:1971-1982. [PMID: 33151389 PMCID: PMC7966193 DOI: 10.1007/s00018-020-03689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/10/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
Understanding how an adult brain reaches an appropriate size and cell composition from a pool of progenitors that proliferates and differentiates is a key question in Developmental Neurobiology. Not only the control of final size but also, the proper arrangement of cells of different embryonic origins is fundamental in this process. Each neural progenitor has to produce a precise number of sibling cells that establish clones, and all these clones will come together to form the functional adult nervous system. Lineage cell tracing is a complex and challenging process that aims to reconstruct the offspring that arise from a single progenitor cell. This tracing can be achieved through strategies based on genetically modified organisms, using either genetic tracers, transfected viral vectors or DNA constructs, and even single-cell sequencing. Combining different reporter proteins and the use of transgenic mice revolutionized clonal analysis more than a decade ago and now, the availability of novel genome editing tools and single-cell sequencing techniques has vastly improved the capacity of lineage tracing to decipher progenitor potential. This review brings together the strategies used to study cell lineages in the brain and the role they have played in our understanding of the functional clonal relationships among neural cells. In addition, future perspectives regarding the study of cell heterogeneity and the ontogeny of different cell lineages will also be addressed.
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Affiliation(s)
- María Figueres-Oñate
- Department of Molecular, Cellular and Development Neurobiology, Instituto Cajal-CSIC, 28002, Madrid, Spain
- Max Planck Research Unit for Neurogenetics, 60438, Frankfurt am Main, Germany
| | - Rebeca Sánchez-González
- Department of Molecular, Cellular and Development Neurobiology, Instituto Cajal-CSIC, 28002, Madrid, Spain
| | - Laura López-Mascaraque
- Department of Molecular, Cellular and Development Neurobiology, Instituto Cajal-CSIC, 28002, Madrid, Spain.
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7
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The art of lineage tracing: From worm to human. Prog Neurobiol 2020; 199:101966. [PMID: 33249090 DOI: 10.1016/j.pneurobio.2020.101966] [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: 08/01/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022]
Abstract
Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.
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8
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Tanaka A, Ishida S, Fuchigami T, Hayashi Y, Kuroda A, Ikenaka K, Fukazawa Y, Hitoshi S. Life-Long Neural Stem Cells Are Fate-Specified at an Early Developmental Stage. Cereb Cortex 2020; 30:6415-6425. [PMID: 32766673 DOI: 10.1093/cercor/bhaa200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
The origin and life-long fate of quiescent neural stem cells (NSCs) in the adult mammalian brain remain largely unknown. A few neural precursor cells in the embryonic brain elongate their cell cycle time and subsequently become quiescent postnatally, suggesting the possibility that life-long NSCs are selected at an early embryonic stage. Here, we utilized a GFP-expressing lentivirus to investigate the fate of progeny from individual lentivirus-infected NSCs by identifying the lentiviral integration site. Our data suggest that NSCs become specified to two or more lineages prior to embryonic day 13.5 in mice: one NSC lineage produces cells only for the cortex and another provides neurons to the olfactory bulb. The majority of neurosphere-forming NSCs in the adult brain are relatively dormant and generate very few cells, if any, in the olfactory bulb or cortex, and this NSC population could serve as a reservoir that is occasionally reactivated later in life.
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Affiliation(s)
- Aoi Tanaka
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Shohei Ishida
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Takahiro Fuchigami
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Yoshitaka Hayashi
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Anri Kuroda
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu 520-2192, Japan
| | - Kazuhiro Ikenaka
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
| | - Yugo Fukazawa
- Department of Histological and Physiological Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Seiji Hitoshi
- Department of Integrative Physiology, Shiga University of Medical Science, Otsu 520-2192, Japan.,Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
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9
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Development of Ependymal and Postnatal Neural Stem Cells and Their Origin from a Common Embryonic Progenitor. Cell Rep 2020; 27:429-441.e3. [PMID: 30970247 DOI: 10.1016/j.celrep.2019.01.088] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/05/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
The adult mouse brain contains an extensive neurogenic niche in the lateral walls of the lateral ventricles. This epithelium, which has a unique pinwheel organization, contains multiciliated ependymal (E1) cells and neural stem cells (B1). This postnatal germinal epithelium develops from the embryonic ventricular zone, but the lineage relationship between E1 and B1 cells remains unknown. Distinct subpopulations of radial glia (RG) cells in late embryonic and early postnatal development either expand their apical domain >11-fold to form E1 cells or retain small apical domains that coalesce into the centers of pinwheels to form B1 cells. Using independent methods of lineage tracing, we show that individual RG cells can give rise to clones containing E1 and B1 cells. This study reveals key developmental steps in the formation of the postnatal germinal niche and the shared cellular origin of E1 and B1 cells.
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10
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Marcy G, Raineteau O. Contributions of Single-Cell Approaches for Probing Heterogeneity and Dynamics of Neural Progenitors Throughout Life: Concise Review. Stem Cells 2019; 37:1381-1388. [DOI: 10.1002/stem.3071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 07/21/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Guillaume Marcy
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208; Bron France
- Neurogenetics Department; Ecole Pratique des Hautes Etudes, PSL Research University; Paris France
| | - Olivier Raineteau
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208; Bron France
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11
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Aalam SMM, Beer PA, Kannan N. Assays for functionally defined normal and malignant mammary stem cells. Adv Cancer Res 2019; 141:129-174. [PMID: 30691682 DOI: 10.1016/bs.acr.2018.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The discovery of rare, heterogeneous self-renewing stem cells with shared developmental and molecular features within epithelial components of mammary gland and breast cancers has provided a conceptual framework to understand cellular composition of these tissues and mechanisms that control their number. These normal mammary epithelial stem cells (MaSCs) and breast cancer stem cells (BCSCs) were identified and analyzed using transplant assays (namely mammary repopulating unit (MRU) assay, mammary tumor-initiating cell (TIC) assay), which reveal their latent ability to regenerate respective normal and malignant epithelial tissues with self-renewing units displaying hierarchical cellular differentiation over multiple generations in recipient mice. "Next-generation" methods using "barcoded" normal and malignant mammary cells, with the help of next-generation sequencing (NGS) technology, have revealed hidden complexity and heterogeneous growth potential of MaSCs and BCSCs. Several single markers or combinations of markers have been reported to prospectively enrich MaSCs and BCSCs. Such markers and the extent to which they enrich for MaSCs and BCSCs activity require a critical appraisal. Also, knowledge of the functional assays and their limitations and harmonious reporting of results is a prerequisite to improve our understanding of MaSCs and BCSCs. This chapter describes evolution of the concept of MaSCs and BCSCs, and specific methodologies to investigate them.
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Affiliation(s)
- Syed Mohammed Musheer Aalam
- Laboratory of Stem Cell and Cancer Biology, Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Philip Anthony Beer
- Laboratory of Stem Cell and Cancer Biology, Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States; Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Nagarajan Kannan
- Laboratory of Stem Cell and Cancer Biology, Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.
