1
|
Sanchez Bosch P, Axelrod JD. Automated counting of Drosophila imaginal disc cell nuclei. Biol Open 2024; 13:bio060254. [PMID: 38345430 PMCID: PMC10903266 DOI: 10.1242/bio.060254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
Automated image quantification workflows have dramatically improved over the past decade, enriching image analysis and enhancing the ability to achieve statistical power. These analyses have proved especially useful for studies in organisms such as Drosophila melanogaster, where it is relatively simple to obtain high sample numbers for downstream analyses. However, the developing wing, an intensively utilized structure in developmental biology, has eluded efficient cell counting workflows due to its highly dense cellular population. Here, we present efficient automated cell counting workflows capable of quantifying cells in the developing wing. Our workflows can count the total number of cells or count cells in clones labeled with a fluorescent nuclear marker in imaginal discs. Moreover, by training a machine-learning algorithm we have developed a workflow capable of segmenting and counting twin-spot labeled nuclei, a challenging problem requiring distinguishing heterozygous and homozygous cells in a background of regionally varying intensity. Our workflows could potentially be applied to any tissue with high cellular density, as they are structure-agnostic, and only require a nuclear label to segment and count cells.
Collapse
Affiliation(s)
- Pablo Sanchez Bosch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey D Axelrod
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
2
|
Zhang M, Liu D, Lan Y, Liu B, Li Z, Ni Y. Hematopoietic stem cell heterogeneity in non-human primates revealed by five-lineage output bias analysis. Blood Sci 2024; 6:e00176. [PMID: 38213824 PMCID: PMC10781131 DOI: 10.1097/bs9.0000000000000176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024] Open
Abstract
Understanding hematopoietic stem cell (HSC) heterogeneity is crucial for treating malignant blood disorders. Compared with mice, we have limited knowledge of the heterogeneity of human HSCs. Fortunately, non-human primates (NHPs) have become the best animal models for studying human HSCs. Here, we employed a public dataset derived from NHP autologous bone marrow transplantation, and focused on a total of 820 HSC clones with reconstitution capacity of all available five lineages (granulocyte, monocyte, B cell, T cell, and natural killer cell) at two time points (11/12 and/or 42/43 months). Intriguingly, unsupervised clustering on these clones revealed six HSC subtypes, including a lymphoid/myeloid balanced (LM-balanced) subtype and five single-lineage-biased subtypes. We also observed that the subtypes of these HSC clones might change over time, and a given subtype could transition into any one of the other five subtypes, albeit with a certain degree of selectivity. Particularly, each of the six subtypes was more likely to turn into lymphoid-biased rather than myeloid-biased ones. Additionally, our five-lineage classification method exhibited strong correlation with traditional lymphoid/myeloid bias classification method. Specifically, our granulocyte- and monocyte-biased subtypes were predominantly attributed to α-HSCs, while LM-balanced, B cell-biased, and T cell-biased subtypes were primarily associated with β-HSCs. The γ-HSCs were composed of a small subset of B cell-biased and T cell-biased subtypes. In summary, our five-lineage classification identifies more finely tuned HSC subtypes based on lineage output bias. These findings enrich our understanding of HSC heterogeneity in NHPs and provide important insights for human research.
Collapse
Affiliation(s)
- Man Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Di Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Senior Department of Hematology, Fifth Medical Center, Medical Innovation Research Department, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
3
|
Zaki ZMM, Kuroda A, Morimura N, Hayashi Y, Hitoshi S. Depletion of transit amplifying cells in the adult brain does not affect quiescent neural stem cell pool size. J Physiol Sci 2023; 73:19. [PMID: 37704979 DOI: 10.1186/s12576-023-00876-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Neural stem cells (NSCs) are maintained in the adult mammalian brain throughout the animal's lifespan. NSCs in the subependymal zone infrequently divide and generate transit amplifying cells, which are destined to become olfactory bulb neurons. When transit amplifying cells are depleted, they are replenished by the quiescent NSC pool. However, the cellular basis for this recovery process remains largely unknown. In this study, we traced NSCs and their progeny after transit amplifying cells were eliminated by intraventricular infusion of cytosine β-D-arabinofuranoside. We found that although the number of neurosphere-forming NSCs decreased shortly after the treatment, they were restored to normal levels 3 weeks after the cessation of treatment. More importantly, the depletion of transit amplifying cells did not induce a significant expansion of the NSC pool by symmetric divisions. Our data suggest that the size of the NSC pool is hardly affected by brain damage due to antimitotic drug treatment.
Collapse
Affiliation(s)
- Zakiyyah Munirah Mohd Zaki
- Department of Integrative Physiology, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Anri Kuroda
- Department of Integrative Physiology, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
- Department of Ophthalmology, Shiga University of Medical Science, Otsu, Japan
| | - Naoko Morimura
- Department of Integrative Physiology, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Yoshitaka Hayashi
- Department of Integrative Physiology, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Seiji Hitoshi
- Department of Integrative Physiology, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan.
| |
Collapse
|
4
|
Ascolani G, Angaroni F, Maspero D, Craighero F, Bhavesh NLS, Piazza R, Damiani C, Ramazzotti D, Antoniotti M, Graudenzi A. LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinformatics 2023; 24:99. [PMID: 36932333 PMCID: PMC10022199 DOI: 10.1186/s12859-023-05221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/03/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit the mutational profiles of single cells generated via variant calling, in order to reconstruct the evolutionary history of a tumor and characterize the impact of therapeutic strategies, such as the administration of drugs. To this end, we have recently developed the LACE framework for the Longitudinal Analysis of Cancer Evolution. RESULTS The LACE 2.0 release aimed at inferring longitudinal clonal trees enhances the original framework with new key functionalities: an improved data management for preprocessing of standard variant calling data, a reworked inference engine, and direct connection to public databases. CONCLUSIONS All of this is accessible through a new and interactive Shiny R graphical interface offering the possibility to apply filters helpful in discriminating relevant or potential driver mutations, set up inferential parameters, and visualize the results. The software is available at: github.com/BIMIB-DISCo/LACE.
Collapse
Affiliation(s)
- Gianluca Ascolani
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy.
| | - Fabrizio Angaroni
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Davide Maspero
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Francesco Craighero
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Narra Lakshmi Sai Bhavesh
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milan-Bicocca, University of Milan-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, University of Milan-Bicocca, Vedano al Lambro, Monza, Italy
| | - Chiara Damiani
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milan-Bicocca, University of Milan-Bicocca, Milan, Italy
| | - Marco Antoniotti
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, University of Milan-Bicocca, Vedano al Lambro, Monza, Italy
| | - Alex Graudenzi
- Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre - B4, University of Milan-Bicocca, Vedano al Lambro, Monza, Italy
| |
Collapse
|
5
|
Sendra M, de Dios Hourcade J, Temiño S, Sarabia AJ, Ocaña OH, Domínguez JN, Torres M. Cre recombinase microinjection for single-cell tracing and localised gene targeting. Development 2023; 150:286898. [PMID: 36734327 PMCID: PMC10110498 DOI: 10.1242/dev.201206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/17/2022] [Indexed: 02/04/2023]
Abstract
Tracing and manipulating cells in embryos are essential to understand development. Lipophilic dye microinjections, viral transfection and iontophoresis have been key to map the origin of the progenitor cells that form the different organs in the post-implantation mouse embryo. These techniques require advanced manipulation skills and only iontophoresis, a demanding approach of limited efficiency, has been used for single-cell labelling. Here, we perform lineage tracing and local gene ablation using cell-permeant Cre recombinase (TAT-Cre) microinjection. First, we map the fate of undifferentiated progenitors to the different heart chambers. Then, we achieve single-cell recombination by titrating the dose of TAT-Cre, which allows clonal analysis of nascent mesoderm progenitors. Finally, injecting TAT-Cre to Mycnflox/flox embryos in the primitive heart tube revealed that Mycn plays a cell-autonomous role in maintaining cardiomyocyte proliferation. This tool will help researchers identify the cell progenitors and gene networks involved in organ development, helping to understand the origin of congenital defects.
