1
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Mold JE, Weissman MH, Ratz M, Hagemann-Jensen M, Hård J, Eriksson CJ, Toosi H, Berghenstråhle J, Ziegenhain C, von Berlin L, Martin M, Blom K, Lagergren J, Lundeberg J, Sandberg R, Michaëlsson J, Frisén J. Clonally heritable gene expression imparts a layer of diversity within cell types. Cell Syst 2024; 15:149-165.e10. [PMID: 38340731 DOI: 10.1016/j.cels.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 05/25/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, heritable differences in gene expression can impart diversity within cells of the same type. Studying clonal human lymphocytes and mouse brain cells, we uncovered a vast diversity of heritable gene expression patterns among different clones of cells of the same type in vivo. We combined chromatin accessibility and RNA profiling on different lymphocyte clones to reveal thousands of regulatory regions exhibiting interclonal variation, which could be directly linked to interclonal variation in gene expression. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging, and disease. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Martin H Weissman
- Mathematics Department, University of California, Santa Cruz, CA, USA.
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Carl-Johan Eriksson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Hosein Toosi
- SciLifeLab, Computational Science and Technology Department, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joseph Berghenstråhle
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Leonie von Berlin
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Stockholm, Sweden
| | - Kim Blom
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Jens Lagergren
- SciLifeLab, Computational Science and Technology Department, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joakim Lundeberg
- SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden.
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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2
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Sun W, Perkins M, Huyghe M, Faraldo MM, Fre S, Perié L, Lyne AM. Extracting, filtering and simulating cellular barcodes using CellBarcode tools. NATURE COMPUTATIONAL SCIENCE 2024; 4:128-143. [PMID: 38374363 PMCID: PMC10899113 DOI: 10.1038/s43588-024-00595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Identifying true DNA cellular barcodes among polymerase chain reaction and sequencing errors is challenging. Current tools are restricted in the diversity of barcode types supported or the analysis strategies implemented. As such, there is a need for more versatile and efficient tools for barcode extraction, as well as for tools to investigate which factors impact barcode detection and which filtering strategies to best apply. Here we introduce the package CellBarcode and its barcode simulation kit, CellBarcodeSim, that allows efficient and versatile barcode extraction and filtering for a range of barcode types from bulk or single-cell sequencing data using a variety of filtering strategies. Using the barcode simulation kit and biological data, we explore the technical and biological factors influencing barcode identification and provide a decision tree on how to optimize barcode identification for different barcode settings. We believe that CellBarcode and CellBarcodeSim have the capability to enhance the reproducibility and interpretation of barcode results across studies.
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Affiliation(s)
- Wenjie Sun
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
| | - Meghan Perkins
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Mathilde Huyghe
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Marisa M Faraldo
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Silvia Fre
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
| | - Anne-Marie Lyne
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
- INSERM U900, Paris, France.
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France.
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3
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Moussion C, Delamarre L. Antigen cross-presentation by dendritic cells: A critical axis in cancer immunotherapy. Semin Immunol 2024; 71:101848. [PMID: 38035643 DOI: 10.1016/j.smim.2023.101848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells that play a key role in shaping adaptive immunity. DCs have a unique ability to sample their environment, capture and process exogenous antigens into peptides that are then loaded onto major histocompatibility complex class I molecules for presentation to CD8+ T cells. This process, called cross-presentation, is essential for initiating and regulating CD8+ T cell responses against tumors and intracellular pathogens. In this review, we will discuss the role of DCs in cancer immunity, the molecular mechanisms underlying antigen cross-presentation by DCs, the immunosuppressive factors that limit the efficiency of this process in cancer, and approaches to overcome DC dysfunction and therapeutically promote antitumoral immunity.
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Affiliation(s)
| | - Lélia Delamarre
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA.
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4
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Bhargava R, Li H, Tsokos GC. Pathogenesis of lupus nephritis: the contribution of immune and kidney resident cells. Curr Opin Rheumatol 2023; 35:107-116. [PMID: 35797522 DOI: 10.1097/bor.0000000000000887] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE OF REVIEW Lupus nephritis is associated with significant mortality and morbidity. We lack effective therapeutics and biomarkers mostly because of our limited understanding of its complex pathogenesis. We aim to present an overview of the recent advances in the field to gain a deeper understanding of the underlying cellular and molecular mechanisms involved in lupus nephritis pathogenesis. RECENT FINDINGS Recent studies have identified distinct roles for each resident kidney cell in the pathogenesis of lupus nephritis. Podocytes share many elements of innate and adaptive immune cells and they can present antigens and participate in the formation of crescents in coordination with parietal epithelial cells. Mesangial cells produce pro-inflammatory cytokines and secrete extracellular matrix contributing to glomerular fibrosis. Tubular epithelial cells modulate the milieu of the interstitium to promote T cell infiltration and formation of tertiary lymphoid organs. Modulation of specific genes in kidney resident cells can ward off the effectors of the autoimmune response including autoantibodies, cytokines and immune cells. SUMMARY The development of lupus nephritis is multifactorial involving genetic susceptibility, environmental triggers and systemic inflammation. However, the role of resident kidney cells in the development of lupus nephritis is becoming more defined and distinct. More recent studies point to the restoration of kidney resident cell function using cell targeted approaches to prevent and treat lupus nephritis.