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12
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Xu M, Wang J, Guo X, Li T, Kuang X, Wu QF. Illumination of neural development by in vivo clonal analysis. CELL REGENERATION (LONDON, ENGLAND) 2018; 7:33-39. [PMID: 30671228 PMCID: PMC6326247 DOI: 10.1016/j.cr.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/22/2018] [Accepted: 09/18/2018] [Indexed: 01/22/2023]
Abstract
Single embryonic and adult neural stem cells (NSCs) are characterized by their self-renewal and differentiation potential. Lineage tracing via clonal analysis allows for specific labeling of a single NSC and tracking of its progeny throughout development. Over the past five decades, a plethora of clonal analysis methods have been developed in tandem with integration of chemical, genetic, imaging and sequencing techniques. Applications of these approaches have gained diverse insights into the heterogeneous behavior of NSCs, lineage relationships between cells, molecular regulation of fate specification and ontogeny of complex neural tissues. In this review, we summarize the history and methods of clonal analysis as well as highlight key findings revealed by single-cell lineage tracking of stem cells in developing and adult brains across different animal models.
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Affiliation(s)
- Mingrui Xu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jingjing Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xize Guo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tingting Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Kuang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing-Feng Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing 100101, China
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13
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Kebschull JM, Zador AM. Cellular barcoding: lineage tracing, screening and beyond. Nat Methods 2018; 15:871-879. [PMID: 30377352 DOI: 10.1038/s41592-018-0185-x] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/26/2018] [Indexed: 01/14/2023]
Abstract
Cellular barcoding is a technique in which individual cells are labeled with unique nucleic acid sequences, termed barcodes, so that they can be tracked through space and time. Cellular barcoding can be used to track millions of cells in parallel, and thus is an efficient approach for investigating heterogeneous populations of cells. Over the past 25 years, cellular barcoding has been used for fate mapping, lineage tracing and high-throughput screening, and has led to important insights into developmental biology and gene function. Driven by plummeting sequencing costs and the power of synthetic biology, barcoding is now expanding beyond traditional applications and into diverse fields such as neuroanatomy and the recording of cellular activity. In this review, we discuss the fundamental principles of cellular barcoding, including the underlying mathematics, and its applications in both new and established fields.
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Affiliation(s)
- Justus M Kebschull
- Watson School of Biological Sciences, Cold Spring Harbor, NY, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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14
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Cerrato V, Parmigiani E, Figueres-Oñate M, Betizeau M, Aprato J, Nanavaty I, Berchialla P, Luzzati F, de’Sperati C, López-Mascaraque L, Buffo A. Multiple origins and modularity in the spatiotemporal emergence of cerebellar astrocyte heterogeneity. PLoS Biol 2018; 16:e2005513. [PMID: 30260948 PMCID: PMC6178385 DOI: 10.1371/journal.pbio.2005513] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 10/09/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
The morphological, molecular, and functional heterogeneity of astrocytes is under intense scrutiny, but how this diversity is ontogenetically achieved remains largely unknown. Here, by quantitative in vivo clonal analyses and proliferation studies, we demonstrate that the major cerebellar astrocyte types emerge according to an unprecedented and remarkably orderly developmental program comprising (i) a time-dependent decline in both clone size and progenitor multipotency, associated with clone allocation first to the hemispheres and then to the vermis(ii) distinctive clonal relationships among astrocyte types, revealing diverse lineage potentials of embryonic and postnatal progenitors; and (iii) stereotyped clone architectures and recurrent modularities that correlate to layer-specific dynamics of postnatal proliferation/differentiation. In silico simulations indicate that the sole presence of a unique multipotent progenitor at the source of the whole astrogliogenic program is unlikely and rather suggest the involvement of additional committed components. Astrocytes are abundant cells of the brain essential to support and shape neuronal activity. They can be grouped in different subclasses based on their remarkable variety of morphologies, molecular profiles, and specialized functions. Although different astrocyte types likely display specialized interactions with distinct neuron categories, the different classes of astrocytes have only partially been unmasked. How astrocyte heterogeneity is ontogenetically achieved remains largely unknown. Here we approached this question by studying the development of the main astrocyte types of the cerebellum. The reconstruction of developmental lineages in the mouse embryo combined with proliferation studies and computational modeling demonstrate that cerebellar astrocyte types emerge according to an unprecedented and remarkably orderly developmental program. Embryonic progenitor cells produce either only a single astrocyte type or more types. These distinct astrocyte lineages display stereotyped architectures and recurrent modularities. Moreover, the generation of astrocytes follows a well-defined spatiotemporal pattern, defined by a time-dependent allocation of astrocytes to distinct cerebellar territories and an inside-out sequence of differentiation, coupled with a decline over time in both progenitor amplification and capability to produce distinct astrocyte types. These results provide the first evidence that an ontogenetic program, tightly regulated in space and time, determines astrocyte heterogeneity.
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Affiliation(s)
- Valentina Cerrato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
| | - Elena Parmigiani
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
| | - María Figueres-Oñate
- Department of Molecular, Cellular, and Developmental Neurobiology, Cajal Institute -CSIC-, Spanish National Research Council, Madrid, Spain
| | - Marion Betizeau
- Brain Research Institute, University of Zurich Irchel, Zurich, Switzerland
| | - Jessica Aprato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
| | - Ishira Nanavaty
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
| | - Paola Berchialla
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Federico Luzzati
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
| | - Claudio de’Sperati
- Laboratory of Action, Perception and Cognition, Vita-Salute San Raffaele University, Milan, Italy
- Experimental Psychology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura López-Mascaraque
- Department of Molecular, Cellular, and Developmental Neurobiology, Cajal Institute -CSIC-, Spanish National Research Council, Madrid, Spain
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, Turin, Italy
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy
- * E-mail:
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15
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Aranyossy T, Thielecke L, Glauche I, Fehse B, Cornils K. Genetic Barcodes Facilitate Competitive Clonal Analyses In Vivo. Hum Gene Ther 2018; 28:926-937. [PMID: 28847169 DOI: 10.1089/hum.2017.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Monitoring the fate of individual cell clones is an important task to better understand normal tissue regeneration, for example after hematopoietic stem cell (HSC) transplantation, but also cancerogenesis. Based on their integration into the host cell's genome, retroviral vectors are commonly used to stably mark target cells and their progeny. The development of genetic barcoding techniques has opened new possibilities to determine clonal composition and dynamics in great detail. A modular genetic barcode was recently introduced consisting of 32 variable positions (BC32) with a customized backbone, and its advantages were demonstrated with regard to barcode calling and quantification. The study presented applied the BC32 system in a complex in vivo situation, namely to analyze clonal reconstitution dynamics for HSC grafts consisting of up to three cell populations with distinguishable barcodes using different alpha- and lentiviral vectors. In a competitive transplantation setup, it was possible to follow the differently marked cell populations within individual animals. This enabled the clonal contribution of the different BC32 constructs during reconstitution and long-term hematopoiesis in the peripheral blood and the spatial distribution in bone marrow and spleen to be identified. Thus, it was demonstrated that the system allows the output of individually marked cells to be tracked in vivo and their influence on clonal dynamics to be analyzed. Successful application of the BC32 system in a complex, competitive in vivo situation provided proof-of-principle that its high complexity and the large Hamming distance between individual barcodes, combined with the easy customization, facilitate efficient and precise quantification, even without prior knowledge of individual barcode sequences. Importantly, simultaneous high-sensitivity analyses of different cell populations in single animals may significantly reduce numbers of animals required to investigate specific scientific questions in accordance with RRR principles. It is concluded that this BC32 system will be excellently suited for various research applications in regenerative medicine and cancer biology.