Collapse
Affiliation(s)
- Miquel Sendra
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Juan de Dios Hourcade
- Transgenesis Unit, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Susana Temiño
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| | - Antonio J Sarabia
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Oscar H Ocaña
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
| | - Jorge N Domínguez
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Miguel Torres
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, CNIC, 28029 Madrid, Spain
| |
Collapse
|
6
|
Lescroart F, Zaffran S. Single Cell Approaches to Understand the Earliest Steps in Heart Development. Curr Cardiol Rep 2022; 24:611-621. [PMID: 35384547 DOI: 10.1007/s11886-022-01681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Cardiac progenitors are the building blocks of the heart. Our knowledge, on how these progenitors build the heart, has considerably increased over the last two decades with the development of single cell approaches. We discuss the lessons learnt from clonal analyses and from single cell sequencing technologies on the understanding of the earliest steps of cardiac specification and lineage segregation. RECENT FINDINGS While experiments were initially performed at the population level, the development of approaches to investigate heart development at the single cell resolution has clearly demonstrated that cardiac progenitors are highly heterogeneous, with different progenitors contributing to different cardiac regions and different cardiac cell types. Some critical transcriptional determinants have also been identified for cardiac progenitor specification. Single cell approaches have finally provided insights into the spatio-temporal specification of unipotent and multipotent cardiac progenitors and provided a framework for investigating congenital heart defects.
Collapse
|
7
|
Morata G, Lawrence P. An exciting period of Drosophila developmental biology: Of imaginal discs, clones, compartments, parasegments and homeotic genes". Dev Biol 2022:S0012-1606(22)00014-8. [PMID: 35120908 DOI: 10.1016/j.ydbio.2022.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/22/2022]
Abstract
In this review we recall a number of important discoveries that took place in Drosophila during seventies and eighties of the last century. The development of cell lineage methods and of powerful modifications of same, such as the Minute technique, led to the discovery of compartments and provided a clearer picture of the body organization: it came to be seen as a chain of metameric lineage units along the A/P body axis. Further, genetic screens allowed the identification of the genes involved in the establishment of the metameric scaffold - the segmentation genes- and also of Hox genes that are responsible for the specific development of individual body parts. As cloning methods became available, many of the most relevant of these developmental genes were cloned and a molecular analysis of development initiated. The discovery of the homeobox, a molecular mark of the Hox and other relevant developmental genes, allowed the finding of Hox genes in animal species, like humans, in which they could not be identified by genetic methods. Analysis of the structure and function of Hox genes provided a general image of the genetic design of the metazoan body.
Collapse
|
8
|
Torres-Martínez HH, Napsucialy-Mendivil S, Dubrovsky JG. Cellular and molecular bases of lateral root initiation and morphogenesis. Curr Opin Plant Biol 2022; 65:102115. [PMID: 34742019 DOI: 10.1016/j.pbi.2021.102115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Lateral root development is essential for the establishment of the plant root system. Lateral root initiation is a multistep process that impacts early primordium morphogenesis and is linked to the formation of a morphogenetic field of pericycle founder cells. Gradual recruitment of founder cells builds this morphogenetic field in an auxin-dependent manner. The complex process of lateral root primordium morphogenesis includes several subprocesses, which are presented in this review. The underlying cellular and molecular mechanisms of these subprocesses are examined.
Collapse
Affiliation(s)
- Héctor H Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, 62210, Morelos, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, 62210, Morelos, Mexico
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, 62210, Morelos, Mexico.
| |
Collapse
|
9
|
Abstract
A central question in neuroscience is how 100 billion neurons come together to build the human brain. The wiring, morphology, survival, and death of each neuron are controlled by genes that encode intrinsic and extrinsic factors. Determining the function of these genes at a high spatiotemporal resolution is a critical step toward understanding brain development and function. Moreover, an increasing number of somatic mutations are being discovered in many brain disorders. However, neurons are embedded in complex networks, making it difficult to distinguish cell-autonomous from non-cell-autonomous function of any given gene in the brain. Here, I describe MADM (mosaic analysis with double markers), a genetic method that allows for labeling and manipulating gene function at the single-cell level within the mouse brain. I present mouse breeding schemes to employ MADM analysis and important considerations for experimental design. This powerful system can be adapted to make fundamental neuroscience discoveries by targeting genetically defined cell types in the mouse brain with high spatiotemporal resolution.
Collapse
Affiliation(s)
- Wei-Hsiang Huang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Montréal, QC, Canada.
| |
Collapse
|
10
|
Devaraju N, Rajendiran V, Ravi NS, Mohankumar KM. Genome Engineering of Hematopoietic Stem Cells Using CRISPR/Cas9 System. Methods Mol Biol 2022; 2429:307-331. [PMID: 35507170 DOI: 10.1007/978-1-0716-1979-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ex vivo genetic manipulation of autologous hematopoietic stem and progenitor cells (HSPCs) is a viable strategy for the treatment of hematologic and primary immune disorders. Targeted genome editing of HSPCs using the CRISPR-Cas9 system provides an effective platform to edit the desired genomic locus for therapeutic purposes with minimal off-target effects. In this chapter, we describe the detailed methodology for the CRISPR-Cas9 mediated gene knockout, deletion, addition, and correction in human HSPCs by viral and nonviral approaches. We also present a comprehensive protocol for the analysis of genome modified HSPCs toward the erythroid and megakaryocyte lineage in vitro and the long-term multilineage reconstitution capacity in the recently developed NBSGW mouse model that supports human erythropoiesis.
Collapse
Affiliation(s)
- Nivedhitha Devaraju
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Mangalore, Karnataka, India
| | - Vignesh Rajendiran
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Nithin Sam Ravi
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Kumarasamypet M Mohankumar
- Centre for Stem Cell Research (a unit of inStem, Bangalore), Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India.
| |
Collapse
|
11
|
Yamamoto R. [ Clonal analysis of hematopoietic stem cells]. Rinsho Ketsueki 2022; 63:999-1005. [PMID: 36198564 DOI: 10.11406/rinketsu.63.999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Hematopoietic stem cells (HSCs) are defined as cells present in the bone marrow that are capable of both self-renewal and multilineage differentiation. The differentiation pathway from HSCs to mature blood cells and HSC self-renewal and differentiation mechanisms still remain unclear and require further elucidation. However, HSCs are a highly diverse population with analysis limitations at the population level. Moreover, molecular and cell biological single-cell analysis has been attracting tremendous attention recently. Herein, we introduce a cell biological single-cell analysis method (single-cell transplantation and cell lineage tracing experiments using genetic techniques) in the field of HSCs.