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Affiliation(s)
- Rhea Bhargava
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard, Medical School, Boston, Massachusetts, USA
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5
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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: 11] [Impact Index Per Article: 5.5] [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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6
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Feng J, Pucella JN, Jang G, Alcántara-Hernández M, Upadhaya S, Adams NM, Khodadadi-Jamayran A, Lau CM, Stoeckius M, Hao S, Smibert P, Tsirigos A, Idoyaga J, Reizis B. Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells. Immunity 2022; 55:405-422.e11. [PMID: 35180378 PMCID: PMC9344860 DOI: 10.1016/j.immuni.2022.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/23/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022]
Abstract
Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s, and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ pro-pDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s.
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Affiliation(s)
- Jue Feng
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Joseph N Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Geunhyo Jang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samik Upadhaya
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Nicholas M Adams
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Colleen M Lau
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Marlon Stoeckius
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Stephanie Hao
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Peter Smibert
- Technology Innovation Laboratory, New York Genome Center, New York, NY 10013, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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7
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Fennell KA, Vassiliadis D, Lam EYN, Martelotto LG, Balic JJ, Hollizeck S, Weber TS, Semple T, Wang Q, Miles DC, MacPherson L, Chan YC, Guirguis AA, Kats LM, Wong ES, Dawson SJ, Naik SH, Dawson MA. Non-genetic determinants of malignant clonal fitness at single-cell resolution. Nature 2021; 601:125-131. [PMID: 34880496 DOI: 10.1038/s41586-021-04206-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 10/30/2021] [Indexed: 12/14/2022]
Abstract
All cancers emerge after a period of clonal selection and subsequent clonal expansion. Although the evolutionary principles imparted by genetic intratumour heterogeneity are becoming increasingly clear1, little is known about the non-genetic mechanisms that contribute to intratumour heterogeneity and malignant clonal fitness2. Here, using single-cell profiling and lineage tracing (SPLINTR)-an expressed barcoding strategy-we trace isogenic clones in three clinically relevant mouse models of acute myeloid leukaemia. We find that malignant clonal dominance is a cell-intrinsic and heritable property that is facilitated by the repression of antigen presentation and increased expression of the secretory leukocyte peptidase inhibitor gene (Slpi), which we genetically validate as a regulator of acute myeloid leukaemia. Increased transcriptional heterogeneity is a feature that enables clonal fitness in diverse tissues and immune microenvironments and in the context of clonal competition between genetically distinct clones. Similar to haematopoietic stem cells3, leukaemia stem cells (LSCs) display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. We demonstrate that LSC clonal output dictates sensitivity to chemotherapy and, although high- and low-output clones adapt differently to therapeutic pressure, they coordinately emerge from minimal residual disease with increased expression of the LSC program. Together, these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness and may inform future therapeutic strategies.
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Affiliation(s)
- Katie A Fennell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Luciano G Martelotto
- The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jesse J Balic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sebastian Hollizeck
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tom S Weber
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy Semple
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Qing Wang
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Denise C Miles
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew A Guirguis
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lev M Kats
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia. .,The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia.
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8
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Zhang S, Afanassiev A, Greenstreet L, Matsumoto T, Schiebinger G. Optimal transport analysis reveals trajectories in steady-state systems. PLoS Comput Biol 2021; 17:e1009466. [PMID: 34860824 PMCID: PMC8691649 DOI: 10.1371/journal.pcbi.1009466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/21/2021] [Accepted: 09/20/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how cells change their identity and behaviour in living systems is an important question in many fields of biology. The problem of inferring cell trajectories from single-cell measurements has been a major topic in the single-cell analysis community, with different methods developed for equilibrium and non-equilibrium systems (e.g. haematopoeisis vs. embryonic development). We show that optimal transport analysis, a technique originally designed for analysing time-courses, may also be applied to infer cellular trajectories from a single snapshot of a population in equilibrium. Therefore, optimal transport provides a unified approach to inferring trajectories that is applicable to both stationary and non-stationary systems. Our method, StationaryOT, is mathematically motivated in a natural way from the hypothesis of a Waddington's epigenetic landscape. We implement StationaryOT as a software package and demonstrate its efficacy in applications to simulated data as well as single-cell data from Arabidopsis thaliana root development.
