1
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Skinner OP, Asad S, Haque A. Advances and challenges in investigating B-cells via single-cell transcriptomics. Curr Opin Immunol 2024; 88:102443. [PMID: 38968762 DOI: 10.1016/j.coi.2024.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024]
Abstract
Single-cell RNA sequencing (scRNAseq) and Variable, Diversity, Joining (VDJ) profiling have improved our understanding of B-cells. Recent scRNAseq-based approaches have led to the discovery of intermediate B-cell states, including preplasma cells and pregerminal centre B-cells, as well as unveiling protective roles for B-cells within tertiary lymphoid structures in respiratory infections and cancers. These studies have improved our understanding of transcriptional and epigenetic control of B-cell development and of atypical and memory B-cell differentiation. Advancements in temporal profiling in parallel with transcriptomic and VDJ sequencing have consolidated our understanding of the trajectory of B-cell clones over the course of infection and vaccination. Challenges remain in studying B-cell states across tissues in humans, in relating spatial location with B-cell phenotype and function, in examining antibody isotype switching events, and in unequivocal determination of clonal relationships. Nevertheless, ongoing multiomic assessments and studies of cellular interactions within tissues promise new avenues for improving humoral immunity and combatting autoimmune conditions.
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Affiliation(s)
- Oliver P Skinner
- Department of Microbiology & Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Parkville, Melbourne, VIC 3000, Australia.
| | - Saba Asad
- Department of Microbiology & Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Parkville, Melbourne, VIC 3000, Australia
| | - Ashraful Haque
- Department of Microbiology & Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Parkville, Melbourne, VIC 3000, Australia.
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2
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Rossmann MP, Palis J. Developmental regulation of primitive erythropoiesis. Curr Opin Hematol 2024; 31:71-81. [PMID: 38415349 DOI: 10.1097/moh.0000000000000806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
PURPOSE OF REVIEW In this review, we present an overview of recent studies of primitive erythropoiesis, focusing on advances in deciphering its embryonic origin, defining species-specific differences in its developmental regulation, and better understanding the molecular and metabolic pathways involved in terminal differentiation. RECENT FINDINGS Single-cell transcriptomics combined with state-of-the-art lineage tracing approaches in unperturbed murine embryos have yielded new insights concerning the origin of the first (primitive) erythroid cells that arise from mesoderm-derived progenitors. Moreover, studies examining primitive erythropoiesis in rare early human embryo samples reveal an overall conservation of primitive erythroid ontogeny in mammals, albeit with some interesting differences such as localization of erythropoietin (EPO) production in the early embryo. Mechanistically, the repertoire of transcription factors that critically regulate primitive erythropoiesis has been expanded to include regulators of transcription elongation, as well as epigenetic modifiers such as the histone methyltransferase DOT1L. For the latter, noncanonical roles aside from enzymatic activity are being uncovered. Lastly, detailed surveys of the metabolic and proteomic landscape of primitive erythroid precursors reveal the activation of key metabolic pathways such as pentose phosphate pathway that are paralleled by a striking loss of mRNA translation machinery. SUMMARY The ability to interrogate single cells in vivo continues to yield new insights into the birth of the first essential organ system of the developing embryo. A comparison of the regulation of primitive and definitive erythropoiesis, as well as the interplay of the different layers of regulation - transcriptional, epigenetic, and metabolic - will be critical in achieving the goal of faithfully generating erythroid cells in vitro for therapeutic purposes.
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Affiliation(s)
- Marlies P Rossmann
- Department of Biomedical Genetics and Wilmot Cancer Institute, University of Rochester Medical Center
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
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3
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In vivo clonal tracking reveals evidence of haemangioblast and haematomesoblast contribution to yolk sac haematopoiesis. Nat Commun 2023; 14:41. [PMID: 36596806 PMCID: PMC9810727 DOI: 10.1038/s41467-022-35744-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
During embryogenesis, haematopoietic and endothelial lineages emerge closely in time and space. It is thought that the first blood and endothelium derive from a common clonal ancestor, the haemangioblast. However, investigation of candidate haemangioblasts in vitro revealed the capacity for mesenchymal differentiation, a feature more compatible with an earlier mesodermal precursor. To date, no evidence for an in vivo haemangioblast has been discovered. Using single cell RNA-Sequencing and in vivo cellular barcoding, we have unravelled the ancestral relationships that give rise to the haematopoietic lineages of the yolk sac, the endothelium, and the mesenchyme. We show that the mesodermal derivatives of the yolk sac are produced by three distinct precursors with dual-lineage outcomes: the haemangioblast, the mesenchymoangioblast, and a previously undescribed cell type: the haematomesoblast. Between E5.5 and E7.5, this trio of precursors seeds haematopoietic, endothelial, and mesenchymal trajectories.