Collapse
Affiliation(s)
- Ryo Yamamoto
- Advanced Study of Human Biology, Kyoto University
| |
Collapse
|
12
|
Gandhi S, Li Y, Tang W, Christensen JB, Urrutia HA, Vieceli FM, Piacentino ML, Bronner ME. A single-plasmid approach for genome editing coupled with long-term lineage analysis in chick embryos. Development 2021; 148:dev193565. [PMID: 33688075 PMCID: PMC8077534 DOI: 10.1242/dev.193565] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
An important strategy for establishing mechanisms of gene function during development is through mutation of individual genes and analysis of subsequent effects on cell behavior. Here, we present a single-plasmid approach for genome editing in chick embryos to study experimentally perturbed cells in an otherwise normal embryonic environment. To achieve this, we have engineered a plasmid that encodes Cas9 protein, gene-specific guide RNA (gRNA), and a fluorescent marker within the same construct. Using transfection- and electroporation-based approaches, we show that this construct can be used to perturb gene function in early embryos as well as human cell lines. Importantly, insertion of this cistronic construct into replication-incompetent avian retroviruses allowed us to couple gene knockouts with long-term lineage analysis. We demonstrate the application of our newly engineered constructs and viruses by perturbing β-catenin in vitro and Sox10, Pax6 and Pax7 in the neural crest, retina, and neural tube and segmental plate in vivo, respectively. Together, this approach enables genes of interest to be knocked out in identifiable cells in living embryos and can be broadly applied to numerous genes in different embryonic tissues.
Collapse
Affiliation(s)
- Shashank Gandhi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuwei Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Weiyi Tang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jens B. Christensen
- Department of Neuroscience, University of Copenhagen, Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Hugo A. Urrutia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Felipe M. Vieceli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael L. Piacentino
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
13
|
Alhashem Z, Portillo MA, Htun MR, Gauert A, Montecinos LB, Härtel S, Linker C. Zebrafish Neural Crest: Lessons and Tools to Study In Vivo Cell Migration. Methods Mol Biol 2021; 2179:79-106. [PMID: 32939715 DOI: 10.1007/978-1-0716-0779-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The study of cell migration has been greatly enhanced by the development of new model systems and analysis protocols to study this process in vivo. Zebrafish embryos have been a principal protagonist because they are easily accessible, genetically tractable, and optically transparent. Neural crest cells, on the other hand, are the ideal system to study cell migration. These cells migrate extensively, using different modalities of movement and sharing many traits with metastatic cancer cells. In this chapter, we present new tools and protocols that allow the study of NC development and migration in vivo.
Collapse
|
14
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
15
|
Abstract
Since its discovery 150 years ago, the neural crest has intrigued investigators owing to its remarkable developmental potential and extensive migratory ability. Cell lineage analysis has been an essential tool for exploring neural crest cell fate and migration routes. By marking progenitor cells, one can observe their subsequent locations and the cell types into which they differentiate. Here, we review major discoveries in neural crest lineage tracing from a historical perspective. We discuss how advancing technologies have refined lineage-tracing studies, and how clonal analysis can be applied to questions regarding multipotency. We also highlight how effective progenitor cell tracing, when combined with recently developed molecular and imaging tools, such as single-cell transcriptomics, single-molecule fluorescence in situ hybridization and high-resolution imaging, can extend the scope of neural crest lineage studies beyond development to regeneration and cancer initiation.
Collapse
Affiliation(s)
- Weiyi Tang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
16
|
Seyed-Safi AG, Daniels JT. A validated porcine corneal organ culture model to study the limbal response to corneal epithelial injury. Exp Eye Res 2020; 197:108063. [PMID: 32417262 DOI: 10.1016/j.exer.2020.108063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/03/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
Abstract
Limbal epithelial stem cells are required for the maintenance and repair of the corneal epithelial surface. The difficulty in obtaining human corneal tissue for research purposes means that animal models for studying the corneal and limbal epithelium are extremely useful. Porcine corneal tissue represents an attractive experimental model, however, functional analysis of the limbal epithelial cell population is needed to validate the use of this tissue. Single cell clonal analysis revealed that holoclone-generating cells were enriched in the limbus as compared with the central cornea (38.3% vs 8.3%) and that label-retaining cells were also enriched in the limbus and compared with the central cornea (44.7 ± 6.4 vs 4.7 ± 1.5). Furthermore, it was demonstrated that in a 3D-printed organ culture system, porcine tissue was capable of maintaining and healing the corneal epithelium. Ki67 staining of corneal sections revealed that in response to central epithelial wounding, a greater proportion of progenitors in the basal limbal epithelium enter an actively dividing state. The authors present a comprehensively validated model system for studying the interactions between limbal niche factors and limbal epithelial stem cell fate.
Collapse
|
17
|
Suzuki H, Harrison CJ, Shimamura M, Kohchi T, Nishihama R. Positional cues regulate dorsal organ formation in the liverwort Marchantia polymorpha. J Plant Res 2020; 133:311-321. [PMID: 32206925 DOI: 10.1007/s10265-020-01180-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/10/2020] [Indexed: 05/05/2023]
Abstract
Bryophytes and vascular plants represent the broadest evolutionary divergence in the land plant lineage, and comparative analyses of development spanning this divergence therefore offer opportunities to identify truisms of plant development in general. In vascular plants, organs are formed repetitively around meristems at the growing tips in response to positional cues. In contrast, leaf formation in mosses and leafy liverworts occurs from clonal groups of cells derived from a daughter cell of the apical stem cell known as merophytes, and cell lineage is a crucial factor in repetitive organ formation. However, it remains unclear whether merophyte lineages are a general feature of repetitive organ formation in bryophytes as patterns of organogenesis in thalloid liverworts are unclear. To address this question, we developed a clonal analysis method for use in the thalloid liverwort Marchantia polymorpha, involving random low-frequency induction of a constitutively expressed nuclear-targeted fluorescent protein by dual heat-shock and dexamethasone treatment. M. polymorpha thalli ultimately derive from stem cells in the apical notch, and the lobes predominantly develop from merophytes cleft to the left and right of the apical cell(s). Sector induction in gemmae and subsequent culture occasionally generated fluorescent sectors that bisected thalli along the midrib and were maintained through several bifurcation events, likely reflecting the border between lateral merophytes. Such thallus-bisecting sectors traversed dorsal air chambers and gemma cups, suggesting that these organs arise independently of merophyte cell lineages in response to local positional cues.
Collapse
Affiliation(s)
- Hidemasa Suzuki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.
| |
Collapse
|
18
|
Salvi M, Cerrato V, Buffo A, Molinari F. Automated segmentation of brain cells for clonal analyses in fluorescence microscopy images. J Neurosci Methods 2019; 325:108348. [PMID: 31283938 DOI: 10.1016/j.jneumeth.2019.108348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 11/26/2022]
Abstract
The understanding of how cell diversity within and across distinct brain regions is ontogenetically achieved is a pivotal topic in neuroscience. Clonal analyses based on multicolor cell labeling represent a powerful tool to tackle this issue and disclose lineage relationships, but produce enormous sets of fluorescence images, leading to time consuming analyses that may be biased by the operator's subjectivity. Thus, time-efficient automated software are needed to analyze images easily, accurately and without subjective bias. In this paper, we present a fully automated method, named FAST ('Fluorescent cell Analysis Segmentation Tool'), for the segmentation of neural cells labeled by multicolor combinations of fluorophores and for their classification into clones. The proposed method was tested on 77 high-magnification fluorescence images of adult mouse cerebellar tissues acquired using a confocal microscope. Automatic results were compared with manual annotations and two open-source software designed for cell detection in microscopic imaging. The algorithm showed very good performance in the cellular detection and in the assignment of the clonal identity. To the best of our knowledge, FAST is the first fully automated technique for the analysis of cellular clones based on combinatorial expression of fluorescent proteins. The proposed approach allows to perform clonal analyses easily, accurately and objectively, overcoming those biases and errors that may result from manual annotations. Moreover, it can be broadly applied to the quantification and colocalization within cells of fluorescent markers, therefore representing a versatile and powerful tool for automated quantitative analyses in fluorescence microscopy.