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Affiliation(s)
- Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Tetsuya Matsumoto
- Department of Mathematics, University of British Columbia, Vancouver, Canada
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9
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In Vivo Tracking of Hematopoietic Stem and Progenitor Cell Ontogeny by Cellular Barcoding. Methods Mol Biol 2021. [PMID: 34057730 DOI: 10.1007/978-1-0716-1425-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cellular barcoding is a powerful technique that allows for high-throughput mapping of the fate of single cells, notably hematopoietic stem and progenitor cells (HSPCs) after transplantation. Unique artificial DNA fragments, termed barcodes, are stably inserted into HSPCs using lentiviral transduction, making sure that each individual cell receives a single unique barcode. Barcoded HSPCs are transplanted into sublethally irradiated mice where they reconstitute the hematopoietic system through proliferation and differentiation. During this process, the barcode of each HSPC is inherited by all of its daughter cells and their subsequent mature hematopoietic cell progeny. After sorting mature hematopoietic cell subsets, their barcodes can be retrieved from genomic DNA through nested PCR and sequencing. Analysis of barcode sequencing results allows for determination of clonal relationships between the mature cells, that is, which cell types were produced by a single barcoded HSPC, as well as the heterogeneity of the initial HSPC population. Here, we give a detailed protocol of a complete HSPC cellular barcoding experiment, starting with barcode lentivirus production, isolation, transduction, and transplantation of HSPCs, isolation of target cells followed by PCR amplification and sequencing of DNA barcodes. Finally, we describe the basic filtering and analysis steps of barcode sequencing data to ensure high-quality results.
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10
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Munoz-Erazo L, Schmidt AJ, Price KM. High-Dimensional Image Analysis using Histocytometry. Curr Protoc 2021; 1:e184. [PMID: 34165879 DOI: 10.1002/cpz1.184] [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] [Indexed: 12/27/2022]
Abstract
Histocytometry is a technique for processing multiparameter microscopy images using computational approaches to identify and quantify cellular phenotypes. It allows for spatial analyses of cellular phenotypes in relation to each other and within defined spatial regions. The benefit of this technique over manual annotation and characterization of cells is a high degree of automation/throughput, significantly decreased user bias, and increased reproducibility. Recently, an increase in freely available software amenable to or deliberately designed for histocytometry has resulted in these complex analyses being available to a broader base of users who have amassed multi-component microscopic imaging data. This article provides an overview of a histocytometry pipeline, focusing on the strategic planning and software requirements to allow readers to perform cell segmentation, phenotyping, and spatial analyses to advance their research outputs. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
| | | | - Kylie M Price
- Malaghan Institute of Medical Research, Wellington, New Zealand
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11
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Tian L, Tomei S, Schreuder J, Weber TS, Amann-Zalcenstein D, Lin DS, Tran J, Audiger C, Chu M, Jarratt A, Willson T, Hilton A, Pang ES, Patton T, Kelly M, Su S, Gouil Q, Diakumis P, Bahlo M, Sargeant T, Kats LM, Hodgkin PD, O'Keeffe M, Ng AP, Ritchie ME, Naik SH. Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development. Immunity 2021; 54:1338-1351.e9. [PMID: 33862015 DOI: 10.1016/j.immuni.2021.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/05/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022]
Abstract
Despite advances in single-cell multi-omics, a single stem or progenitor cell can only be tested once. We developed clonal multi-omics, in which daughters of a clone act as surrogates of the founder, thereby allowing multiple independent assays per clone. With SIS-seq, clonal siblings in parallel "sister" assays are examined either for gene expression by RNA sequencing (RNA-seq) or for fate in culture. We identified, and then validated using CRISPR, genes that controlled fate bias for different dendritic cell (DC) subtypes. This included Bcor as a suppressor of plasmacytoid DC (pDC) and conventional DC type 2 (cDC2) numbers during Flt3 ligand-mediated emergency DC development. We then developed SIS-skew to examine development of wild-type and Bcor-deficient siblings of the same clone in parallel. We found Bcor restricted clonal expansion, especially for cDC2s, and suppressed clonal fate potential, especially for pDCs. Therefore, SIS-seq and SIS-skew can reveal the molecular and cellular mechanisms governing clonal fate.