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Affiliation(s)
- Tim Aranyossy
- 1 Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf , Hamburg, Germany
| | - Lars Thielecke
- 2 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ingmar Glauche
- 2 Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Boris Fehse
- 1 Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf , Hamburg, Germany
| | - Kerstin Cornils
- 1 Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf , Hamburg, Germany .,3 Department of Pediatric Hematology and Oncology, Division Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf , Hamburg, Germany .,4 Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
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16
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Ma J, Shen Z, Yu YC, Shi SH. Neural lineage tracing in the mammalian brain. Curr Opin Neurobiol 2018; 50:7-16. [PMID: 29125960 PMCID: PMC5938148 DOI: 10.1016/j.conb.2017.10.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/08/2017] [Accepted: 10/17/2017] [Indexed: 01/05/2023]
Abstract
Delineating the lineage of neural cells that captures the progressive steps in their specification is fundamental to understanding brain development, organization, and function. Since the earliest days of embryology, lineage questions have been addressed with methods of increasing specificity, capacity, and resolution. Yet, a full realization of individual cell lineages remains challenging for complex systems. A recent explosion of technical advances in genome-editing and single-cell sequencing has enabled lineage analysis in an unprecedented scale, speed, and depth across different species. In this review, we discuss the application of available as well as future genetic labeling techniques for tracking neural lineages in vivo in the mammalian nervous system.
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Affiliation(s)
- Jian Ma
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhongfu Shen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Chun Yu
- Institute of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Song-Hai Shi
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, U.S.A
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17
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Carlone DL. Identifying Adult Stem Cells Using Cre‐Mediated Lineage Tracing. ACTA ACUST UNITED AC 2018; 36:5A.2.1-5A.2.18. [DOI: 10.1002/9780470151808.sc05a02s36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Diana L. Carlone
- Boston Children's Hospital, Harvard Medical School, Harvard Stem Cell Institute Boston Massachusetts
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18
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Pelkey KA, Chittajallu R, Craig MT, Tricoire L, Wester JC, McBain CJ. Hippocampal GABAergic Inhibitory Interneurons. Physiol Rev 2017; 97:1619-1747. [PMID: 28954853 DOI: 10.1152/physrev.00007.2017] [Citation(s) in RCA: 495] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/16/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022] Open
Abstract
In the hippocampus GABAergic local circuit inhibitory interneurons represent only ~10-15% of the total neuronal population; however, their remarkable anatomical and physiological diversity allows them to regulate virtually all aspects of cellular and circuit function. Here we provide an overview of the current state of the field of interneuron research, focusing largely on the hippocampus. We discuss recent advances related to the various cell types, including their development and maturation, expression of subtype-specific voltage- and ligand-gated channels, and their roles in network oscillations. We also discuss recent technological advances and approaches that have permitted high-resolution, subtype-specific examination of their roles in numerous neural circuit disorders and the emerging therapeutic strategies to ameliorate such pathophysiological conditions. The ultimate goal of this review is not only to provide a touchstone for the current state of the field, but to help pave the way for future research by highlighting where gaps in our knowledge exist and how a complete appreciation of their roles will aid in future therapeutic strategies.
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Affiliation(s)
- Kenneth A Pelkey
- Porter Neuroscience Center, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratories, University of Exeter, Exeter, United Kingdom; and Sorbonne Universités, UPMC University of Paris, INSERM, CNRS, Neurosciences Paris Seine-Institut de Biologie Paris Seine, Paris, France
| | - Ramesh Chittajallu
- Porter Neuroscience Center, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratories, University of Exeter, Exeter, United Kingdom; and Sorbonne Universités, UPMC University of Paris, INSERM, CNRS, Neurosciences Paris Seine-Institut de Biologie Paris Seine, Paris, France
| | - Michael T Craig
- Porter Neuroscience Center, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratories, University of Exeter, Exeter, United Kingdom; and Sorbonne Universités, UPMC University of Paris, INSERM, CNRS, Neurosciences Paris Seine-Institut de Biologie Paris Seine, Paris, France
| | - Ludovic Tricoire
- Porter Neuroscience Center, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratories, University of Exeter, Exeter, United Kingdom; and Sorbonne Universités, UPMC University of Paris, INSERM, CNRS, Neurosciences Paris Seine-Institut de Biologie Paris Seine, Paris, France
| | - Jason C Wester
- Porter Neuroscience Center, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratories, University of Exeter, Exeter, United Kingdom; and Sorbonne Universités, UPMC University of Paris, INSERM, CNRS, Neurosciences Paris Seine-Institut de Biologie Paris Seine, Paris, France
| | - Chris J McBain
- Porter Neuroscience Center, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratories, University of Exeter, Exeter, United Kingdom; and Sorbonne Universités, UPMC University of Paris, INSERM, CNRS, Neurosciences Paris Seine-Institut de Biologie Paris Seine, Paris, France
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19
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Sultan KT, Han Z, Zhang XJ, Xianyu A, Li Z, Huang K, Shi SH. Clonally Related GABAergic Interneurons Do Not Randomly Disperse but Frequently Form Local Clusters in the Forebrain. Neuron 2017; 92:31-44. [PMID: 27710787 DOI: 10.1016/j.neuron.2016.09.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 11/16/2022]
Abstract
Progenitor cells in the medial ganglionic eminence (MGE) and preoptic area (PoA) give rise to GABAergic inhibitory interneurons that are distributed in the forebrain, largely in the cortex, hippocampus, and striatum. Two previous studies suggest that clonally related interneurons originating from individual MGE/PoA progenitors frequently form local clusters in the cortex. However, Mayer et al. and Harwell et al. recently argued that MGE/PoA-derived interneuron clones disperse widely and populate different forebrain structures. Here, we report further analysis of the spatial distribution of clonally related interneurons and demonstrate that interneuron clones do not non-specifically disperse in the forebrain. Around 70% of clones are restricted to one brain structure, predominantly the cortex. Moreover, the regional distribution of clonally related interneurons exhibits a clear clustering feature, which cannot occur by chance from a random diffusion. These results confirm that lineage relationship influences the spatial distribution of inhibitory interneurons in the forebrain. This Matters Arising paper is in response to Harwell et al. (2015) and Mayer et al. (2015), published in Neuron. See also the response by Turrero García et al. (2016) and Mayer et al. (2016), published in this issue.