Collapse
Affiliation(s)
- Massimo Salvi
- Biolab, Department of Electronics and Telecommunications, Politecnico di Torino, Turin, Italy.
| | - Valentina Cerrato
- Department of Neuroscience Rita Levi-Montalcini, University of Turin and Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy.
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi-Montalcini, University of Turin and Neuroscience Institute Cavalieri Ottolenghi, Orbassano, Turin, Italy.
| | - Filippo Molinari
- Biolab, Department of Electronics and Telecommunications, Politecnico di Torino, Turin, Italy.
| |
Collapse
|
19
|
Nguyen NB, Chen CH, Zhang Y, Zhao P, Wu BM, Ardehali R. Harnessing the versatility of PLGA nanoparticles for targeted Cre-mediated recombination. Nanomedicine 2019; 19:106-114. [PMID: 31026512 DOI: 10.1016/j.nano.2019.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/28/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
Ligand-dependent Cre recombinases are pivotal tools for the generation of inducible somatic mutants. This method enables spatial and temporal control of gene activity through tamoxifen administration, providing new avenues for studying gene function and establishing animal models of human diseases. While this paved the way for developmental studies previously deemed impractical, the generation of tissue-specific transgenic mouse lines can be time-consuming and costly. Herein, we design a 'smart', biocompatible, and biodegradable nanoparticle system encapsulated with tamoxifen that is actively targeted to specific cell types in vivo through surface conjugation of antibodies. We demonstrate that these nanoparticles bind to cells of interest and activate Cre recombinase, resulting in tissue-specific Cre activation. This system provides a versatile, yet powerful approach to induce recombination in a ubiquitious Cre system for various biomedical applications and sets the stage for a time- and cost-effective strategy of generating new transgenic mouse lines.
Collapse
Affiliation(s)
- Ngoc B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA; Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cheng-Han Chen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yulong Zhang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peng Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA
| | - Benjamin M Wu
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Reza Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA; Molecular, Cellular and Integrative Physiology Graduate Program, University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
20
|
Affan A, Al-Jezani N, Railton P, Powell JN, Krawetz RJ. Multiple mesenchymal progenitor cell subtypes with distinct functional potential are present within the intimal layer of the hip synovium. BMC Musculoskelet Disord 2019; 20:125. [PMID: 30909916 PMCID: PMC6434889 DOI: 10.1186/s12891-019-2495-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/05/2019] [Indexed: 12/18/2022] Open
Abstract
Background The synovial membrane adjacent to the articular cartilage is home to synovial mesenchymal progenitor cell (sMPC) populations that have the ability to undergo chondrogenesis. While it has been hypothesized that multiple subtypes of stem and progenitor cells exist in vivo, there is little evidence supporting this hypothesis in human tissues. Furthermore, in most of the published literature on this topic, the cells are cultured before derivation of clonal populations. This gap in the literature makes it difficult to determine if there are distinct MPC subtypes in human synovial tissues, and if so, if these sMPCs express any markers in vivo/in situ that provide information in regards to the function of specific MPC subtypes (e.g. cells with increased chondrogenic capacity)? Therefore, the current study was undertaken to determine if any of the classical MPC cell surface markers provide insight into the differentiation capacity of sMPCs. Methods Clonal populations of sMPCs were derived from a cohort of patients with hip osteoarthritis (OA) and patients at high risk to develop OA using indexed cell sorting. Tri-differentiation potential and cell surface receptor expression of the resultant clones was determined. Results A number of clones with distinct differentiation potential were derived from this cohort, yet the most common cell surface marker profile on MPCs (in situ) that demonstrated chondrogenic potential was determined to be CD90+/CD44+/CD73+. A validation cohort was employed to isolate cells with only this cell surface profile. Isolating cells directly from human synovial tissue with these three markers alone, did not enrich for cells with chondrogenic capacity. Conclusions Therefore, additional markers are required to further discriminate the heterogeneous subtypes of MPCs and identify sMPCs with functional properties that are believed to be advantageous for clinical application. Electronic supplementary material The online version of this article (10.1186/s12891-019-2495-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Asmaa Affan
- McCaig Institute for Bone and Joint Health, Faculty of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,University of Calgary, Biomedical Engineering Graduate Program, Calgary, Canada
| | - Nedaa Al-Jezani
- McCaig Institute for Bone and Joint Health, Faculty of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,University of Calgary, Medical Science Graduate Program, Calgary, AB, Canada
| | - Pamela Railton
- University of Calgary, Department of Surgery, Calgary, Alberta, Canada.,Charles Sturt University, Orange, Australia
| | - James N Powell
- McCaig Institute for Bone and Joint Health, Faculty of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada.,University of Calgary, Department of Surgery, Calgary, Alberta, Canada
| | - Roman J Krawetz
- McCaig Institute for Bone and Joint Health, Faculty of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada. .,University of Calgary, Biomedical Engineering Graduate Program, Calgary, Canada. .,University of Calgary, Department of Surgery, Calgary, Alberta, Canada. .,University of Calgary, Department of Anatomy and Cell Biology, Calgary, Alberta, Canada.
| |
Collapse
|
21
|
Gilles AF, Schinko JB, Schacht MI, Enjolras C, Averof M. Clonal analysis by tunable CRISPR-mediated excision. Development 2019; 146:dev.170969. [PMID: 30552128 DOI: 10.1242/dev.170969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/26/2018] [Indexed: 01/05/2023]
Abstract
Clonal marking techniques based on the Cre/lox and Flp/FRT systems are widely used in multicellular model organisms to mark individual cells and their progeny, in order to study their morphology, growth properties and developmental fates. The same tools can be adapted to introduce specific genetic changes in a subset of cells within the body, i.e. to perform mosaic genetic analysis. Marking and manipulating distinct cell clones requires control over the frequency of clone induction, which is sometimes difficult to achieve. Here, we present Valcyrie, a new method that replaces the conventional Cre or Flp recombinase-mediated excision of a marker cassette by CRISPR-mediated excision. A major advantage of this approach is that CRISPR efficiency can be tuned in a predictable fashion by manipulating the degree of sequence complementarity between the CRISPR guide RNA and its targets. We establish the method in the beetle Tribolium castaneum We demonstrate that clone marking frequency can be tuned to generate embryos that carry single marked clones. The Valcyrie approach can be applied to a wide range of experimental settings, for example to modulate clone frequency with existing tools in established model organisms and to introduce clonal analysis in emerging experimental models.