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4
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Serrano A, Berthelet J, Naik SH, Merino D. Mastering the use of cellular barcoding to explore cancer heterogeneity. Nat Rev Cancer 2022; 22:609-624. [PMID: 35982229 DOI: 10.1038/s41568-022-00500-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/13/2022] [Indexed: 11/09/2022]
Abstract
Tumours are often composed of a multitude of malignant clones that are genomically unique, and only a few of them may have the ability to escape cancer therapy and grow as symptomatic lesions. As a result, tumours with a large degree of genomic diversity have a higher chance of leading to patient death. However, clonal fate can be driven by non-genomic features. In this context, new technologies are emerging not only to track the spatiotemporal fate of individual cells and their progeny but also to study their molecular features using various omics analysis. In particular, the recent development of cellular barcoding facilitates the labelling of tens to millions of cancer clones and enables the identification of the complex mechanisms associated with clonal fate in different microenvironments and in response to therapy. In this Review, we highlight the recent discoveries made using lentiviral-based cellular barcoding techniques, namely genetic and optical barcoding. We also emphasize the strengths and limitations of each of these technologies and discuss some of the key concepts that must be taken into consideration when one is designing barcoding experiments. Finally, we suggest new directions to further improve the use of these technologies in cancer research.
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Affiliation(s)
- Antonin Serrano
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Jean Berthelet
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Shalin H Naik
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Delphine Merino
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Victoria, Australia.
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5
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Chen C, Liao Y, Peng G. Connecting past and present: single-cell lineage tracing. Protein Cell 2022; 13:790-807. [PMID: 35441356 PMCID: PMC9237189 DOI: 10.1007/s13238-022-00913-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/06/2022] [Indexed: 01/16/2023] Open
Abstract
Central to the core principle of cell theory, depicting cells’ history, state and fate is a fundamental goal in modern biology. By leveraging clonal analysis and single-cell RNA-seq technologies, single-cell lineage tracing provides new opportunities to interrogate both cell states and lineage histories. During the past few years, many strategies to achieve lineage tracing at single-cell resolution have been developed, and three of them (integration barcodes, polylox barcodes, and CRISPR barcodes) are noteworthy as they are amenable in experimentally tractable systems. Although the above strategies have been demonstrated in animal development and stem cell research, much care and effort are still required to implement these methods. Here we review the development of single-cell lineage tracing, major characteristics of the cell barcoding strategies, applications, as well as technical considerations and limitations, providing a guide to choose or improve the single-cell barcoding lineage tracing.
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Affiliation(s)
- Cheng Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yuanxin Liao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangdun Peng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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6
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Shen S, Sun Y, Matsumoto M, Shim WJ, Sinniah E, Wilson SB, Werner T, Wu Z, Bradford ST, Hudson J, Little MH, Powell J, Nguyen Q, Palpant NJ. Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends Mol Med 2021; 27:1135-1158. [PMID: 34657800 DOI: 10.1016/j.molmed.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022]
Abstract
Pluripotent stem cells underpin a growing sector that leverages their differentiation potential for research, industry, and clinical applications. This review evaluates the landscape of methods in single-cell transcriptomics that are enabling accelerated discovery in stem cell science. We focus on strategies for scaling stem cell differentiation through multiplexed single-cell analyses, for evaluating molecular regulation of cell differentiation using new analysis algorithms, and methods for integration and projection analysis to classify and benchmark stem cell derivatives against in vivo cell types. By discussing the available methods, comparing their strengths, and illustrating strategies for developing integrated analysis pipelines, we provide user considerations to inform their implementation and interpretation.
