1
|
Waterfall JJ, Midoun A, Perié L. A computational tool suite to facilitate single-cell lineage tracing analyses. Cell Rep Methods 2024:100780. [PMID: 38744285 DOI: 10.1016/j.crmeth.2024.100780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Tracking the lineage relationships of cell populations is of increasing interest in diverse biological contexts. In this issue of Cell Reports Methods, Holze et al. present a suite of computational tools to facilitate such analyses and encourage their broader application.
Collapse
Affiliation(s)
- Joshua J Waterfall
- Institut Curie, Université PSL, INSERM U830, Paris, France; Institut Curie, Université PSL, Department of Translational Research, Paris, France.
| | - Adil Midoun
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique de la Cellule et du Cancer, Paris, France
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique de la Cellule et du Cancer, Paris, France.
| |
Collapse
|
2
|
Cosgrove J, Marçais A, Hartmann FJ, Bergthaler A, Zanoni I, Corrado M, Perié L, Cabezas-Wallscheid N, Bousso P, Alexandrov T, Kielian T, Martínez-Martín N, Opitz CA, Lyssiotis CA, Argüello RJ, Van den Bossche J. A call for accessible tools to unlock single-cell immunometabolism research. Nat Metab 2024:10.1038/s42255-024-01031-w. [PMID: 38605184 DOI: 10.1038/s42255-024-01031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie, (Team Lyacts), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Felix J Hartmann
- German Cancer Research Center (DKFZ), Heidelberg, Systems Immunology & Single-Cell Biology, Germany and German Cancer Consortium (DKTK), DKFZ, Core Center Heidelberg, Heidelberg, Germany
| | - Andreas Bergthaler
- Institute of Hygiene and Applied Immunology, Department of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ivan Zanoni
- Division of Immunology, Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mauro Corrado
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Institute for Genetics, University of Cologne, Cologne, Germany
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | | | - Philippe Bousso
- Institut Pasteur, Université Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Paris, France
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Bio Studio, BioInnovation Institute, Copenhagen, Denmark
| | - Tammy Kielian
- Department of Pathology, Microbiology, and Immunology University of Nebraska Medical Center, Omaha, NE, USA
| | - Nuria Martínez-Martín
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
| | - Christiane A Opitz
- German Cancer Research Center (DKFZ), Heidelberg, Division of Metabolic Crosstalk in Cancer and the German Cancer Consortium (DKTK), DKFZ Core Center Heidelberg, Heidelberg, Germany
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, Department of Internal Medicine, Division of Gastroenterology and Hepatology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Rafael J Argüello
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Centre for Living Systems, Marseille, France
| | - Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Institute for Infection and Immunity, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
3
|
Sun W, Perkins M, Huyghe M, Faraldo MM, Fre S, Perié L, Lyne AM. Extracting, filtering and simulating cellular barcodes using CellBarcode tools. Nat Comput Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
4
|
Gerber-Ferder Y, Cosgrove J, Duperray-Susini A, Missolo-Koussou Y, Dubois M, Stepaniuk K, Pereira-Abrantes M, Sedlik C, Lameiras S, Baulande S, Bendriss-Vermare N, Guermonprez P, Passaro D, Perié L, Piaggio E, Helft J. Breast cancer remotely imposes a myeloid bias on haematopoietic stem cells by reprogramming the bone marrow niche. Nat Cell Biol 2023; 25:1736-1745. [PMID: 38036749 DOI: 10.1038/s41556-023-01291-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Myeloid cell infiltration of solid tumours generally associates with poor patient prognosis and disease severity1-13. Therefore, understanding the regulation of myeloid cell differentiation during cancer is crucial to counteract their pro-tumourigenic role. Bone marrow (BM) haematopoiesis is a tightly regulated process for the production of all immune cells in accordance to tissue needs14. Myeloid cells differentiate during haematopoiesis from multipotent haematopoietic stem and progenitor cells (HSPCs)15-17. HSPCs can sense inflammatory signals from the periphery during infections18-21 or inflammatory disorders22-27. In these settings, HSPC expansion is associated with increased myeloid differentiation28,29. During carcinogenesis, the elevation of haematopoietic growth factors supports the expansion and differentiation of committed myeloid progenitors5,30. However, it is unclear whether cancer-related inflammation also triggers demand-adapted haematopoiesis at the level of multipotent HSPCs. In the BM, HSPCs reside within the haematopoietic niche which delivers HSC maintenance and differentiation cues31-35. Mesenchymal stem cells (MSCs) are a major cellular component of the BM niche and contribute to HSC homeostasis36-41. Modifications of MSCs in systemic disorders have been associated with HSC differentiation towards myeloid cells22,42. It is unknown if MSCs are regulated in the context of solid tumours and if their myeloid supportive activity is impacted by cancer-induced systemic changes. Here, using unbiased transcriptomic analysis and in situ imaging of HSCs and the BM niche during breast cancer, we show that both HSCs and MSCs are transcriptionally and spatially modified. We demonstrate that breast tumour can distantly remodel the cellular cross-talks in the BM niche leading to increased myelopoiesis.