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Affiliation(s)
- Khadeejah T Sultan
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Neuroscience Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Zhi Han
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA; College of Software, Nankai University, Tianjin 300071, PR China
| | - Xin-Jun Zhang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Anjin Xianyu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Physiology, Biophysics, and Systems Biology Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Zhizhong Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Kun Huang
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA.
| | - Song-Hai Shi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Neuroscience Graduate Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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20
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Turrero García M, Harwell CC. Radial glia in the ventral telencephalon. FEBS Lett 2017; 591:3942-3959. [PMID: 28862741 DOI: 10.1002/1873-3468.12829] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/31/2022]
Abstract
The ventral telencephalon is the developmental origin of the basal ganglia and the source of neuronal and glial cells that integrate into developing circuits in other areas of the brain. Radial glia in the embryonic subpallium give rise to an enormous diversity of mature cell types, either directly or through other transit-amplifying progenitors. Here, we review current knowledge about these subpallial neural stem cells and their progeny, focusing on the period of neurogenesis. We describe their cell biological features and the extrinsic and intrinsic molecular codes that guide their fate specification in defined temporal and spatial sequences. We also discuss the role of clonal lineage in the organization and specification of mature neurons.
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Affiliation(s)
| | - Corey C Harwell
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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21
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Woodworth MB, Girskis KM, Walsh CA. Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat Rev Genet 2017; 18:230-244. [PMID: 28111472 PMCID: PMC5459401 DOI: 10.1038/nrg.2016.159] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Resolving lineage relationships between cells in an organism is a fundamental interest of developmental biology. Furthermore, investigating lineage can drive understanding of pathological states, including cancer, as well as understanding of developmental pathways that are amenable to manipulation by directed differentiation. Although lineage tracking through the injection of retroviral libraries has long been the state of the art, a recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible. In this Review, we discuss these techniques for cell lineage tracking, with attention both to those that trace lineage forwards from experimental labelling, and those that trace backwards across the life history of an organism.
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Affiliation(s)
- Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Kelly M Girskis
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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22
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Figueres-Oñate M, García-Marqués J, López-Mascaraque L. UbC-StarTrack, a clonal method to target the entire progeny of individual progenitors. Sci Rep 2016; 6:33896. [PMID: 27654510 PMCID: PMC5031994 DOI: 10.1038/srep33896] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/05/2016] [Indexed: 01/02/2023] Open
Abstract
Clonal cell analysis defines the potential of single cells and the diversity they can produce. To achieve this, we have developed a novel adaptation of the genetic tracing strategy, UbC-StarTrack, which attributes a specific and unique color-code to single neural precursors, allowing all their progeny to be tracked. We used integrable fluorescent reporters driven by a ubiquitous promoter in PiggyBac-based vectors to achieve inheritable and stable clonal cell labeling. In addition, coupling this to an inducible Cre-LoxP system avoids the expression of non-integrated reporters. To assess the utility of this system, we first analyzed images of combinatorial expression of fluorescent reporters in transfected cells and their progeny. We also validated the efficiency of the UbC-StarTrack to trace cell lineages through in vivo, in vitro and ex vivo strategies. Finally, progenitors located in the lateral ventricles were targeted at embryonic or postnatal stages to determine the diversity of neurons and glia they produce, and their clonal relationships. In this way we demonstrate that UbC-StarTrack can be used to identify all the progeny of a single cell and that it can be employed in a wide range of contexts.
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23
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Weber TS, Perié L, Duffy KR. Inferring average generation via division-linked labeling. J Math Biol 2016; 73:491-523. [PMID: 26733310 DOI: 10.1007/s00285-015-0963-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 10/01/2015] [Indexed: 12/30/2022]
Abstract
For proliferating cells subject to both division and death, how can one estimate the average generation number of the living population without continuous observation or a division-diluting dye? In this paper we provide a method for cell systems such that at each division there is an unlikely, heritable one-way label change that has no impact other than to serve as a distinguishing marker. If the probability of label change per cell generation can be determined and the proportion of labeled cells at a given time point can be measured, we establish that the average generation number of living cells can be estimated. Crucially, the estimator does not depend on knowledge of the statistics of cell cycle, death rates or total cell numbers. We explore the estimator's features through comparison with physiologically parameterized stochastic simulations and extrapolations from published data, using it to suggest new experimental designs.
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Affiliation(s)
- Tom S Weber
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Leïla Perié
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland.
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24
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Bystrykh LV, Belderbos ME. Clonal Analysis of Cells with Cellular Barcoding: When Numbers and Sizes Matter. Methods Mol Biol 2016; 1516:57-89. [PMID: 27044044 DOI: 10.1007/7651_2016_343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cellular barcoding is a recently rediscovered tool to trace the clonal output of individual cells with genetically distinct and heritable DNA sequences. Each year a few dozens of papers are published using the cellular barcoding technique. Those publications largely focus on mutually related issues, namely: counting cells capable of clonal proliferation and expansion, monitoring clonal dynamics in time, tracing the origin of differentiated cells, characterizing the differentiation potential of stem cells and similar topics. Apart from their biological content, claims and conclusions, these studies show remarkable diversity in technical aspects of the barcoding method and sometimes in major conclusions. Although a diversity of approaches is quite usual in data analysis, deviant handling of barcode data might directly affect experimental results and their biological interpretation. Here, we will describe typical challenges and caveats in cellular barcoding publications available so far.
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Affiliation(s)
- Leonid V Bystrykh
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Building 3226, Groningen, 9713, AV, The Netherlands.
| | - Mirjam E Belderbos
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Building 3226, Groningen, 9713, AV, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
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25
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Abstract
In select areas of the brain, neural stem cells produce new neurons throughout life. An elegant new study in this issue of Cell reveals the origins of a stem cell population that persists into adulthood and uncovers a surprising relationship between neurons born in the mature brain and those generated early in development.
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Affiliation(s)
- Mazen A Kheirbek
- Department of Psychiatry, Columbia University, New York, NY 10032, USA; Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA.
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26
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Fuentealba LC, Rompani SB, Parraguez JI, Obernier K, Romero R, Cepko CL, Alvarez-Buylla A. Embryonic Origin of Postnatal Neural Stem Cells. Cell 2015; 161:1644-55. [PMID: 26091041 DOI: 10.1016/j.cell.2015.05.041] [Citation(s) in RCA: 380] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 03/08/2015] [Accepted: 05/04/2015] [Indexed: 11/18/2022]
Abstract
Adult neural stem/progenitor (B1) cells within the walls of the lateral ventricles generate different types of neurons for the olfactory bulb (OB). The location of B1 cells determines the types of OB neurons they generate. Here we show that the majority of mouse B1 cell precursors are produced between embryonic days (E) 13.5 and 15.5 and remain largely quiescent until they become reactivated postnatally. Using a retroviral library carrying over 100,000 genetic tags, we found that B1 cells share a common progenitor with embryonic cells of the cortex, striatum, and septum, but this lineage relationship is lost before E15.5. The regional specification of B1 cells is evident as early as E11.5 and is spatially linked to the production of neurons that populate different areas of the forebrain. This study reveals an early embryonic regional specification of postnatal neural stem cells and the lineage relationship between them and embryonic progenitor cells.