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Affiliation(s)
- Luyi Tian
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sara Tomei
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Jaring Schreuder
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Tom S Weber
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Daniela Amann-Zalcenstein
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Single Cell Open Research Endeavour (SCORE), The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Dawn S Lin
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Jessica Tran
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Cindy Audiger
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Mathew Chu
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Andrew Jarratt
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Tracy Willson
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Adrienne Hilton
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Ee Shan Pang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Timothy Patton
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Madison Kelly
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Shian Su
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Quentin Gouil
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter Diakumis
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Toby Sargeant
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Lev M Kats
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Philip D Hodgkin
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Meredith O'Keeffe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ashley P Ng
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Matthew E Ritchie
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Shalin H Naik
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Single Cell Open Research Endeavour (SCORE), The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.
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12
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Espinoza DA, Mortlock RD, Koelle SJ, Wu C, Dunbar CE. Interrogation of clonal tracking data using barcodetrackR. NATURE COMPUTATIONAL SCIENCE 2021; 1:280-289. [PMID: 37621673 PMCID: PMC10449013 DOI: 10.1038/s43588-021-00057-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/17/2021] [Indexed: 08/26/2023]
Abstract
Clonal tracking methods provide quantitative insights into the cellular output of genetically labelled progenitor cells across time and cellular compartments. In the context of gene and cell therapies, clonal tracking methods have enabled the tracking of progenitor cell output both in humans receiving therapies and in corresponding animal models, providing valuable insight into lineage reconstitution, clonal dynamics, and vector genotoxicity. However, the absence of a toolbox for analysis of clonal tracking data has precluded the development of standardized analytical frameworks within the field. Thus, we developed barcodetrackR, an R package and accompanying Shiny app containing diverse tools for the analysis and visualization of clonal tracking data. We demonstrate the utility of barcodetrackR in exploring longitudinal clonal patterns and lineage relationships in a number of clonal tracking studies of hematopoietic stem and progenitor cells (HSPCs) in humans receiving HSPC gene therapy and in animals receiving lentivirally transduced HSPC transplants or tumor cells.
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Affiliation(s)
- Diego A. Espinoza
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryland D. Mortlock
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samson J. Koelle
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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13
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Lin DS, Tian L, Tomei S, Amann-Zalcenstein D, Baldwin TM, Weber TS, Schreuder J, Stonehouse OJ, Rautela J, Huntington ND, Taoudi S, Ritchie ME, Hodgkin PD, Ng AP, Nutt SL, Naik SH. Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development. Nat Cell Biol 2021; 23:219-231. [PMID: 33649477 DOI: 10.1038/s41556-021-00636-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/19/2021] [Indexed: 01/31/2023]
Abstract
Regulation of haematopoietic stem and progenitor cell (HSPC) fate is crucial during homeostasis and under stress conditions. Here we examine the aetiology of the Flt3 ligand (Flt3L)-mediated increase of type 1 conventional dendritic cells (cDC1s). Using cellular barcoding we demonstrate this occurs through selective clonal expansion of HSPCs that are primed to produce cDC1s and not through activation of cDC1 fate by other HSPCs. In particular, multi/oligo-potent clones selectively amplify their cDC1 output, without compromising the production of other lineages, via a process we term tuning. We then develop Divi-Seq to simultaneously profile the division history, surface phenotype and transcriptome of individual HSPCs. We discover that Flt3L-responsive HSPCs maintain a proliferative 'early progenitor'-like state, leading to the selective expansion of multiple transitional cDC1-primed progenitor stages that are marked by Irf8 expression. These findings define the mechanistic action of Flt3L through clonal tuning, which has important implications for other models of 'emergency' haematopoiesis.
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Affiliation(s)
- Dawn S Lin
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Luyi Tian
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Sara Tomei
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Daniela Amann-Zalcenstein
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Tracey M Baldwin
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Blood Cells and Blood Cancer Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Tom S Weber
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jaring Schreuder
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Olivia J Stonehouse
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Jai Rautela
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Nicholas D Huntington
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Samir Taoudi
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Matthew E Ritchie
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Philip D Hodgkin
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Ashley P Ng
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Blood Cells and Blood Cancer Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
| | - Stephen L Nutt
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Shalin H Naik
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute, Parkville, VIC, Australia.
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14
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Stadler T, Pybus OG, Stumpf MPH. Phylodynamics for cell biologists. Science 2021; 371:371/6526/eaah6266. [PMID: 33446527 DOI: 10.1126/science.aah6266] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how "tree thinking" is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data.
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Affiliation(s)
- T Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
| | - M P H Stumpf
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia.