Collapse
Affiliation(s)
- Yohan Gerber-Ferder
- Institut Curie, Immunity and Cancer, PSL University, INSERM U932, Paris, France
- Université Paris Cité, INSERM U932, Paris, France
| | - Jason Cosgrove
- PSL University, Institut Curie Research Center, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Aleria Duperray-Susini
- Institut Cochin, Leukemia and Niche Dynamics Laboratory, Université Paris Cité, INSERM, CNRS, Paris, France
| | | | - Marine Dubois
- Institut Curie, Immunity and Cancer, PSL University, INSERM U932, Paris, France
| | - Kateryna Stepaniuk
- Institut Cochin, Phagocytes and Cancer Immunology Laboratory, Université Paris Cité, INSERM U1016, CNRS UMR8104, Paris, France
| | - Manuela Pereira-Abrantes
- Cancer Research Center of Lyon, Centre Léon Bérard, Université Claude Bernard Lyon 1, UMR INSERM 1052 CNRS 5286, Lyon, France
| | - Christine Sedlik
- Institut Curie, Immunity and Cancer, PSL University, INSERM U932, Paris, France
| | - Sonia Lameiras
- Institut Curie, ICGex Next-Generation Sequencing Platform, PSL University, Paris, France
- Institut Curie, Single Cell Initiative, PSL University, Paris, France
| | - Sylvain Baulande
- Institut Curie, ICGex Next-Generation Sequencing Platform, PSL University, Paris, France
- Institut Curie, Single Cell Initiative, PSL University, Paris, France
| | - Nathalie Bendriss-Vermare
- Cancer Research Center of Lyon, Centre Léon Bérard, Université Claude Bernard Lyon 1, UMR INSERM 1052 CNRS 5286, Lyon, France
| | - Pierre Guermonprez
- Institut Pasteur, Dendritic Cells and Adaptive Immunity Unit, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Paris, France
| | - Diana Passaro
- Institut Cochin, Leukemia and Niche Dynamics Laboratory, Université Paris Cité, INSERM, CNRS, Paris, France
| | - Leïla Perié
- PSL University, Institut Curie Research Center, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Eliane Piaggio
- Institut Curie, Immunity and Cancer, PSL University, INSERM U932, Paris, France
| | - Julie Helft
- Institut Cochin, Phagocytes and Cancer Immunology Laboratory, Université Paris Cité, INSERM U1016, CNRS UMR8104, Paris, France.
| |
Collapse
|
5
|
Urbanus J, Cosgrove J, Beltman JB, Elhanati Y, Moral RA, Conrad C, van Heijst JW, Tubeuf E, Velds A, Kok L, Merle C, Magnusson JP, Guyonnet L, Frisén J, Fre S, Walczak AM, Mora T, Jacobs H, Schumacher TN, Perié L. DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age. Nat Commun 2023; 14:2184. [PMID: 37069150 PMCID: PMC10110593 DOI: 10.1038/s41467-023-37167-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we present an in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis rather than the increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remains constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.