Collapse
Affiliation(s)
- Anna F Gilles
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France .,BMIC graduate programme, Université Claude Bernard/Lyon 1, France.,TriGenes gUG, Biberach University of Applied Sciences, Hubertus-Liebrecht-Str. 35, 88400 Biberach/Riss, Germany
| | - Johannes B Schinko
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France .,TriGenes gUG, Biberach University of Applied Sciences, Hubertus-Liebrecht-Str. 35, 88400 Biberach/Riss, Germany.,Centre National de la Recherche Scientifique (CNRS), France
| | - Magdalena I Schacht
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France.,Department of Evolutionary Developmental Genetics, Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Camille Enjolras
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France.,Centre National de la Recherche Scientifique (CNRS), France
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 32 avenue Tony Garnier, 69007 Lyon, France .,Centre National de la Recherche Scientifique (CNRS), France
| |
Collapse
|
22
|
Merryweather-Clarke AT, Cook D, Lara BJ, Hua P, Repapi E, Ashley N, Lim SY, Watt SM. Does osteogenic potential of clonal human bone marrow mesenchymal stem/stromal cells correlate with their vascular supportive ability? Stem Cell Res Ther 2018; 9:351. [PMID: 30567594 PMCID: PMC6300038 DOI: 10.1186/s13287-018-1095-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human bone marrow-derived mesenchymal stem/stromal cells (hBM MSCs) have multiple functions, critical for skeletal formation and function. Their functional heterogeneity, however, represents a major challenge for their isolation and in developing potency and release assays to predict their functionality prior to transplantation. Additionally, potency, biomarker profiles and defining mechanisms of action in a particular clinical setting are increasing requirements of Regulatory Agencies for release of hBM MSCs as Advanced Therapy Medicinal Products for cellular therapies. Since the healing of bone fractures depends on the coupling of new blood vessel formation with osteogenesis, we hypothesised that a correlation between the osteogenic and vascular supportive potential of individual hBM MSC-derived CFU-F (colony forming unit-fibroblastoid) clones might exist. METHODS We tested this by assessing the lineage (i.e. adipogenic (A), osteogenic (O) and/or chondrogenic (C)) potential of individual hBM MSC-derived CFU-F clones and determining if their osteogenic (O) potential correlated with their vascular supportive profile in vitro using lineage differentiation assays, endothelial-hBM MSC vascular co-culture assays and transcriptomic (RNAseq) analyses. RESULTS Our results demonstrate that the majority of CFU-F (95%) possessed tri-lineage, bi-lineage or uni-lineage osteogenic capacity, with 64% of the CFU-F exhibiting tri-lineage AOC potential. We found a correlation between the osteogenic and vascular tubule supportive activity of CFU-F clones, with the strength of this association being donor dependent. RNAseq of individual clones defined gene fingerprints relevant to this correlation. CONCLUSIONS This study identified a donor-dependent correlation between osteogenic and vascular supportive potential of hBM MSCs and important gene signatures that support these functions that are relevant to their bone regenerative properties.
Collapse
Affiliation(s)
- Alison T. Merryweather-Clarke
- Stem Cell Research, Nuffield Division of Clinical Laboratory Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9BQ UK
- Stem Cell Research, NHS Blood and Transplant, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| | - David Cook
- Stem Cell Research, Nuffield Division of Clinical Laboratory Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9BQ UK
- Stem Cell Research, NHS Blood and Transplant, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| | - Barbara Joo Lara
- Stem Cell Research, Nuffield Division of Clinical Laboratory Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9BQ UK
- Stem Cell Research, NHS Blood and Transplant, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| | - Peng Hua
- Stem Cell Research, Nuffield Division of Clinical Laboratory Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9BQ UK
- Stem Cell Research, NHS Blood and Transplant, John Radcliffe Hospital, Oxford, OX3 9BQ UK
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| | - Emmanouela Repapi
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| | - Neil Ashley
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| | - Shiang Y. Lim
- Department of Surgery, University of Melbourne, Fitzroy, Victoria 3065 Australia
- O’Brien Institute Department, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065 Australia
| | - Suzanne M. Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9BQ UK
- Stem Cell Research, NHS Blood and Transplant, John Radcliffe Hospital, Oxford, OX3 9BQ UK
| |
Collapse
|
23
|
Miyoshi G. Elucidating the developmental trajectories of GABAergic cortical interneuron subtypes. Neurosci Res 2019; 138:26-32. [PMID: 30227162 DOI: 10.1016/j.neures.2018.09.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022]
Abstract
GABAergic interneurons in the neocortex play pivotal roles in the feedforward and feedback inhibition that control higher order information processing and thus, malfunction in the inhibitory circuits often leads to neurodevelopmental disorders. Very interestingly, a large diversity of morphology, synaptic targeting specificity, electrophysiological properties and molecular expression profiles are found in cortical interneurons, which originate within the distantly located embryonic ganglionic eminences. Here, I will review the still ongoing effort to understand the developmental trajectories of GABAergic cortical interneuron subtypes.
Collapse
|
24
|
Dobreva MP, Abon Escalona V, Lawson KA, Sanchez MN, Ponomarev LC, Pereira PNG, Stryjewska A, Criem N, Huylebroeck D, Chuva de Sousa Lopes SM, Aerts S, Zwijsen A. Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling. Development 2018; 145:dev.157222. [PMID: 29884675 DOI: 10.1242/dev.157222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 05/30/2018] [Indexed: 12/18/2022]
Abstract
Upon gastrulation, the mammalian conceptus transforms rapidly from a simple bilayer into a multilayered embryo enveloped by its extra-embryonic membranes. Impaired development of the amnion, the innermost membrane, causes major malformations. To clarify the origin of the mouse amnion, we used single-cell labelling and clonal analysis. We identified four clone types with distinct clonal growth patterns in amniotic ectoderm. Two main types have progenitors in extreme proximal-anterior epiblast. Early descendants initiate and expand amniotic ectoderm posteriorly, while descendants of cells remaining anteriorly later expand amniotic ectoderm from its anterior side. Amniogenesis is abnormal in embryos deficient in the bone morphogenetic protein (BMP) signalling effector SMAD5, with delayed closure of the proamniotic canal, and aberrant amnion and folding morphogenesis. Transcriptomics of individual Smad5 mutant amnions isolated before visible malformations and tetraploid chimera analysis revealed two amnion defect sets. We attribute them to impairment of progenitors of the two main cell populations in amniotic ectoderm and to compromised cuboidal-to-squamous transition of anterior amniotic ectoderm. In both cases, SMAD5 is crucial for expanding amniotic ectoderm rapidly into a stretchable squamous sheet to accommodate exocoelom expansion, axial growth and folding morphogenesis.
Collapse
Affiliation(s)
- Mariya P Dobreva
- VIB-KU Leuven Center for Brain and Disease Research, Leuven 3000, Belgium .,Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Vanesa Abon Escalona
- VIB-KU Leuven Center for Brain and Disease Research, Leuven 3000, Belgium.,Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Cardiovascular Sciences, KU Leuven, Leuven 3000, Belgium
| | - Kirstie A Lawson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Ljuba C Ponomarev
- Department of Cardiovascular Sciences, KU Leuven, Leuven 3000, Belgium
| | - Paulo N G Pereira
- VIB-KU Leuven Center for Brain and Disease Research, Leuven 3000, Belgium.,Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Nathan Criem
- VIB-KU Leuven Center for Brain and Disease Research, Leuven 3000, Belgium.,Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Cardiovascular Sciences, KU Leuven, Leuven 3000, Belgium
| | - Danny Huylebroeck
- Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | | | - Stein Aerts
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - An Zwijsen
- VIB-KU Leuven Center for Brain and Disease Research, Leuven 3000, Belgium .,Department of Human Genetics, KU Leuven, Leuven 3000, Belgium.,Department of Cardiovascular Sciences, KU Leuven, Leuven 3000, Belgium
| |
Collapse
|
25
|
Kirschen GW, Ge S, Park IM. Probability of viral labeling of neural stem cells in vivo. Neurosci Lett 2018; 681:17-18. [PMID: 29777716 DOI: 10.1016/j.neulet.2018.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/05/2018] [Accepted: 05/09/2018] [Indexed: 10/16/2022]
Abstract
In the neuroscience field over the past several decades, viral vectors have become powerful gene delivery systems to study neural populations of interest. For neural stem cell (NSC) biology, such viruses are often used to birth-date and track NSCs over developmental time in lineage tracing experiments. Yet, the probability of successful infection of a given stem cell in vivo remains unknown. This information would be helpful to inform investigators interested in titrating their viruses to selectively target sparsely-populated clusters of cells in the nervous system. Here, we describe a novel approach to calculate the probability of successful viral infection of NSCs using experimentally-derived cell cluster data from our newly-developed method to sparsely label adult NSCs, and a simple statistical derivation. Others interested in precisely defining their viral infection efficiency can use this method for a variety of basic and translational studies.