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Affiliation(s)
- Luis C Fuentealba
- Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Santiago B Rompani
- Departments of Genetics and Ophthalmology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jose I Parraguez
- Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Kirsten Obernier
- Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Ricardo Romero
- Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Constance L Cepko
- Departments of Genetics and Ophthalmology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Arturo Alvarez-Buylla
- Department of Neurological Surgery and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.
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27
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Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries. Neuron 2015; 87:989-98. [PMID: 26299473 DOI: 10.1016/j.neuron.2015.07.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/29/2015] [Accepted: 07/15/2015] [Indexed: 02/06/2023]
Abstract
The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute.
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28
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Peikon ID, Gizatullina DI, Zador AM. In vivo generation of DNA sequence diversity for cellular barcoding. Nucleic Acids Res 2014; 42:e127. [PMID: 25013177 PMCID: PMC4176322 DOI: 10.1093/nar/gku604] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/08/2014] [Accepted: 06/23/2014] [Indexed: 11/14/2022] Open
Abstract
Heterogeneity is a ubiquitous feature of biological systems. A complete understanding of such systems requires a method for uniquely identifying and tracking individual components and their interactions with each other. We have developed a novel method of uniquely tagging individual cells in vivo with a genetic 'barcode' that can be recovered by DNA sequencing. Our method is a two-component system comprised of a genetic barcode cassette whose fragments are shuffled by Rci, a site-specific DNA invertase. The system is highly scalable, with the potential to generate theoretical diversities in the billions. We demonstrate the feasibility of this technique in Escherichia coli. Currently, this method could be employed to track the dynamics of populations of microbes through various bottlenecks. Advances of this method should prove useful in tracking interactions of cells within a network, and/or heterogeneity within complex biological samples.
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Affiliation(s)
- Ian D Peikon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Anthony M Zador
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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29
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García-Moreno F, Vasistha NA, Begbie J, Molnár Z. CLoNe is a new method to target single progenitors and study their progeny in mouse and chick. Development 2014; 141:1589-98. [PMID: 24644261 PMCID: PMC3957378 DOI: 10.1242/dev.105254] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/02/2014] [Indexed: 01/20/2023]
Abstract
Cell lineage analysis enables us to address pivotal questions relating to: the embryonic origin of cells and sibling cell relationships in the adult body; the contribution of progenitors activated after trauma or disease; and the comparison across species in evolutionary biology. To address such fundamental questions, several techniques for clonal labelling have been developed, each with its shortcomings. Here, we report a novel method, CLoNe that is designed to work in all vertebrate species and tissues. CLoNe uses a cocktail of labelling, targeting and transposition vectors that enables targeting of specific subpopulations of progenitor types with a combination of fluorophores resulting in multifluorescence that describes multiple clones per specimen. Furthermore, transposition into the genome ensures the longevity of cell labelling. We demonstrate the robustness of this technique in mouse and chick forebrain development, and show evidence that CLoNe will be broadly applicable to study clonal relationships in different tissues and species.
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Affiliation(s)
- Fernando García-Moreno
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Navneet A. Vasistha
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Jo Begbie
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK
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30
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Jiang H, Wang L, Beier KT, Cepko CL, Fekete DM, Brigande JV. Lineage analysis of the late otocyst stage mouse inner ear by transuterine microinjection of a retroviral vector encoding alkaline phosphatase and an oligonucleotide library. PLoS One 2013; 8:e69314. [PMID: 23935981 PMCID: PMC3723842 DOI: 10.1371/journal.pone.0069314] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/12/2013] [Indexed: 12/23/2022] Open
Abstract
The mammalian inner ear subserves the special senses of hearing and balance. The auditory and vestibular sensory epithelia consist of mechanically sensitive hair cells and associated supporting cells. Hearing loss and balance dysfunction are most frequently caused by compromise of hair cells and/or their innervating neurons. The development of gene- and cell-based therapeutics will benefit from a thorough understanding of the molecular basis of patterning and cell fate specification in the mammalian inner ear. This includes analyses of cell lineages and cell dispersals across anatomical boundaries (such as sensory versus nonsensory territories). The goal of this study was to conduct retroviral lineage analysis of the embryonic day 11.5(E11.5) mouse otic vesicle. A replication-defective retrovirus encoding human placental alkaline phosphatase (PLAP) and a variable 24-bp oligonucleotide tag was microinjected into the E11.5 mouse otocyst. PLAP-positive cells were microdissected from cryostat sections of the postnatal inner ear and subjected to nested PCR. PLAP-positive cells sharing the same sequence tag were assumed to have arisen from a common progenitor and are clonally related. Thirty five multicellular clones consisting of an average of 3.4 cells per clone were identified in the auditory and vestibular sensory epithelia, ganglia, spiral limbus, and stria vascularis. Vestibular hair cells in the posterior crista were related to one another, their supporting cells, and nonsensory epithelial cells lining the ampulla. In the organ of Corti, outer hair cells were related to a supporting cell type and were tightly clustered. By contrast, spiral ganglion neurons, interdental cells, and Claudius' cells were related to cells of the same type and could be dispersed over hundreds of microns. These data contribute new information about the developmental potential of mammalian otic precursors in vivo.
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Affiliation(s)
- Han Jiang
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
- Jilin Province Key Laboratory of Animal Embryo Engineering, College of Animal Science and Veterinary Medicine, Jilin University, Changchun, China
| | - Lingyan Wang
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Kevin T. Beier
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Constance L. Cepko
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donna M. Fekete
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - John V. Brigande
- Department of Otolaryngology, Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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31
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Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X. Nanotools for neuroscience and brain activity mapping. ACS NANO 2013; 7:1850-66. [PMID: 23514423 PMCID: PMC3665747 DOI: 10.1021/nn4012847] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.