Collapse
Affiliation(s)
- Jos Urbanus
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Joost B Beltman
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Rafael A Moral
- Department of Mathematics and Statistics, Maynooth University, Maynooth, Ireland
| | - Cecile Conrad
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Jeroen W van Heijst
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emilie Tubeuf
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Arno Velds
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lianne Kok
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Candice Merle
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Jens P Magnusson
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Léa Guyonnet
- Cytometry Platform, Institut Curie, 75005, Paris, France
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Silvia Fre
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École Normale Supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'École Normale Supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, Paris, France
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
| |
Collapse
|
6
|
Donada A, Tak T, Prevedello G, Milo I, Duffy KR, Perié L. Simultaneous Assessment of Kinship, Division Number, and Phenotype via Flow Cytometry for Hematopoietic Stem and Progenitor Cells. J Vis Exp 2023. [PMID: 37036235 DOI: 10.3791/64918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
Few techniques can assess phenotype and fate for the same cell simultaneously. Most of the current protocols used to characterize phenotype, although able to generate large datasets, necessitate the destruction of the cell of interest, making it impossible to assess its functional fate. Heterogeneous biological differentiating systems like hematopoiesis are therefore difficult to describe. Building on cell division tracking dyes, we further developed a protocol to simultaneously determine kinship, division number, and differentiation status for many single hematopoietic progenitors. This protocol allows the assessment of the ex vivo differentiation potential of murine and human hematopoietic progenitors, isolated from various biological sources. Moreover, as it is based on flow cytometry and a limited number of reagents, it can quickly generate a large amount of data, at the single-cell level, in a relatively inexpensive manner. We also provide the analytical pipeline for single-cell analysis, combined with a robust statistical framework. As this protocol allows the linking of cell division and differentiation at the single-cell level, it can be used to quantitatively assess symmetric and asymmetric fate commitment, the balance between self-renewal and differentiation, and the number of divisions for a given commitment fate. Altogether, this protocol can be used in experimental designs aiming to unravel the biological differences between hematopoietic progenitors, from a single-cell perspective.
Collapse
Affiliation(s)
| | - Tamar Tak
- Quantitative Immuno-hematology, CNRS UMR168, Institut Curie
| | - Giulio Prevedello
- Quantitative Immuno-hematology, CNRS UMR168, Institut Curie; Hamilton Institute, Maynooth University; Institut Curie, PSL Research University, CNRS UMR 3348, Orsay; Université Paris-Sud, Université Paris-Saclay, CNRS UMR 3348, Orsay
| | - Idan Milo
- Quantitative Immuno-hematology, CNRS UMR168, Institut Curie
| | | | - Leïla Perié
- Quantitative Immuno-hematology, CNRS UMR168, Institut Curie;
| |
Collapse
|
7
|
Hadj Abed L, Tak T, Cosgrove J, Perié L. CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data. Front Med (Lausanne) 2022; 9:919345. [PMID: 36275810 PMCID: PMC9581332 DOI: 10.3389/fmed.2022.919345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.
Collapse
Affiliation(s)
- Louisa Hadj Abed
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Centre de Bio-Informatique, MINES ParisTech, Institut Curie, PSL University, Paris, France
| | - Tamar Tak
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,*Correspondence: Jason Cosgrove,
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Leïla Perié,
| |
Collapse
|
8
|
Murakami S, Barroca V, Perié L, Bravard A, Bernardino-Sgherri J, Tisserand A, Devanand C, Edmond V, Magniez A, Tenreira Bento S, Torres C, Pasquier F, Plo I, Vainchenker W, Villeval JL, Roméo PH, Lewandowski D. In Vivo Monitoring of Polycythemia Vera Development Reveals Carbonic Anhydrase 1 as a Potent Therapeutic Target. Blood Cancer Discov 2022; 3:285-297. [PMID: 35290450 PMCID: PMC9327731 DOI: 10.1158/2643-3230.bcd-21-0039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/21/2021] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Current murine models of myeloproliferative neoplasms (MPNs) cannot examine how MPNs progress from a single bone marrow source to the entire hematopoietic system. Thus, using transplantation of knock-in JAK2V617F hematopoietic cells into a single irradiated leg, we show development of polycythemia vera (PV) from a single anatomic site in immunocompetent mice. Barcode experiments reveal that grafted JAK2V617F stem/progenitor cells migrate from the irradiated leg to nonirradiated organs such as the contralateral leg and spleen, which is strictly required for development of PV. Mutant cells colonizing the nonirradiated leg efficiently induce PV in nonconditioned recipient mice and contain JAK2V617F hematopoietic stem/progenitor cells that express high levels of carbonic anhydrase 1 (CA1), a peculiar feature also found in CD34+ cells from patients with PV. Finally, genetic and pharmacologic inhibition of CA1 efficiently suppresses PV development and progression in mice and decreases PV patients' erythroid progenitors, strengthening CA1 as a potent therapeutic target for PV. SIGNIFICANCE Follow-up of hematopoietic malignancies from their initiating anatomic site is crucial for understanding their development and discovering new therapeutic avenues. We developed such an approach, used it to characterize PV progression, and identified CA1 as a promising therapeutic target of PV. This article is highlighted in the In This Issue feature, p. 265.