Collapse
Affiliation(s)
- Gregory W Kirschen
- Medical Scientist Training Program (MSTP), Stony Brook School of Medicine, United States; Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY, 11794, United States
| | - Shaoyu Ge
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY, 11794, United States
| | - Il Memming Park
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY, 11794, United States.
| |
Collapse
|
26
|
Abstract
Stem cells, which both self-renew and produce differentiated progeny, represent fundamental biological units for the development, growth, maintenance, and regeneration of adult tissues. Characterization of stem cell lineage potential can be accomplished with clonal assays that interrogate stem cell output at the single-cell level. Here we present two methods for clonal analysis of individual proliferative cells (neoblasts) in the planarian Schmidtea mediterranea. The first method utilizes "subtotal" gamma irradiation to study rare surviving neoblasts and their clonal descendants in their native environment. The second method utilizes a fluorescent-activated cell sorting (FACS) strategy to obtain neoblast-enriched cell fractions, followed by single-cell transplantation into lethally irradiated hosts. Together, these methods provide a framework for generation and analysis of stem cell-derived clones in planarians.
Collapse
Affiliation(s)
- Irving E Wang
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel E Wagner
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter W Reddien
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
27
|
Tornini VA, Thompson JD, Allen RL, Poss KD. Live fate-mapping of joint-associated fibroblasts visualizes expansion of cell contributions during zebrafish fin regeneration. Development 2017; 144:2889-2895. [PMID: 28811310 DOI: 10.1242/dev.155655] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/04/2017] [Indexed: 02/03/2023]
Abstract
The blastema is a mass of progenitor cells responsible for regeneration of amputated salamander limbs and fish fins. Previous studies have indicated that resident cell sources producing the blastema contribute lineage-restricted progeny to regenerating tissue. However, these studies have labeled general cell types rather than granular cell subpopulations, and they do not explain the developmental transitions that must occur for distal structures to arise from cells with proximal identities in the appendage stump. Here, we find that regulatory sequences of tph1b, which encodes an enzyme that synthesizes serotonin, mark a subpopulation of fibroblast-like cells restricted to the joints of uninjured adult zebrafish fins. Amputation stimulates serotonin production in regenerating fin fibroblasts, yet targeted tph1b mutations abrogating this response do not disrupt fin regeneration. In uninjured animals, tph1b-expressing cells contribute fibroblast progeny that remain restricted to joints throughout life. By contrast, upon amputation, tph1b+ joint cells give rise to fibroblasts that distribute across the entire lengths of regenerating fin rays. Our experiments visualize and quantify how incorporation into an appendage blastema broadens the progeny contributions of a cellular subpopulation that normally has proximodistal restrictions.
Collapse
Affiliation(s)
- Valerie A Tornini
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.,Regeneration Next, Duke University, Durham, NC 27710, USA
| | - John D Thompson
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.,Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Raymond L Allen
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA .,Regeneration Next, Duke University, Durham, NC 27710, USA
| |
Collapse
|
28
|
Foglia MJ, Cao J, Tornini VA, Poss KD. Multicolor mapping of the cardiomyocyte proliferation dynamics that construct the atrium. Development 2016; 143:1688-96. [PMID: 26989176 DOI: 10.1242/dev.136606] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/08/2016] [Indexed: 01/13/2023]
Abstract
The orchestrated division of cardiomyocytes assembles heart chambers of distinct morphology. To understand the structural divergence of the cardiac chambers, we determined the contributions of individual embryonic cardiomyocytes to the atrium in zebrafish by multicolor fate-mapping and we compare our analysis to the established proliferation dynamics of ventricular cardiomyocytes. We find that most atrial cardiomyocytes become rod-shaped in the second week of life, generating a single-muscle-cell-thick myocardial wall with a striking webbed morphology. Inner pectinate myofibers form mainly by direct branching, unlike delamination events that create ventricular trabeculae. Thus, muscle clones assembling the atrial chamber can extend from wall to lumen. As zebrafish mature, atrial wall cardiomyocytes proliferate laterally to generate cohesive patches of diverse shapes and sizes, frequently with dominant clones that comprise 20-30% of the wall area. A subpopulation of cardiomyocytes that transiently express atrial myosin heavy chain (amhc) contributes substantially to specific regions of the ventricle, suggesting an unappreciated level of plasticity during chamber formation. Our findings reveal proliferation dynamics and fate decisions of cardiomyocytes that produce the distinct architecture of the atrium.
Collapse
Affiliation(s)
- Matthew J Foglia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingli Cao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Valerie A Tornini
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
29
|
Wan Y, Almeida AD, Rulands S, Chalour N, Muresan L, Wu Y, Simons BD, He J, Harris WA. The ciliary marginal zone of the zebrafish retina: clonal and time-lapse analysis of a continuously growing tissue. Development 2016; 143:1099-107. [PMID: 26893352 PMCID: PMC4852496 DOI: 10.1242/dev.133314] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/09/2016] [Indexed: 01/07/2023]
Abstract
Clonal analysis is helping us understand the dynamics of cell replacement in homeostatic adult tissues (Simons and Clevers, 2011). Such an analysis, however, has not yet been achieved for continuously growing adult tissues, but is essential if we wish to understand the architecture of adult organs. The retinas of lower vertebrates grow throughout life from retinal stem cells (RSCs) and retinal progenitor cells (RPCs) at the rim of the retina, called the ciliary marginal zone (CMZ). Here, we show that RSCs reside in a niche at the extreme periphery of the CMZ and divide asymmetrically along a radial (peripheral to central) axis, leaving one daughter in the peripheral RSC niche and the other more central where it becomes an RPC. We also show that RPCs of the CMZ have clonal sizes and compositions that are statistically similar to progenitor cells of the embryonic retina and fit the same stochastic model of proliferation. These results link embryonic and postembryonic cell behaviour, and help to explain the constancy of tissue architecture that has been generated over a lifetime. Summary: A quantitative study of cell proliferation and fate choice in the zebrafish retina - a continuously growing neural tissue - reveals key features of late retinal neurogenesis.
Collapse
Affiliation(s)
- Yinan Wan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Alexandra D Almeida
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Steffen Rulands
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Cavendish Laboratory, Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE, UK Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Naima Chalour
- Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leila Muresan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Yunmin Wu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE, UK Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jie He
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - William A Harris
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| |
Collapse
|
30
|
Abstract
The invention of new mouse molecular genetics techniques, initiated in the 1980s, has repeatedly expanded our ability to tackle exciting developmental biology problems. The brain is the most complex organ, and as such the more sophisticated the molecular genetics technique, the more impact they have on uncovering new insights into how our brain functions. I provide a general time line for the introduction of new techniques over the past 30 years and give examples of new discoveries in the neural development field that emanated from them. I include a look to what the future holds and argue that we are at the dawn of a very exciting age for young scientists interested in studying how the nervous system is constructed and functions with such precision.