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Affiliation(s)
- A. Paul Alivisatos
- Department of Chemistry, University of California, Berkeley, California 94720, and Lawrence Berkeley Laboratory, Berkeley, California 94720-1460
| | - Anne M. Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Psychiatry, and Semel Institute for Neuroscience & Human Behavior, Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095
| | - Edward S. Boyden
- Media Laboratory, Department of Biological Engineering, Brain and Cognitive Sciences, and McGovern Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | | | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University, Boston, Massachusetts 02115
| | - Karl Deisseroth
- Howard Hughes Medical Institute, Stanford University, Stanford California 94305
- Departments of Bioengineering and Psychiatry, Stanford University, Stanford California 94305
| | - John P. Donoghue
- Department of Neuroscience, Division of Engineering, Department of Computer Science, Brown University, Providence, Rhode Island 02912
| | - Scott E. Fraser
- Departments of Biological Sciences, Biomedical Engineering, Physiology and Biophysics, Stem Cell Biology and Regenerative Medicine, and Pediatrics, Radiology and Ophthalmology, University of Southern California, Los Angeles, California 90089
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia 20147
| | - Sotiris Masmanidis
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Neurobiology, University of California, Los Angeles, California 90095
- Address correspondence to , , ,
| | - Paul L. McEuen
- Department of Physics, Laboratory of Atomic and Solid State Physics, and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853
| | - Arto V. Nurmikko
- Department of Physics and Division of Engineering, Brown University, Providence, Rhode Island 02912
| | - Hongkun Park
- Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138
| | - Darcy S. Peterka
- Howard Hughes Medical Institute and Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Clay Reid
- Allen Institute for Brain Science, Seattle, Washington 98103
| | - Michael L. Roukes
- Kavli Nanoscience Institute, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Departments of Physics, Applied Physics, and Bioengineering, California Institute of Technology, MC 149-33, Pasadena, California 91125
| | - Axel Scherer
- Kavli Nanoscience Institute, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Departments of Electrical Engineering, Applied Physics, and Physics, California Institute of Technology, MC 149-33, Pasadena, California 91125
- Address correspondence to , , ,
| | - Mark Schnitzer
- Howard Hughes Medical Institute, Stanford University, Stanford California 94305
- Departments of Applied Physics and Biology, James H. Clark Center, Stanford University, Stanford, California 94305
| | - Terrence J. Sejnowski
- Howard Hughes Medical Institute, Computational Neurobiology Laboratory, Salk Institute, La Jolla, California 92037, and Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, New York 10027
| | - Doris Tsao
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Gina Turrigiano
- Department of Biology and Center for Complex Systems, Brandeis University, Waltham, Massachusetts 02254
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095
- Department of Chemistry & Biochemistry, Department of Materials Science & Engineering, University of California, Los Angeles, California 90095
- Address correspondence to , , ,
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853
| | - Rafael Yuste
- Howard Hughes Medical Institute and Department of Biological Sciences, Columbia University, New York, New York 10027
- Kavli Institute for Brain Science, Columbia University, New York, New York 10027
- Address correspondence to , , ,
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Departments of Chemistry and Chemical Biology and Physics, Harvard University, Cambridge, Massachusetts 02138
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Abstract
Reconstructing the lineage of cells is central to understanding development and is now also an important issue in stem cell research. Technological advances in genetically engineered permanent cell labeling, together with a multiplicity of fluorescent markers and sophisticated imaging, open new possibilities for prospective and retrospective clonal analysis.
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Affiliation(s)
- Margaret E Buckingham
- Molecular Genetics of Development Unit, CNRS URA 2578, Department of Developmental Biology, Institut Pasteur, Paris, France.
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34
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Bower DV, Sato Y, Lansford R. Dynamic lineage analysis of embryonic morphogenesis using transgenic quail and 4D multispectral imaging. Genesis 2011; 49:619-43. [PMID: 21509927 DOI: 10.1002/dvg.20754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/27/2011] [Accepted: 03/28/2011] [Indexed: 12/17/2022]
Abstract
We describe the development of transgenic quail that express various fluorescent proteins in targeted manners and their use as a model system that integrates advanced imaging approaches with conventional and emerging molecular genetics technologies. We also review the progression and complications of past fate mapping techniques that led us to generate transgenic quail, which permit dynamic imaging of amniote embryogenesis with unprecedented subcellular resolution.
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Affiliation(s)
- Danielle V Bower
- Department of Biology and the Biological Imaging Center, California Institute of Technology, Pasadena, California 91125, USA
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Beier KT, Samson MES, Matsuda T, Cepko CL. Conditional expression of the TVA receptor allows clonal analysis of descendents from Cre-expressing progenitor cells. Dev Biol 2011; 353:309-20. [PMID: 21397594 DOI: 10.1016/j.ydbio.2011.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/29/2011] [Accepted: 03/04/2011] [Indexed: 12/26/2022]
Abstract
An understanding of the number and types of progeny produced by progenitor cells during development provides a foundation for studies of when and where cell fate determination takes place. Lineal relationships can be revealed by the identification of descendents of cells that express a recombinase, such as Cre or Flp. This method provides data concerning gene expression history, but does not provide clonal resolution among the descendents. An alternative method employs retroviral labeling, which permits the identification of clones, but does not allow for the tracking of gene expression history. Here we report a combination of these methods to circumvent each method's limitations. By employing the specificity of Cre expression, and by selecting only a subset of cells with a Cre history for retroviral infection, clones with a gene expression history can be labeled. The method utilizes a conditional allele of the avian tumor virus receptor A (TVA), which allows infection of mouse cells following Cre activity, with mammalian retroviral vectors pseudotyped with the ASLV-A envelope glycoprotein (EnvA). We quantified the efficiency and specificity of this system in vivo and in vitro. We also generated a series of retroviral vectors encoding a variety of histochemical and fluorescent reporter genes that enable the tracking of mixtures of clones, thus enabling better resolution of clonal boundaries. This method and new vectors can be used to further our understanding of the gene expression patterns of progenitor cells that make particular daughter cells, as well as provide a platform for manipulating identified subsets of developing cells.
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Affiliation(s)
- Kevin T Beier
- Department of Genetics, Department of Ophthamology, Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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36
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Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, DiMaio D. Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering. Protein Eng Des Sel 2011; 24:311-20. [PMID: 21149273 PMCID: PMC3038463 DOI: 10.1093/protein/gzq112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 10/29/2010] [Accepted: 11/14/2010] [Indexed: 11/12/2022] Open
Abstract
Genetic selection from libraries expressing proteins with randomized amino acid segments is a powerful approach to identify proteins with novel biological activities. Here, we assessed the utility of deep DNA sequencing to characterize the composition, diversity, size and stability of such randomized libraries. We used 454 pyrosequencing to sequence a retroviral library expressing small proteins with randomized transmembrane domains. Despite the potential for unintended random mutagenesis during its construction, the overall hydrophobic composition and diversity of the proteins encoded by the sequenced library conformed well to its design. In addition, our sequencing results allowed us to calculate a more accurate estimate of the number of different proteins encoded by the library and suggested that the traditional methods for estimating the size of randomized libraries may overestimate their true size. Our results further demonstrated that no significant genetic bottlenecks exist in the methods used to express complex retrovirus libraries in mammalian cells and recover library sequences from these cells. These findings suggest that deep sequencing can be used to determine the quality and content of other libraries with randomized segments and to follow individual sequences during selection.