Collapse
Affiliation(s)
- Shohei Murakami
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Vilma Barroca
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Leïla Perié
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Anne Bravard
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Jacqueline Bernardino-Sgherri
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | | | - Caroline Devanand
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Valérie Edmond
- Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - Aurélie Magniez
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | | | - Claire Torres
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | | | - Isabelle Plo
- Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | | | | | - Paul-Henri Roméo
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| | - Daniel Lewandowski
- CEA-INSERM UMR1274, Institut de Radiobiologie Cellulaire et Moléculaire (iRCM), Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), CEA, Fontenay aux Roses, France
- Université Paris Diderot, Paris, France
- Université Paris Saclay, Gif-sur-Yvette, France
| |
Collapse
|
9
|
Marsolier J, Prompsy P, Durand A, Lyne AM, Landragin C, Trouchet A, Bento ST, Eisele A, Foulon S, Baudre L, Grosselin K, Bohec M, Baulande S, Dahmani A, Sourd L, Letouzé E, Salomon AV, Marangoni E, Perié L, Vallot C. H3K27me3 conditions chemotolerance in triple-negative breast cancer. Nat Genet 2022; 54:459-468. [PMID: 35410383 PMCID: PMC7612638 DOI: 10.1038/s41588-022-01047-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
Abstract
The persistence of cancer cells resistant to therapy remains a major clinical challenge. In triple-negative breast cancer, resistance to chemotherapy results in the highest recurrence risk among breast cancer subtypes. The drug-tolerant state seems largely defined by nongenetic features, but the underlying mechanisms are poorly understood. Here, by monitoring epigenomes, transcriptomes and lineages with single-cell resolution, we show that the repressive histone mark H3K27me3 (trimethylation of histone H3 at lysine 27) regulates cell fate at the onset of chemotherapy. We report that a persister expression program is primed with both H3K4me3 (trimethylation of histone H3 at lysine 4) and H3K27me3 in unchallenged cells, with H3K27me3 being the lock to its transcriptional activation. We further demonstrate that depleting H3K27me3 enhances the potential of cancer cells to tolerate chemotherapy. Conversely, preventing H3K27me3 demethylation simultaneously to chemotherapy inhibits the transition to a drug-tolerant state, and delays tumor recurrence in vivo. Our results highlight how chromatin landscapes shape the potential of cancer cells to respond to initial therapy.
Collapse
Affiliation(s)
- Justine Marsolier
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Pacôme Prompsy
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Adeline Durand
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Anne-Marie Lyne
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Camille Landragin
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Amandine Trouchet
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Single Cell Initiative, Institut Curie, PSL University, Paris, France
| | | | - Almut Eisele
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Sophie Foulon
- CNRS UMR8231, ESPCI Paris, PSL University, Paris, France
| | - Léa Baudre
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Kevin Grosselin
- CNRS UMR8231, ESPCI Paris, PSL University, Paris, France,HiFiBio SAS, Paris, France,Current Affiliation: Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Mylène Bohec
- Single Cell Initiative, Institut Curie, PSL University, Paris, France,Genomics of Excellence (ICGex) Platform, Institut Curie, PSL University, Paris, France
| | - Sylvain Baulande
- Single Cell Initiative, Institut Curie, PSL University, Paris, France,Genomics of Excellence (ICGex) Platform, Institut Curie, PSL University, Paris, France
| | - Ahmed Dahmani
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Laura Sourd
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Eric Letouzé
- Functional Genomics of Solid Tumors laboratory, Centre de Recherche des Cordeliers, Sorbonne University, Inserm, USPC, Paris Descartes University, Paris Diderot University, Paris, France
| | - Anne-Vincent Salomon
- Pathology-Genetics-Immunology Department, Institut Curie, PSL Research University, Paris, France,INSERM U934, Institut Curie, PSL Research University, Paris, France
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Leïla Perié
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France. .,Translational Research Department, Institut Curie, PSL University, Paris, France.