Collapse
Affiliation(s)
- Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, USA.
| |
Collapse
|
31
|
Abstract
Cell lineage is the framework for understanding cellular diversity, stability of differentiation, and its relationship to pluripotency. The special condition of in utero development in mammals has presented challenges to developmental biologists in tracing cell lineages but modern imaging and cell marking techniques have allowed the gradual elucidation of lineage relationships. Early experimental embryology approaches had limited resolution and relied of suboptimal cell markers and considerable disturbance to the embryos. Transgenic technology introduced genetic markers, particularly fluorescent proteins that, combined with sophisticated imaging modalities, greatly increase resolution and allow clonal analysis within lineages. The concept of cell lineage has also undergone evolution as it became possible to trace the lineage of cells based not only on their physical location or attributes but also on their gene expression pattern, thus opening up mechanistic lines of investigation into the determinants of cell lineage.
Collapse
Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, USA.
| |
Collapse
|
32
|
Abstract
Skeletal muscle stem cells are satellite cells that play crucial roles in tissue repair and regeneration after muscle injury. Accumulating evidence indicates that satellite cells are genetically and functionally heterogeneous, even within the same muscle. A small population of satellite cells possesses "stemness" and exhibits the remarkable ability to regenerate through robust self-renewal when transplanted into a regenerating muscle niche. In contrast, not all satellite cells self-renew. For example, some cells are committed myogenic progenitors that immediately undergo myogenic differentiation with minimal cell division after activation. Recent studies illuminate the cellular and molecular characteristics of the functional heterogeneity among satellite cells. To evaluate heterogeneity and stem cell dynamics, here we describe methods to conduct a clonal analysis of satellite cells and to visualize a slowly dividing cell population.
Collapse
Affiliation(s)
- Yasuo Kitajima
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Shizuka Ogawa
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Yusuke Ono
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan.
| |
Collapse
|
33
|
Abstract
Since its introduction in 1993, the GAL4 system has become an essential part of the Drosophila geneticist's toolkit. Widely used to drive gene expression in a multitude of cell- and tissue-specific patterns, the system has been adapted and extended to form the basis of many modern tools for the manipulation of gene expression in Drosophila and other model organisms.
Collapse
|
34
|
Sikorski DJ, Caron NJ, VanInsberghe M, Zahn H, Eaves CJ, Piret JM, Hansen CL. Clonal analysis of individual human embryonic stem cell differentiation patterns in microfluidic cultures. Biotechnol J 2015; 10:1546-54. [PMID: 26059045 DOI: 10.1002/biot.201500035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/04/2015] [Accepted: 06/05/2015] [Indexed: 01/23/2023]
Abstract
Heterogeneity in the clonal outputs of individual human embryonic stem cells (hESCs) confounds analysis of their properties in studies of bulk populations and how to manipulate them for clinical applications. To circumvent this problem we developed a microfluidic device that supports the robust generation of colonies derived from single ESCs. This microfluidic system contains 160 individually addressable chambers equipped for perfusion culture of individual hESCs that could be shown to match the growth rates, marker expression and colony morphologies obtained in conventional cultures. Use of this microfluidic device to analyze the clonal growth kinetics of multiple individual hESCs induced to differentiation revealed variable shifts in the growth rate, area per cell and expression of OCT4 in the progeny of individual hESCs. Interestingly, low OCT4 expression, a slower growth rate and low nuclear to cytoplasmic ratios were found to be correlated responses. This study demonstrates how microfluidic systems can be used to enable large scale live-cell imaging of isolated hESCs exposed to changing culture conditions, to examine how different aspects of their variable responses are correlated.
Collapse
Affiliation(s)
- Darek J Sikorski
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Nicolas J Caron
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michael VanInsberghe
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Hans Zahn
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - James M Piret
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Carl L Hansen
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada. .,Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
35
|
Rebollo E, Karkali K, Mangione F, Martín-Blanco E. Live imaging in Drosophila: The optical and genetic toolkits. Methods 2014; 68:48-59. [PMID: 24814031 DOI: 10.1016/j.ymeth.2014.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/19/2022] Open
Abstract
Biological imaging based on light microscopy comes at the core of the methods that let us understanding morphology and its dynamics in synergy to the spatiotemporal distribution of cellular and molecular activities as the organism develops and becomes functional. Non-linear optical tools and superesolution methodologies are under constant development and their applications to live imaging of whole organisms keep improving as we speak. Genetically coded biosensors, multicolor clonal methods and optogenetics in different organisms and, in particular, in Drosophila follow equivalent paths. We anticipate a brilliant future for live imaging providing the roots for the holistic understanding, rather than for individual parts, of development and function at the whole-organism level.
Collapse
Affiliation(s)
- Elena Rebollo
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Cientific de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Katerina Karkali
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Cientific de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Federica Mangione
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Cientific de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Enrique Martín-Blanco
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Cientific de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain.
| |
Collapse
|
36
|
Archacka K, Pozzobon M, Repele A, Rossi CA, Campanella M, De Coppi P. Culturing muscle fibres in hanging drop: a novel approach to solve an old problem. Biol Cell 2014; 106:72-82. [PMID: 24405025 DOI: 10.1111/boc.201300028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 11/05/2013] [Indexed: 11/25/2022]
Abstract
BACKGROUND INFORMATION The satellite cells (SCs) associated with muscle fibres play a key role in postnatal growth and regeneration of skeletal muscle. Commonly used methods of isolation and in vitro culture of SCs lead to the mixture of their subpopulations that exist within muscle. To solve this problem, we used the well established technique, the hanging drop system, to culture SCs in a three-dimensional environment and thus, to monitor them in their original niche. RESULTS Using hanging drop technique, we were able to culture SCs associated with the fibre at least for 9 days with one transfer of fibres to the fresh drops. In comparison, in the classical method of myofibres culture, that is, on the dishes coated with Matrigel, SCs leave the fibres within 3 days after the isolation. Cells cultured in both systems differed in expression of Pax7 and MyoD. While almost all cells cultured in adhesion system expressed MyoD before the fifth day of the culture, the majority of SCs cultured in hanging drop still maintained expression of Pax7 and were not characterised by the presence of MyoD. Among the cells cultured with single myofibre for up to 9 days, we identified two different subclones of SCs: low proliferative clone and high proliferative clone, which differed in proliferation rate and membrane potential. CONCLUSIONS The hanging drop enables the myofibres to be kept in suspension for at least 9 days, and thus, allows SCs and their niche to interact each other for prolonged time. In a consequence, SCs cultured in hanging drop maintain expression of Pax7 while those cultured in a traditional adhesion culture, that is, devoid of signals from the original niche, activate and preferentially undergo differentiation as manifested by expression of MyoD. Thus, the innovative method of SCs culturing in the hanging drop system may serve as a useful tool to study the fate of different subpopulations of these cells in their anatomical location and to determine reciprocal interactions between them and their niche.
Collapse
Affiliation(s)
- Karolina Archacka
- Stem Cells and Regenerative Medicine Lab, Foundation Institute of Pediatic Research Città della Speranza, Padua, 35127, Italy; Department of Cytology, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | | | | | | | | | | |
Collapse
|
37
|
Wang LL, Yao GY, Zhao ZS, Wei XL, Xu RJ. Clonality analysis of neuroendocrine cells in gastric adenocarcinoma. World J Gastroenterol 2013; 19:5340-5346. [PMID: 23983439 PMCID: PMC3752570 DOI: 10.3748/wjg.v19.i32.5340] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/05/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To achieve a better understanding of the origination of neuroendocrine (NE) cells in gastric adenocarcinoma.