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Affiliation(s)
- Sara A. Marlatt
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 300 George Street, 8th Floor, New Haven, CT 06511-6624, USA
- Keck Biotechnology Resource Laboratory, Yale University, 300 George Street, Box 201, New Haven, CT 06511, USA
| | - Tobin J. Cammett
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Present address: Alexion Pharmaceuticals, 352 Knotter Drive, Cheshire, CT 06410, USA
| | - Gregory Korbel
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Present address: The Wharton School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Yale Comprehensive Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, PO Box 208005, New Haven, CT 06520-8005, USA
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, 300 George Street, 8th Floor, New Haven, CT 06511-6624, USA
- Department of Therapeutic Radiology, Yale School of Medicine, PO Box 208040, New Haven, CT 06520-8040, USA
- Yale Comprehensive Cancer Center, PO Box 208028, New Haven, CT 06520-8028, USA
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37
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38
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Abstract
Understanding how cells are assembled in three dimensions to generate an organ, or a whole organism, is a pivotal question in developmental biology. Similarly, it is critical to understand how adult stem cells integrate into an existing organ during regeneration or in response to injury. Key to discovering the answers to these questions is being able to study the various behaviors of distinct cell types during development or regeneration. Fate mapping techniques are fundamental to studying cell behaviors such as proliferation, movement, and lineage segregation, as the techniques allow precursor cells to be marked and their descendants followed and characterized over time. The generation of transgenic mice, combined with the use of site-specific recombinases (SSR) in the mouse genome, has provided a means to develop powerful genetic fate mapping approaches. A key advantage of genetic fate mapping is that it allows cells to be genetically marked, and therefore the mark is transmitted to all the descendants of the initially marked cells. By making modifications to the SSRs that render their enzymatic activity inducible, and the development of an assortment of reporter alleles for marking cells, increasingly sophisticated genetic fate mapping studies can be performed. In this chapter, we review the four main genetic fate mapping methods that utilize intrachromosomal recombination to mark cells (cumulative, inducible, clonal, and intersectional) and one interchromosomal method, the tools required to carry out each approach, and the practical considerations that have to be taken into account before embarking on each type of genetic fate mapping study.
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Affiliation(s)
- Emilie Legué
- Memorial Sloan-Kettering Cancer Center, New York, USA
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39
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Postinjury niches induce temporal shifts in progenitor fates to direct lesion repair after spinal cord injury. J Neurosci 2009; 29:6722-33. [PMID: 19458241 DOI: 10.1523/jneurosci.4538-08.2009] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Progenitors that express NG2-proteoglycan are the predominant self-renewing cells within the CNS. NG2 progenitors replenish oligodendrocyte populations within the intact stem cell niche, and cycling NG2 cells are among the first cells to react to CNS insults. We investigated the role of NG2 progenitors after spinal cord injury and how bone morphogen protein signals remodel the progressive postinjury (PI) niche. Progeny labeled by an NG2-specific reporter virus undergo a coordinated shift in differentiation profile. NG2 progeny born 24 h PI produce scar-forming astrocytes and transient populations of novel phagocytic astrocytes shown to contain denatured myelin within cathepsin-D-labeled endosomes, but NG2 progenitors born 7 d PI differentiate into oligodendrocytes and express myelin on processes that wrap axons. Analysis of spinal cord mRNA shows a temporal shift in the niche transcriptome of ligands that affect PI remodeling and direct progenitor differentiation. We conclude that NG2 progeny are diverse lineages that obey progressive cues after trauma to replenish the injured niche.
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40
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Carlone DL. Functional analysis of adult stem cells using Cre-mediated lineage tracing. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2009; Chapter 5:Unit 5A.2. [PMID: 19455543 DOI: 10.1002/9780470151808.sc05a02s9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Lineage-tracing has been used for decades to establish cell fate maps during development. Recently, with the advent of genetic lineage-tracing techniques (employing Cre-lox recombination), it has been possible to permanently mark progenitor/stem cell populations within somatic tissues. In addition, pulse-chase studies have shown that only stem cells are capable of producing labeled progeny after an extensive period of chase. This unit focuses on the protocols used to target putative adult stem cells in vivo. Using these techniques, one should be able to functionally confirm or deny the stem cell capacity of a given cell population.
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Affiliation(s)
- Diana L Carlone
- Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts
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41
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Gordon CT, Rodda FA, Farlie PG. The RCAS retroviral expression system in the study of skeletal development. Dev Dyn 2009; 238:797-811. [DOI: 10.1002/dvdy.21907] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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42
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Satoh T, Fekete DM. Lineage analysis of inner ear cells using genomic tags for clonal identification. Methods Mol Biol 2009; 493:47-63. [PMID: 18839341 DOI: 10.1007/978-1-59745-523-7_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
To understand the mechanisms of development of the inner ear, it is important to know the lineal relationships among the different cell types and the migrational boundaries of individual clones within the inner ear. This chapter details the basic methods for performing lineage analysis of the inner ear using replication-defective retroviral vectors in chicken embryos. Protocols are provided for generating avian retroviruses pseudotyped with vesicular stomatitis virus (VSV) envelopes to improve infectivity in early embryos. Moreover, we include the pioneering methods of the Cepko laboratory, whereby a library of DNA tags was developed to allow clonal relationships to be confirmed by PCR amplification and sequencing of the tag in dispersed clonal progeny. By varying the site and time of viral delivery, these methods are appropriate to study cell lineages in other tissues of the developing chicken.
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Affiliation(s)
- Takunori Satoh
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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43
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Schepers K, Swart E, van Heijst JWJ, Gerlach C, Castrucci M, Sie D, Heimerikx M, Velds A, Kerkhoven RM, Arens R, Schumacher TNM. Dissecting T cell lineage relationships by cellular barcoding. ACTA ACUST UNITED AC 2008; 205:2309-18. [PMID: 18809713 PMCID: PMC2556794 DOI: 10.1084/jem.20072462] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
T cells, as well as other cell types, are composed of phenotypically and functionally distinct subsets. However, for many of these populations it is unclear whether they develop from common or separate progenitors. To address such issues, we developed a novel approach, termed cellular barcoding, that allows the dissection of lineage relationships. We demonstrate that the labeling of cells with unique identifiers coupled to a microarray-based detection system can be used to analyze family relationships between the progeny of such cells. To exemplify the potential of this technique, we studied migration patterns of families of antigen-specific CD8+ T cells in vivo. We demonstrate that progeny of individual T cells rapidly seed independent lymph nodes and that antigen-specific CD8+ T cells present at different effector sites are largely derived from a common pool of precursors. These data show how locally primed T cells disperse and provide a technology for kinship analysis with wider utility.
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Affiliation(s)
- Koen Schepers
- Division of Immunology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
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44
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Pearse RV, Scherz PJ, Campbell JK, Tabin CJ. A cellular lineage analysis of the chick limb bud. Dev Biol 2007; 310:388-400. [PMID: 17888899 PMCID: PMC2940718 DOI: 10.1016/j.ydbio.2007.08.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 08/01/2007] [Accepted: 08/01/2007] [Indexed: 10/23/2022]
Abstract
The chick limb bud has been used as a model system for studying pattern formation and tissue development for more than 50 years. However, the lineal relationships among the different cell types and the migrational boundaries of individual cells within the limb mesenchyme have not been explored. We have used a retroviral lineage analysis system to track the fate of single limb bud mesenchymal cells at different times in early limb development. We find that progenitor cells labeled at stage 19-22 can give rise to multiple cell types including clones containing cells of all five of the major lateral plate mesoderm-derived tissues (cartilage, perichondrium, tendon, muscle connective tissue, and dermis). There is a bias, however, such that clones are more likely to contain the cell types of spatially adjacent tissues such as cartilage/perichondrium and tendon/muscle connective tissue. It has been recently proposed that distinct proximodistal segments are established early in limb development; however our analysis suggests that there is not a strict barrier to cellular migration along the proximodistal axis in the early stage 19-22 limb buds. Finally, our data indicate the presence of a dorsal/ventral boundary established by stage 16 that is inhibitory to cellular mixing. This boundary is demarcated by the expression of the LIM-homeodomain factor lmx1b.