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Affiliation(s)
- Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Maika Matsumoto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Sean B Wilson
- Murdoch Children's Research Institute, Melbourne, Australia
| | - Tessa Werner
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Zhixuan Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - James Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Joseph Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia; UNSW Cellular Genomics Futures Institute, UNSW, Sydney, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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7
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Michki NS, Li Y, Sanjasaz K, Zhao Y, Shen FY, Walker LA, Cao W, Lee CY, Cai D. The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis. Cell Rep 2021; 35:109039. [PMID: 33909998 PMCID: PMC8139287 DOI: 10.1016/j.celrep.2021.109039] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/19/2021] [Accepted: 04/06/2021] [Indexed: 01/16/2023] Open
Abstract
The Drosophila type II neuroblast lineages present an attractive model to investigate the neurogenesis and differentiation process as they adapt to a process similar to that in the human outer subventricular zone. We perform targeted single-cell mRNA sequencing in third instar larval brains to study this process of the type II NB lineage. Combining prior knowledge, in silico analyses, and in situ validation, our multi-informatic investigation describes the molecular landscape from a single developmental snapshot. 17 markers are identified to differentiate distinct maturation stages. 30 markers are identified to specify the stem cell origin and/or cell division numbers of INPs, and at least 12 neuronal subtypes are identified. To foster future discoveries, we provide annotated tables of pairwise gene-gene correlation in single cells and MiCV, a web tool for interactively analyzing scRNA-seq datasets. Taken together, these resources advance our understanding of the neural differentiation process at the molecular level.
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Affiliation(s)
- Nigel S Michki
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA
| | - Ye Li
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kayvon Sanjasaz
- Molecular, Cellular, and Developmental Biology LS&A, University of Michigan, Ann Arbor, MI, USA
| | - Yimeng Zhao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fred Y Shen
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Logan A Walker
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA
| | - Wenjia Cao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Cheng-Yu Lee
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dawen Cai
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA.
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8
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Hausmann A, Hardt WD. Elucidating host-microbe interactions in vivo by studying population dynamics using neutral genetic tags. Immunology 2020; 162:341-356. [PMID: 32931019 PMCID: PMC7968395 DOI: 10.1111/imm.13266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/21/2020] [Accepted: 08/29/2020] [Indexed: 12/14/2022] Open
Abstract
Host–microbe interactions are highly dynamic in space and time, in particular in the case of infections. Pathogen population sizes, microbial phenotypes and the nature of the host responses often change dramatically over time. These features pose particular challenges when deciphering the underlying mechanisms of these interactions experimentally, as traditional microbiological and immunological methods mostly provide snapshots of population sizes or sparse time series. Recent approaches – combining experiments using neutral genetic tags with stochastic population dynamic models – allow more precise quantification of biologically relevant parameters that govern the interaction between microbe and host cell populations. This is accomplished by exploiting the patterns of change of tag composition in the microbe or host cell population under study. These models can be used to predict the effects of immunodeficiencies or therapies (e.g. antibiotic treatment) on populations and thereby generate hypotheses and refine experimental designs. In this review, we present tools to study population dynamics in vivo using genetic tags, explain examples for their implementation and briefly discuss future applications.
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Affiliation(s)
- Annika Hausmann
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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9
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Pucella JN, Upadhaya S, Reizis B. The Source and Dynamics of Adult Hematopoiesis: Insights from Lineage Tracing. Annu Rev Cell Dev Biol 2020; 36:529-550. [PMID: 32580566 DOI: 10.1146/annurev-cellbio-020520-114601] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The generation of all blood cell lineages (hematopoiesis) is sustained throughout the entire life span of adult mammals. Studies using cell transplantation identified the self-renewing, multipotent hematopoietic stem cells (HSCs) as the source of hematopoiesis in adoptive hosts and delineated a hierarchy of HSC-derived progenitors that ultimately yield mature blood cells. However, much less is known about adult hematopoiesis as it occurs in native hosts, i.e., without transplantation. Here we review recent advances in our understanding of native hematopoiesis, focusing in particular on the application of genetic lineage tracing in mice. The emerging evidence has established HSCs as the major source of native hematopoiesis, helped to define the kinetics of HSC differentiation, and begun exploring native hematopoiesis in stress conditions such as aging and inflammation. Major outstanding questions about native hematopoiesis still remain, such as its clonal composition, the nature of lineage commitment, and the dynamics of the process in humans.