METHODS: In this study, 120 cases of gastric adenocarcinoma were obtained. First, frozen section-immunohistochemistrical samples were selected from a large quantity of neuroendocrine cells. Second, laser capture microdissection was used to get target cells from gastric adenocarcinoma and whole genome amplification was applied to get a large quantity of DNA for further study. Third, genome-wide microsatellite abnormalities [microsatellite instability (MSI), loss of heterozygosity (LOH)] and p53 mutation were detected by polymerase chain reaction (PCR)-single-strand conformation polymer- phism-silver staining and PCR-sequencing in order to identify the clonality of NE cells.
RESULTS: The total incidence rate of MSI was 27.4%, while LOH was 17.9%. Ten cases had a highest concordance for the two types of cells. The other samples had similar microsatellite changes, except for cases 7 and 10. Concordant p53 mutations exhibited in sample 4, 14, 21 and 27, and there were different mutations between two kinds of cells in case 7. In case 17, mutation took place only in adenocarcinoma cells. p53 mutation was closely related with degree of differentiation, tumor-node-metastasis stage, vessel invasion and lymph node metastasis. In brief, NE and adenocarcinoma cells showed the same MSI, LOH or p53 mutation in most cases (27/30). In the other three cases, different MSI, LOH or p53 mutation occurred.
CONCLUSION: NE and the gastric adenocarcinoma cells may mainly derive from the same stem cells, but the remaining cases showing different origin needs further investigation.
Collapse
|
38
|
Pan YA, Freundlich T, Weissman TA, Schoppik D, Wang XC, Zimmerman S, Ciruna B, Sanes JR, Lichtman JW, Schier AF. Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish. Development 2013; 140:2835-46. [PMID: 23757414 DOI: 10.1242/dev.094631] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Advances in imaging and cell-labeling techniques have greatly enhanced our understanding of developmental and neurobiological processes. Among vertebrates, zebrafish is uniquely suited for in vivo imaging owing to its small size and optical translucency. However, distinguishing and following cells over extended time periods remains difficult. Previous studies have demonstrated that Cre recombinase-mediated recombination can lead to combinatorial expression of spectrally distinct fluorescent proteins (RFP, YFP and CFP) in neighboring cells, creating a 'Brainbow' of colors. The random combination of fluorescent proteins provides a way to distinguish adjacent cells, visualize cellular interactions and perform lineage analyses. Here, we describe Zebrabow (Zebrafish Brainbow) tools for in vivo multicolor imaging in zebrafish. First, we show that the broadly expressed ubi:Zebrabow line provides diverse color profiles that can be optimized by modulating Cre activity. Second, we find that colors are inherited equally among daughter cells and remain stable throughout embryonic and larval stages. Third, we show that UAS:Zebrabow lines can be used in combination with Gal4 to generate broad or tissue-specific expression patterns and facilitate tracing of axonal processes. Fourth, we demonstrate that Zebrabow can be used for long-term lineage analysis. Using the cornea as a model system, we provide evidence that embryonic corneal epithelial clones are replaced by large, wedge-shaped clones formed by centripetal expansion of cells from the peripheral cornea. The Zebrabow tool set presented here provides a resource for next-generation color-based anatomical and lineage analyses in zebrafish.
Collapse
Affiliation(s)
- Y Albert Pan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Sánchez L, Nöthiger R. Clonal analysis ofsex-lethal, a gene needed for female sexual development inDrosophila melanogaster. Wilehm Roux Arch Dev Biol 1982; 191:211-214. [PMID: 28305387 DOI: 10.1007/bf00848339] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/1982] [Accepted: 04/06/1982] [Indexed: 11/30/2022]
Abstract
The mutationSxl f , located on the X-chromosome, is a sex-limited recessive lethal that specifically kills 2X; 2A flies while it does not affect X; 2A flies (Cline 1978). We have analyzed the role ofSxl f on sex determination by a clonal analysis of a new spontaneous allele,Sxl fLS . Female embryos and larvae heterozygous forSxl fLS were irradiated at different times of development to generate homozygousSxl fLS clones which were recognized by linked marker mutations. We have studied the phenotype of such clones on sexually dimorphic regions of the fly (foreleg basitarsus, 5th, 6th and 7th tergites, analia and external genitalia). Despite their female (2X; 2A) chromosomal constitution, clones homozygous forSxl fLS differentiated male structures. These results confirm and extend the preliminary report of Cline (1979). They show that the wildtype product ofSxl f is required for female development.
Collapse
Affiliation(s)
- Lucas Sánchez
- Zoologisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Rolf Nöthiger
- Zoologisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| |
Collapse
|
40
|
Haynie JL, Bryant PJ. The effects of X-rays on the proliferation dynamics of cells in the imaginal wing disc ofDrosophila melanogaster. ACTA ACUST UNITED AC 1977; 183:85-100. [PMID: 28304897 DOI: 10.1007/bf00848779] [Citation(s) in RCA: 174] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/1976] [Accepted: 06/17/1977] [Indexed: 10/26/2022]
Abstract
We report on the size distribution of clones marked by mitotic recombination induced by several different doses of X-rays applied to 72 h oldDrosophila larvae. The results indicate that the radiation significantly reduces the number of cells which undergo normal proliferation in the imaginal wing disc. We estimate that 1000 r reduces by 40-60% the number of cells capable of making a normal contribution to the development of the adult wing. Part of this reduction is due to severe curtailment in the proliferative ability of cells which nevertheless remain capable of adult differentiation; this effect is possibly due to radiation-induced aneuploidy. Cytological evidence suggests that immediate cell death also occurs as a result of radiation doses as low as 100 r. The surviving cells are stimulated to undergo additional proliferation in response to the X-ray damage so that the result is the differentiation of a normal wing.
Collapse
Affiliation(s)
- John L Haynie
- Department of Developmental and Cell Biology and Center for Pathobiology, University of California, 92717, Irvine, California, USA
| | - Peter J Bryant
- Department of Developmental and Cell Biology and Center for Pathobiology, University of California, 92717, Irvine, California, USA
| |
Collapse
|
41
|
Steiner E. Establishment of compartments in the developing leg imaginal discs ofDrosophila melanogaster. ACTA ACUST UNITED AC 1976; 180:9-30. [PMID: 28304893 DOI: 10.1007/BF00848882] [Citation(s) in RCA: 170] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/1976] [Accepted: 04/13/1976] [Indexed: 10/26/2022]
Abstract
-cells they can fill large areas within the compartments of an imaginal disc.The present studies concentrated mainly on the three leg discs. Clones were induced by doses of 1000 r at ages ranging from 3±0.5 h after oviposition to 144 h.All clones induced later than the blastoderm stage were absolutely restricted to either the anterior or the posterior compartment of a disc. The border between the anterior and posterior compartment runs as a straight line along the entire leg and at the distal end separates the two claws (Figs. 5, 6, 7). A further subdivision of the anterior compartment is indicated by clones initiated in the second larval instar (Fig. 11). A parallel subdivision could not be detected in the posterior compartment. Irradiation in the early third instar led to clones which were restricted to single longitudinal bristle rows and leg segments. But no clear-cut compartment borders could be found; in particular a proximo-distal separation appears to be absent.Among the 318 clones induced at the blastoderm stage eleven extended from the wing into the second leg (Fig. 8), or from the haltere into the third leg.With the exception of 3 clones that apparently occupied the anterior as well as the posterior compartment of a wing or a leg, all clones remained confined to either the anterior or the posterior compartment.Frequently clones overlapped left and right forelegs (Fig. 9). Intersegmental overlaps were not observed.The results show that the earliest compartment borders appear in all thoracic discs. This suggests that compartmentalization is a fundamental process common to all discs.
Collapse
|