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15
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A new lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics. Nat Immunol 2020; 21:1574-1584. [PMID: 33077975 DOI: 10.1038/s41590-020-0799-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 08/27/2020] [Indexed: 12/21/2022]
Abstract
A classical view of blood cell development is that multipotent hematopoietic stem and progenitor cells (HSPCs) become lineage-restricted at defined stages. Lin-c-Kit+Sca-1+Flt3+ cells, termed lymphoid-primed multipotent progenitors (LMPPs), have lost megakaryocyte and erythroid potential but are heterogeneous in their fate. Here, through single-cell RNA sequencing, we identify the expression of Dach1 and associated genes in this fraction as being coexpressed with myeloid/stem genes but inversely correlated with lymphoid genes. Through generation of Dach1-GFP reporter mice, we identify a transcriptionally and functionally unique Dach1-GFP- subpopulation within LMPPs with lymphoid potential with low to negligible classic myeloid potential. We term these 'lymphoid-primed progenitors' (LPPs). These findings define an early definitive branch point of lymphoid development in hematopoiesis and a means for prospective isolation of LPPs.
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16
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Audiger C, Lesage S. FLT3 Ligand Is Dispensable for the Final Stage of Type 1 Conventional Dendritic Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2020; 205:2117-2127. [PMID: 32887750 DOI: 10.4049/jimmunol.2000742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/10/2020] [Indexed: 12/29/2022]
Abstract
Conventional dendritic cells (cDCs) are comprised of two major subsets, type 1 cDC (cDC1) and type 2 cDC (cDC2). As each cDC subset differentially influences the nature of immune responses, we sought factors that would allow the manipulation of their relative abundance. Notably, cDC1 are less abundant than cDC2 in both lymphoid and nonlymphoid organs. We demonstrate that this bias is already apparent in bone marrow precommitted precursors. However, comparison of five common inbred strains revealed a disparity in precursor-product relationship, in which mice with fewer precursors to cDC1 had more cDC1. This disparity associated with contrasting variations in CD135 (FLT3) expression on cDC subsets. Hence, we characterized the response to FLT3 ligand during cDC1 and cDC2 lineage differentiation and find that although FLT3 ligand is required throughout cDC2 differentiation, it is surprisingly dispensable during late-stage cDC1 differentiation. Overall, we find that tight regulation of FLT3 ligand levels throughout cDC differentiation dictates the cDC1 to cDC2 ratio in lymphoid organs.
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Affiliation(s)
- Cindy Audiger
- Department of Immunology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada; and Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
| | - Sylvie Lesage
- Department of Immunology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec H1T 2M4, Canada; and Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec H3C 3J7, Canada
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17
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Carrelha J, Lin DS, Rodriguez-Fraticelli AE, Luis TC, Wilkinson AC, Cabezas-Wallscheid N, Tremblay CS, Haas S. Single-cell lineage tracing approaches in hematology research: technical considerations. Exp Hematol 2020; 89:26-36. [PMID: 32735908 PMCID: PMC7894992 DOI: 10.1016/j.exphem.2020.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023]
Abstract
The coordinated differentiation of hematopoietic stem and progenitor cells (HSPCs) into the various mature blood cell types is responsible for sustaining blood and immune system homeostasis. The cell fate decisions underlying this important biological process are made at the level of single cells. Methods to trace the fate of single cells are therefore essential for understanding hematopoietic system activity in health and disease and have had a major impact on how we understand and represent hematopoiesis. Here, we discuss the basic methodologies and technical considerations for three important clonal assays: single-cell transplantation, lentiviral barcoding, and Sleeping Beauty barcoding. This perspective is a synthesis of presentations and discussions from the 2019 International Society for Experimental Hematology (ISEH) Annual Meeting New Investigator Technology Session and the 2019 ISEH Winter Webinar.
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Affiliation(s)
- Joana Carrelha
- Haematopoietic Stem Cell Laboratory, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Dawn S Lin
- Immunology, The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Alejo E Rodriguez-Fraticelli
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Tiago C Luis
- Department of Life Sciences, Imperial College London, London, UK
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Cedric S Tremblay
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
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18
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Abstract
Animals begin life as a single cell that divides and differentiates to form a complex body. In doing so, cells make a sequence of fate decisions, often depicted as a tree. A goal in developmental biology is to chart the structure of this tree across tissues, typically by tagging cells and tracking their offspring. Recent advances in DNA sequencing enable tracking thousands of cells simultaneously using unique DNA barcodes, but one can construct false differentiation hierarchies from barcode data. Here, we apply the theory of branching processes to derive conditions under which barcode statistics correctly encode developmental hierarchy. We use this formal basis to develop a practical pipeline for analyzing lineage barcoding experiments. The pipeline is demonstrated in studying hematopoiesis. A central task in developmental biology is to learn the sequence of fate decisions that leads to each mature cell type in a tissue or organism. Recently, clonal labeling of cells using DNA barcodes has emerged as a powerful approach for identifying cells that share a common ancestry of fate decisions. Here we explore the idea that stochasticity of cell fate choice during tissue development could be harnessed to read out lineage relationships after a single step of clonal barcoding. By considering a generalized multitype branching process, we determine the conditions under which the final distribution of barcodes over observed cell types encodes their bona fide lineage relationships. We then propose a method for inferring the order of fate decisions. Our theory predicts a set of symmetries of barcode covariance that serves as a consistency check for the validity of the method. We show that broken symmetries may be used to detect multiple paths of differentiation to the same cell types. We provide computational tools for general use. When applied to barcoding data in hematopoiesis, these tools reconstruct the classical hematopoietic hierarchy and detect couplings between monocytes and dendritic cells and between erythrocytes and basophils that suggest multiple pathways of differentiation for these lineages.