| |
Collapse
|
10
|
Eisele AS, Cosgrove J, Magniez A, Tubeuf E, Tenreira Bento S, Conrad C, Cayrac F, Tak T, Lyne AM, Urbanus J, Perié L. Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells. eLife 2022; 11:66922. [PMID: 35166672 PMCID: PMC8884727 DOI: 10.7554/elife.66922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The cytokine erythropoietin (EPO) is a potent inducer of erythrocyte development and one of the most prescribed biopharmaceuticals. The action of EPO on erythroid progenitor cells is well established, but its direct action on hematopoietic stem and progenitor cells (HSPCs) is still debated. Here, using cellular barcoding, we traced the differentiation of hundreds of single murine HSPCs, after ex vivo EPO-exposure and transplantation, in five different hematopoietic cell lineages, and observed the transient occurrence of high-output Myeloid-Erythroid-megaKaryocyte (MEK)-biased and Myeloid-B-cell-Dendritic cell (MBDC)-biased clones. Single-cell RNA sequencing (ScRNAseq) analysis of ex vivo EPO-exposed HSPCs revealed that EPO induced the upregulation of erythroid associated genes in a subset of HSPCs, overlapping with multipotent progenitor (MPP) 1 and MPP2. Transplantation of Barcoded EPO-exposed-MPP2 confirmed their enrichment in Myeloid-Erythroid-biased clones. Collectively, our data show that EPO does act directly on MPP independent of the niche, and modulates fate by remodeling the clonal composition of the MPP pool.
Collapse
Affiliation(s)
- Almut S Eisele
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| | - Jason Cosgrove
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| | | | - Emilie Tubeuf
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| | | | - Cecile Conrad
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| | - Fanny Cayrac
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| | - Tamar Tak
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| | | | - Jos Urbanus
- Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Leïla Perié
- CNRS UMR168, Physico-chimie, Institut Curie, Paris, France
| |
Collapse
|
11
|
Hustin L, Cosgrove J, de Boer R, Perié L. 3101 – HEMATOPOIESIS IN NUMBERS. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
12
|
Donada A, Hermange G, Milo I, Abed LH, Tenreira-Bento S, Vargaftig J, Michonneau D, Cournéde PH, Perié L. 3073 – HUMAN HAEMATOPOIETIC STEM AND PROGENITOR CELLS FORM KINSHIPS THAT ARE SIMILAR IN FATE AND SYNCHRONOUS IN DIVISION. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
13
|
Cosgrove J, Hustin LSP, de Boer RJ, Perié L. Hematopoiesis in numbers. Trends Immunol 2021; 42:1100-1112. [PMID: 34742656 DOI: 10.1016/j.it.2021.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 12/16/2022]
Abstract
Hematopoiesis is a dynamic process in which stem and progenitor cells give rise to the ~1013 blood and immune cells distributed throughout the human body. We argue that a quantitative description of hematopoiesis can help consolidate existing data, identify knowledge gaps, and generate new hypotheses. Here, we review known numbers in murine and, where possible, human hematopoiesis, and consolidate murine numbers into a set of reference values. We present estimates of cell numbers, division and differentiation rates, cell size, and macromolecular composition for each hematopoietic cell type. We also propose guidelines to improve the reporting of measurements and highlight areas in which quantitative data are lacking. Overall, we show how quantitative approaches can be used to understand key properties of hematopoiesis.
Collapse
Affiliation(s)
- Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Lucie S P Hustin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France.
| |
Collapse
|
14
|
Sommerkamp P, Romero-Mulero MC, Narr A, Ladel L, Hustin L, Schönberger K, Renders S, Altamura S, Zeisberger P, Jäcklein K, Klimmeck D, Rodriguez-Fraticelli A, Camargo F, Perié L, Trumpp A, Cabezas-Wallscheid N. 3032 – MOUSE MULTIPOTENT PROGENITOR 5 CELLS ARE LOCATED AT THE INTERPHASE BETWEEN HEMATOPOIETIC STEM AND PROGENITOR CELLS. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
15
|
Tak T, Prevedello G, Simon G, Paillon N, Benlabiod C, Marty C, Plo I, Duffy KR, Perié L. HSPCs display within-family homogeneity in differentiation and proliferation despite population heterogeneity. eLife 2021; 10:60624. [PMID: 34002698 PMCID: PMC8175087 DOI: 10.7554/elife.60624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
High-throughput single-cell methods have uncovered substantial heterogeneity in the pool of hematopoietic stem and progenitor cells (HSPCs), but how much instruction is inherited by offspring from their heterogeneous ancestors remains unanswered. Using a method that enables simultaneous determination of common ancestor, division number, and differentiation status of a large collection of single cells, our data revealed that murine cells that derived from a common ancestor had significant similarities in their division progression and differentiation outcomes. Although each family diversifies, the overall collection of cell types observed is composed of homogeneous families. Heterogeneity between families could be explained, in part, by differences in ancestral expression of cell surface markers. Our analyses demonstrate that fate decisions of cells are largely inherited from ancestor cells, indicating the importance of common ancestor effects. These results may have ramifications for bone marrow transplantation and leukemia, where substantial heterogeneity in HSPC behavior is observed.