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Affiliation(s)
- Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; , ,
| | - Samik Upadhaya
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; , ,
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; , ,
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10
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Pei W, Wang X, Rössler J, Feyerabend TB, Höfer T, Rodewald HR. Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nat Protoc 2019; 14:1820-1840. [PMID: 31110297 DOI: 10.1038/s41596-019-0163-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/12/2019] [Indexed: 01/02/2023]
Abstract
Fate mapping is a powerful genetic tool for linking stem or progenitor cells with their progeny, and hence for defining cell lineages in vivo. The resolution of fate mapping depends on the numbers of distinct markers that are introduced in the beginning into stem or progenitor cells; ideally, numbers should be sufficiently large to allow the tracing of output from individual cells. Highly diverse genetic barcodes can serve this purpose. We recently developed an endogenous genetic barcoding system, termed Polylox. In Polylox, random DNA recombination can be induced by transient activity of Cre recombinase in a 2.1-kb-long artificial recombination substrate that has been introduced into a defined locus in mice (Rosa26Polylox reporter mice). Here, we provide a step-by-step protocol for the use of Polylox, including barcode induction and estimation of induction efficiency, barcode retrieval with single-molecule real-time (SMRT) DNA sequencing followed by computational barcode identification, and the calculation of barcode-generation probabilities, which is key for estimations of single-cell labeling for a given number of stem cells. Thus, Polylox barcoding enables high-resolution fate mapping in essentially all tissues in mice for which inducible Cre driver lines are available. Alternative methods include ex vivo cell barcoding, inducible transposon insertion and CRISPR-Cas9-based barcoding; Polylox currently allows combining non-invasive and cell-type-specific labeling with high label diversity. The execution time of this protocol is ~2-3 weeks for experimental data generation and typically <2 d for computational Polylox decoding and downstream analysis.
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Affiliation(s)
- Weike Pei
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Xi Wang
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Jens Rössler
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany. .,Bioquant Center, University of Heidelberg, Heidelberg, Germany.
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
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11
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Li Y, Wu Y, Ma L, Guo Z, Xiao W, Yuan Y. Loss of heterozygosity by SCRaMbLEing. SCIENCE CHINA-LIFE SCIENCES 2019; 62:381-393. [PMID: 30900161 DOI: 10.1007/s11427-019-9504-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Abstract
Genetic variation drives phenotypic evolution within populations. Genetic variation can be divided into different forms according to the size of genomic changes. However, study of large-scale genomic variation such as structural variation and aneuploidy is still limited and mainly based on the static, predetermined feature of individual genomes. Here, using SCRaMbLE, different levels of loss of heterozygosity (LOH) events including short-range LOH, long-range LOH and whole chromosome LOH were detected in evolved strains. By contrast, using rapid adaptive evolution, aneuploidy was detected in the adaptive strains. It was further found that deletion of gene GLN3, long-range LOH in the left arm of synthetic chromosome X, whole chromosome LOH of synthetic chromosome X, and duplication of chromosome VIII (trisomy) lead to increased rapamycin resistance in synthetic yeast. Comparative analysis of genome stability of evolved strains indicates that the aneuploid strain has a higher frequency of degeneration than the SCRaMbLEd strain. These findings enrich our understanding of genetic mechanism of rapamycin resistance in yeast, and provide valuable insights into yeast genome architecture and function.