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19
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Naik SH. Dendritic cell development at a clonal level within a revised 'continuous' model of haematopoiesis. Mol Immunol 2020; 124:190-197. [PMID: 32593782 DOI: 10.1016/j.molimm.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/15/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022]
Abstract
Understanding development of the dendritic cell (DC) subtypes continues to evolve. The origin and relationship of conventional DC type 1 (cDC1), cDC type 2 (cDC2) and plasmacytoid DCs (pDCs) to each other, and in relation to classic myeloid and lymphoid cells, has had a long and controversial history and is still not fully resolved. This review summarises the technological developments and findings that have been achieved at a clonal level, and how that has enhanced our knowledge of the process. It summarises the single cell lineage tracing technologies that have emerged, their application in in vitro and in vivo studies, in both mouse and human settings, and places the findings in a wider context of understanding haematopoiesis at a single cell or clonal level. In particular, it addresses the fate heterogeneity observed in many phenotypically defined progenitor subsets and how these findings have led to a departure from the classic ball-and-stick models of haematopoiesis to the emerging continuous model. Prior contradictions in DC development may be reconciled if they are framed within this revised model, where commitment to a lineage or cell type does not occur in an all-or-nothing process in defined progenitors but rather can occur at many stages of haematopoiesis in a dynamic process.
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Affiliation(s)
- Shalin H Naik
- Immunology Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia; The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
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20
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Nutt SL, Chopin M. Transcriptional Networks Driving Dendritic Cell Differentiation and Function. Immunity 2020; 52:942-956. [DOI: 10.1016/j.immuni.2020.05.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/23/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022]
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21
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Luo XL, Dalod M. The quest for faithful in vitro models of human dendritic cells types. Mol Immunol 2020; 123:40-59. [PMID: 32413788 DOI: 10.1016/j.molimm.2020.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/06/2020] [Accepted: 04/16/2020] [Indexed: 12/13/2022]
Abstract
Dendritic cells (DCs) are mononuclear phagocytes that are specialized in the induction and functional polarization of effector lymphocytes, thus orchestrating immune defenses against infections and cancer. The population of DC encompasses distinct cell types that vary in their efficacy for complementary functions and are thus likely involved in defending the body against different threats. Plasmacytoid DCs specialize in the production of high levels of the antiviral cytokines type I interferons. Type 1 conventional DCs (cDC1s) excel in the activation of cytotoxic CD8+ T cells (CTLs) which are critical for defense against cancer and infections by intracellular pathogens. Type 2 conventional DCs (cDC2s) prime helper CD4+ T cells for the production of type 2 cytokines underpinning immune defenses against worms or of IL-17 promoting control of infections by extracellular bacteria or fungi. Hence, clinically manipulating the development and functions of DC types could have a major impact for improving treatments against many diseases. However, the rarity and fragility of human DC types is impeding advancement towards this goal. To overcome this roadblock, major efforts are ongoing to generate in vitro large numbers of distinct human DC types. We review here the current state of this research field, emphasizing recent breakthrough and proposing future priorities. We also pinpoint the necessity to develop a consensus nomenclature and rigorous methodologies to ensure proper identification and characterization of human DC types. Finally, we elaborate on how faithful in vitro models of human DC types can accelerate our understanding of the biology of these cells and the engineering of next generation vaccines or immunotherapies against viral infections or cancer.
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Affiliation(s)
- Xin-Long Luo
- Aix Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, Marseille, France
| | - Marc Dalod
- Aix Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, Marseille, France.
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22
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Wells CA, Choi J. Transcriptional Profiling of Stem Cells: Moving from Descriptive to Predictive Paradigms. Stem Cell Reports 2020; 13:237-246. [PMID: 31412285 PMCID: PMC6700522 DOI: 10.1016/j.stemcr.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Transcriptional profiling is a powerful tool commonly used to benchmark stem cells and their differentiated progeny. As the wealth of stem cell data builds in public repositories, we highlight common data traps, and review approaches to combine and mine this data for new cell classification and cell prediction tools. We touch on future trends for stem cell profiling, such as single-cell profiling, long-read sequencing, and improved methods for measuring molecular modifications on chromatin and RNA that bring new challenges and opportunities for stem cell analysis.