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Affiliation(s)
- R V Pearse
- Department of Genetics NRB 360, Boston, MA 02115, USA
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45
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Satoh T, Fekete DM. Clonal analysis of the relationships between mechanosensory cells and the neurons that innervate them in the chicken ear. Development 2005; 132:1687-97. [PMID: 15743876 DOI: 10.1242/dev.01730] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In vertebrates, hair-cell-bearing mechanosensory organs and the neurons that innervate them share a common placodal origin. In the inner ear, the peripheral neurons for both auditory and vestibular systems emigrate from the otic placode as neuroblasts, and divide, differentiate and innervate only one of six to eight distinct sensory organs. How these neurons find their correct target is unknown, although one suggestion is that they synapse with clonally related cells. To test this idea for both the middle and inner ears of chicken embryos, lineage analysis was initiated at the time of neuroblast delamination by labeling progenitors with replication-defective retroviruses. The vast majority (89%) of clones were restricted to a single anatomical subdivision of the sensory periphery or its associated ganglia, indicating limited clonal dispersion. Among the remaining clones, we found evidence of a shared neurosensory lineage in the middle ear. Likewise, in the inner ear, neurons could be related to cells of the otic epithelium, although the latter cells were not widely distributed. Rather, they were restricted to a region in or near the utricular macula. None of the other seven sensory organs was related to the ganglion neurons, suggesting that a common lineage between neurons and their targets is not a general mechanism of establishing synaptic connections in the inner ear. This conclusion is further strengthened by finding a shared lineage between the vestibular and acoustic ganglia, revealing the presence of a common progenitor for the two functional classes of neurons.
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Affiliation(s)
- Takunori Satoh
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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46
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Goings GE, Sahni V, Szele FG. Migration patterns of subventricular zone cells in adult mice change after cerebral cortex injury. Brain Res 2004; 996:213-26. [PMID: 14697499 DOI: 10.1016/j.brainres.2003.10.034] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The subventricular zone (SVZ) generates the largest number of migratory cells in the adult brain. SVZ neuroblasts migrate to the olfactory bulbs (OB) in the adult, whereas during development, SVZ cells migrate into many adjacent nuclei. Previously, we showed that cerebral cortex injury in the adult causes molecular and cellular changes which may recapitulate the developmental migratory directions. Consistent with this, growth factors, as well as models of illness or injury can cause adult SVZ cells to migrate into non-olfactory bulb nuclei. Here, we tested the hypothesis that cerebral cortex injury in the adult mouse induces changes in migration, by labeling adult SVZ cells with a retroviral vector and examining the distribution of cells 4 days and 3 weeks later. Four days after cortical lesions, disproportionately fewer retrovirally-labeled cells had migrated to the olfactory bulb in lesioned mice than in controls. Conversely, the number of cells found in non-olfactory bulb regions (primarily the area of the lesion and the corpus callosum) was increased in lesioned mice. The morphology of these emigrated cells suggested that they were differentiating into glial cells. Three weeks after cortical injury, the majority of retrovirally-labeled cells in both groups of mice had migrated into the granule and periglomerular layers of the olfactory bulb. At 3 weeks, we still observed retrovirally-labeled glial cells in the corpus callosum and in the area of the injury in lesioned mice. These results suggest that cortical lesions cause a transient change in migration patterns of SVZ progeny, which is characterized by decreases in migration to the olfactory bulb but increased migration towards the injury. Our studies also suggest that cortical lesions induce the production of new glial cells which survive for at least 3 weeks after injury. The data support the concept that in the adult, SVZ cells can generate progeny that migrate towards injured areas and thus potentially be harnessed for neural repair.
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Affiliation(s)
- Gwendolyn E Goings
- CMIER Neurobiology Program, Department of Pediatrics, 2300 Children's Plaza, No. 209, Children's Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60614-3394, USA
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47
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48
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Ishii Y, Reese DE, Mikawa T. Somatic transgenesis using retroviral vectors in the chicken embryo. Dev Dyn 2004; 229:630-42. [PMID: 14991718 DOI: 10.1002/dvdy.10484] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The avian embryo is an excellent model system for experimental studies because of its accessibility and ease of microsurgical manipulations. While the complete chicken genome sequence will soon be determined, a comprehensive germ cell transmission-based genetic approach is not available for this animal model. Several techniques of somatic cell transgenesis have been developed in the past decade. Of these, the retroviral shuttle vector system provides both (1) stable integration of exogenous genes into the host cell genome, and (2) constant expression levels in a target cell population over the course of development. This review summarizes retroviral vectors available for the avian model and outlines the uses of retroviral-mediated gene transfer for cell lineage analysis as well as functional studies of genes and proteins in the chick embryo.
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Affiliation(s)
- Yasuo Ishii
- Department of Cell and Developmental Biology, Cornell University Medical College, New York, New York 10021, USA
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Brown WRA, Hubbard SJ, Tickle C, Wilson SA. The chicken as a model for large-scale analysis of vertebrate gene function. Nat Rev Genet 2003; 4:87-98. [PMID: 12560806 DOI: 10.1038/nrg998] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- William R A Brown
- Institute of Genetics, Nottingham University, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Kil SH, Collazo A. A review of inner ear fate maps and cell lineage studies. JOURNAL OF NEUROBIOLOGY 2002; 53:129-42. [PMID: 12382271 DOI: 10.1002/neu.10127] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A renewed interest in the development of the inner ear has provided more data on the fate and cell lineage relationships of the tissues making up this complex structure. The inner ear develops from a simple ectodermal thickening of the head called the otic placode, which undergoes a great deal of growth and differentiation to form a multichambered nonsensory epithelium that houses the six to nine sensory organs of the inner ear. Despite a large number of studies examining otic development, there have been surprisingly few fate maps generated. The published fate maps encompass four species and range from preotic to otocyst stages. Although some of these studies were consistent with a compartment and boundary model, other studies reveal extensive cell mixing during development. Cell lineage studies have been done in fewer species. At the single cell level the resulting clones in both chicks and frogs appear somewhat restricted in terms of distribution. We conclude that up until late placode stages there are no clear lineage restriction boundaries, meaning that cells seem to mix extensively at these early stages. At late placode stages, when the otic cup has formed, there are at least two boundaries located dorsally in the forming otocyst but none ventrally. These conclusions are consistent with all the fate maps and reconciles the chick and frog data. These results suggest that genes involved in patterning the inner ear may have dynamic and complex expression patterns.
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Affiliation(s)
- Sung-Hee Kil
- Leslie and Susan Gonda (Goldschmied) Department of Cell and Molecular Biology, House Ear Institute, 2100 West Third St, Los Angeles, California 90057, USA
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