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Affiliation(s)
- Yunxiang Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yi Wu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Lu Ma
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Zhou Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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12
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Pei W, Feyerabend TB, Rössler J, Wang X, Postrach D, Busch K, Rode I, Klapproth K, Dietlein N, Quedenau C, Chen W, Sauer S, Wolf S, Höfer T, Rodewald HR. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature 2017; 548:456-460. [PMID: 28813413 PMCID: PMC5905670 DOI: 10.1038/nature23653] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 07/19/2017] [Indexed: 01/03/2023]
Abstract
Developmental deconvolution of complex organs and tissues at the level of
individual cells remains challenging. Non-invasive genetic fate mapping1 has been widely used, but the low number
of distinct fluorescent marker proteins limits its resolution. Much higher
numbers of cell markers have been generated using viral integration sites2, viral barcodes3, and strategies based on transposons4 and CRISPR/Cas9 genome editing5; however, temporal and tissue-specific induction of
barcodes in situ has not been achieved. Here we report the development of an
artificial DNA recombination locus (termed Polylox) that
enables broadly applicable endogenous barcoding based on the
Cre-loxP recombination system6,7. Polylox
recombination in situ reaches a practical diversity of several hundred thousand
barcodes, allowing tagging of single cells. We have used this experimental
system, combined with fate mapping, to assess haematopoietic stem cell (HSC)
fates in vivo. Classical models of haematopoietic lineage specification assume a
tree with few major branches. More recently, driven in part by the development
of more efficient single-cell assays and improved transplantation efficiencies,
different models have been proposed, in which unilineage priming may occur in
mice and humans at the level of HSCs8–10. We have
introduced barcodes into HSC progenitors in embryonic mice, and found that the
adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which
are unexpectedly large. Most HSC clones gave rise to multilineage or
oligolineage fates, arguing against unilineage priming, and suggesting coherent
usage of the potential of cells in a clone. The spreading of barcodes, both
after induction in embryos and in adult mice, revealed a basic split between
common myeloid-erythroid development and common lymphocyte development,
supporting the long-held but contested view of a tree-like haematopoietic
structure.
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Affiliation(s)
- Weike Pei
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Jens Rössler
- Division of Theoretical Systems Biology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Xi Wang
- Division of Theoretical Systems Biology, German Cancer Research Center, D-69120 Heidelberg, Germany.,Max Delbrück Center, Scientific Genomics Platforms (BIMSB/BIH), D-13125 Berlin, Germany
| | - Daniel Postrach
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Katrin Busch
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Immanuel Rode
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Kay Klapproth
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Nikolaus Dietlein
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Claudia Quedenau
- Max Delbrück Center, Scientific Genomics Platforms (BIMSB/BIH), D-13125 Berlin, Germany
| | - Wei Chen
- Max Delbrück Center, Scientific Genomics Platforms (BIMSB/BIH), D-13125 Berlin, Germany
| | - Sascha Sauer
- Max Delbrück Center, Scientific Genomics Platforms (BIMSB/BIH), D-13125 Berlin, Germany
| | - Stephan Wolf
- Genomics &Proteomics Core Facilities, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, D-69120 Heidelberg, Germany.,Bioquant Center, University of Heidelberg, D-69120 Heidelberg, Germany
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, D-69120 Heidelberg, Germany
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Krueger A, Ziętara N, Łyszkiewicz M. T Cell Development by the Numbers. Trends Immunol 2016; 38:128-139. [PMID: 27842955 DOI: 10.1016/j.it.2016.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023]
Abstract
T cells are continually generated in the thymus in a highly dynamic process comprising discrete steps of lineage commitment, T cell receptor (TCR) gene rearrangement, and selection. These steps are linked to distinct rates of proliferation, survival, and cell death, but a quantitative picture of T cell development is only beginning to emerge. Here we summarize recent technical advances, including genetic fate mapping, barcoding, and molecular timers, that have allowed the implementation of computational models to quantify developmental dynamics in the thymus. Coupling new techniques with mathematical models has recently resulted in the emergence of new paradigms in early hematopoiesis and might similarly open new perspectives on T cell development.
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Affiliation(s)
- Andreas Krueger
- Institute of Molecular Medicine, Goethe University Frankfurt am Main, 60590 Frankfurt am Main, Germany.
| | - Natalia Ziętara
- Dr von Hauner Children's Hospital, Ludwig Maximilian University, 80337 Munich, Germany
| | - Marcin Łyszkiewicz
- Dr von Hauner Children's Hospital, Ludwig Maximilian University, 80337 Munich, Germany
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