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Affiliation(s)
- Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia.
| | - Jarny Choi
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville 3010, Australia
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23
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Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science 2020; 367:science.aaw3381. [PMID: 31974159 DOI: 10.1126/science.aaw3381] [Citation(s) in RCA: 345] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
A challenge in biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Here, we used expressed DNA barcodes to clonally trace transcriptomes over time and applied this to study fate determination in hematopoiesis. We identified states of primed fate potential and located them on a continuous transcriptional landscape. We identified two routes of monocyte differentiation that leave an imprint on mature cells. Analysis of sister cells also revealed cells to have intrinsic fate biases not detectable by single-cell RNA sequencing. Finally, we benchmarked computational methods of dynamic inference from single-cell snapshots, showing that fate choice occurs earlier than is detected by state-of the-art algorithms and that cells progress steadily through pseudotime with precise and consistent dynamics.
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Affiliation(s)
- Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alejo Rodriguez-Fraticelli
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fernando D Camargo
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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24
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Guermonprez P, Gerber-Ferder Y, Vaivode K, Bourdely P, Helft J. Origin and development of classical dendritic cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 349:1-54. [PMID: 31759429 DOI: 10.1016/bs.ircmb.2019.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Classical dendritic cells (cDCs) are mononuclear phagocytes of hematopoietic origin specialized in the induction and regulation of adaptive immunity. Initially defined by their unique T cell activation potential, it became quickly apparent that cDCs would be difficult to distinguish from other phagocyte lineages, by solely relying on marker-based approaches. Today, cDCs definition increasingly embed their unique ontogenetic features. A growing consensus defines cDCs on multiple criteria including: (1) dependency on the fms-like tyrosine kinase 3 ligand hematopoietic growth factor, (2) development from the common DC bone marrow progenitor, (3) constitutive expression of the transcription factor ZBTB46 and (4) the ability to induce, after adequate stimulation, the activation of naïve T lymphocytes. cDCs are a heterogeneous cell population that contains two main subsets, named type 1 and type 2 cDCs, arising from divergent ontogenetic pathways and populating multiple lymphoid and non-lymphoid tissues. Here, we present recent knowledge on the cellular and molecular pathways controlling the specification and commitment of cDC subsets from murine and human hematopoietic stem cells.
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Affiliation(s)
- Pierre Guermonprez
- King's College London, Centre for Inflammation Biology and Cancer Immunology, The Peter Gorer Department of Immmunobiology, London, United Kingdom; Université de Paris, CNRS ERL8252, INSERM1149, Centre for Inflammation Research, Paris, France.
| | - Yohan Gerber-Ferder
- Institut Curie, PSL Research University, INSERM U932, SiRIC «Translational Immunotherapy Team», Paris, France; Université de Paris, Immunity and Cancer Department, INSERM U932, Institut Curie, Paris, France
| | - Kristine Vaivode
- King's College London, Centre for Inflammation Biology and Cancer Immunology, The Peter Gorer Department of Immmunobiology, London, United Kingdom
| | - Pierre Bourdely
- King's College London, Centre for Inflammation Biology and Cancer Immunology, The Peter Gorer Department of Immmunobiology, London, United Kingdom
| | - Julie Helft
- Institut Curie, PSL Research University, INSERM U932, SiRIC «Translational Immunotherapy Team», Paris, France; Université de Paris, Immunity and Cancer Department, INSERM U932, Institut Curie, Paris, France.
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25
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Musumeci A, Lutz K, Winheim E, Krug AB. What Makes a pDC: Recent Advances in Understanding Plasmacytoid DC Development and Heterogeneity. Front Immunol 2019; 10:1222. [PMID: 31191558 PMCID: PMC6548821 DOI: 10.3389/fimmu.2019.01222] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 05/13/2019] [Indexed: 12/16/2022] Open
Abstract
Dendritic cells (DCs) are professional antigen presenting cells (APCs) that originate in the bone marrow and are continuously replenished from hematopoietic progenitor cells. Conventional DCs (cDCs) and plasmacytoid DCs (pDCs) are distinguished by morphology and function, and can be easily discriminated by surface marker expression, both in mouse and man. Classification of DCs based on their ontology takes into account their origin as well as their requirements for transcription factor (TF) expression. cDCs and pDCs of myeloid origin differentiate from a common DC progenitor (CDP) through committed pre-DC stages. pDCs have also been shown to originate from a lymphoid progenitor derived IL-7R+ FLT3+ precursor population containing cells with pDC or B cell potential. Technological advancements in recent years have allowed unprecedented resolution in the analysis of cell states, down to the single cell level, providing valuable information on the commitment, and dynamics of differentiation of all DC subsets. However, the heterogeneity and functional diversification of pDCs still raises the question whether different ontogenies generate restricted pDC subsets, or fully differentiated pDCs retain plasticity in response to challenges. The emergence of novel techniques for the integration of high-resolution data in individual cells promises interesting discoveries regarding DC development and plasticity in the near future.
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Affiliation(s)
- Andrea Musumeci
- Institute for Immunology, Biomedical Center, Ludwig-Maximilian-University, Munich, Germany
| | - Konstantin Lutz
- Institute for Immunology, Biomedical Center, Ludwig-Maximilian-University, Munich, Germany
| | - Elena Winheim
- Institute for Immunology, Biomedical Center, Ludwig-Maximilian-University, Munich, Germany
| | - Anne Barbara Krug
- Institute for Immunology, Biomedical Center, Ludwig-Maximilian-University, Munich, Germany
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Rhodes JW, Tong O, Harman AN, Turville SG. Human Dendritic Cell Subsets, Ontogeny, and Impact on HIV Infection. Front Immunol 2019; 10:1088. [PMID: 31156637 PMCID: PMC6532592 DOI: 10.3389/fimmu.2019.01088] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
Dendritic cells (DCs) play important roles in orchestrating host immunity against invading pathogens, representing one of the first responders to infection by mucosal invaders. From their discovery by Ralph Steinman in the 1970s followed shortly after with descriptions of their in vivo diversity and distribution by Derek Hart, we are still continuing to progressively elucidate the spectrum of DCs present in various anatomical compartments. With the power of high-dimensional approaches such as single-cell sequencing and multiparameter cytometry, recent studies have shed new light on the identities and functions of DC subtypes. Notable examples include the reclassification of plasmacytoid DCs as purely interferon-producing cells and re-evaluation of intestinal conventional DCs and macrophages as derived from monocyte precursors. Collectively, these observations have changed how we view these cells not only in steady-state immunity but also during disease and infection. In this review, we will discuss the current landscape of DCs and their ontogeny, and how this influences our understanding of their roles during HIV infection.
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Affiliation(s)
- Jake William Rhodes
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Orion Tong
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Andrew Nicholas Harman
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Discipline of Applied Medical Sciences, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Stuart Grant Turville
- University of New South Wales, Sydney, NSW, Australia.,Kirby Institute, Kensington, NSW, Australia
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28
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Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer. Nat Commun 2019; 10:766. [PMID: 30770823 PMCID: PMC6377663 DOI: 10.1038/s41467-019-08595-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 01/18/2019] [Indexed: 12/23/2022] Open
Abstract
Primary triple negative breast cancers (TNBC) are prone to dissemination but sub-clonal relationships between tumors and resulting metastases are poorly understood. Here we use cellular barcoding of two treatment-naïve TNBC patient-derived xenografts (PDXs) to track the spatio-temporal fate of thousands of barcoded clones in primary tumors, and their metastases. Tumor resection had a major impact on reducing clonal diversity in secondary sites, indicating that most disseminated tumor cells lacked the capacity to 'seed', hence originated from 'shedders' that did not persist. The few clones that continued to grow after resection i.e. 'seeders', did not correlate in frequency with their parental clones in primary tumors. Cisplatin treatment of one BRCA1-mutated PDX model to non-palpable levels had a surprisingly minor impact on clonal diversity in the relapsed tumor yet purged 50% of distal clones. Therefore, clonal features of shedding, seeding and drug resistance are important factors to consider for the design of therapeutic strategies.
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29
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Reizis B. Plasmacytoid Dendritic Cells: Development, Regulation, and Function. Immunity 2019; 50:37-50. [PMID: 30650380 PMCID: PMC6342491 DOI: 10.1016/j.immuni.2018.12.027] [Citation(s) in RCA: 369] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Plasmacytoid dendritic cells (pDCs) are a unique sentinel cell type that can detect pathogen-derived nucleic acids and respond with rapid and massive production of type I interferon. This review summarizes our current understanding of pDC biology, including transcriptional regulation, heterogeneity, role in antiviral immune responses, and involvement in immune pathology, particularly in autoimmune diseases, immunodeficiency, and cancer. We also highlight the remaining gaps in our knowledge and important questions for the field, such as the molecular basis of unique interferon-producing capacity of pDCs. A better understanding of cell type-specific positive and negative control of pDC function should pave the way for translational applications focused on this immune cell type.
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Affiliation(s)
- Boris Reizis
- Department of Pathology and Department of Medicine, New York University School of Medicine, New York, NY 10016, USA.
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