Collapse
Affiliation(s)
- Tamar Tak
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Giulio Prevedello
- Institut Curie, PSL Research University, CNRS, Orsay, France.,Université Paris-Saclay, Saclay, France
| | - Gaël Simon
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Noémie Paillon
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Camélia Benlabiod
- INSERM, UMR1287, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France.,Université de Paris, Paris, France
| | - Caroline Marty
- Université Paris-Saclay, Saclay, France.,INSERM, UMR1287, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Isabelle Plo
- Université Paris-Saclay, Saclay, France.,INSERM, UMR1287, Gustave Roussy, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Co Kildare, Ireland
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| |
Collapse
|
16
|
Kok L, Dijkgraaf FE, Urbanus J, Bresser K, Vredevoogd DW, Cardoso RF, Perié L, Beltman JB, Schumacher TN. A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool. J Exp Med 2021; 217:151985. [PMID: 32728699 PMCID: PMC7537386 DOI: 10.1084/jem.20191711] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/01/2020] [Accepted: 06/16/2020] [Indexed: 11/29/2022] Open
Abstract
An increasing body of evidence emphasizes the role of tissue-resident memory T cells (TRM) in the defense against recurring pathogens and malignant neoplasms. However, little is known with regard to the origin of these cells and their kinship to other CD8+ T cell compartments. To address this issue, we followed the antigen-specific progeny of individual naive CD8+ T cells to the T effector (TEFF), T circulating memory (TCIRCM), and TRM pools by lineage-tracing and single-cell transcriptome analysis. We demonstrate that a subset of T cell clones possesses a heightened capacity to form TRM, and that enriched expression of TRM–fate-associated genes is already apparent in the circulating TEFF offspring of such clones. In addition, we demonstrate that the capacity to generate TRM is permanently imprinted at the clonal level, before skin entry. Collectively, these data provide compelling evidence for early stage TRM fate decisions and the existence of committed TRM precursor cells in the circulatory TEFF compartment.
Collapse
Affiliation(s)
- Lianne Kok
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Feline E Dijkgraaf
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jos Urbanus
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kaspar Bresser
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rebeca F Cardoso
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Leïla Perié
- Institut Curie, Université Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique UMR168, Paris, France
| | - Joost B Beltman
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| |
Collapse
|
17
|
Lyne AM, Kent DG, Laurenti E, Cornils K, Glauche I, Perié L. A track of the clones: new developments in cellular barcoding. Exp Hematol 2018; 68:15-20. [DOI: 10.1016/j.exphem.2018.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 11/30/2022]
|
18
|
Perié L, Duffy KR. Retracing thein vivohaematopoietic tree using single-cell methods. FEBS Lett 2016; 590:4068-4083. [DOI: 10.1002/1873-3468.12299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/08/2016] [Accepted: 07/09/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Leïla Perié
- Institut Curie; PSL Research University; CNRS UMR168; Paris France
- Sorbonne Universités; UPMC Univ Paris 06; France
| | - Ken R. Duffy
- Hamilton Institute; Maynooth University; Co Kildare Ireland
| |
Collapse
|
19
|
Perié L, Duffy KR, Kok L, de Boer RJ, Schumacher TN. The Branching Point in Erythro-Myeloid Differentiation. Cell 2016; 163:1655-62. [PMID: 26687356 DOI: 10.1016/j.cell.2015.11.059] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/18/2015] [Accepted: 11/28/2015] [Indexed: 12/17/2022]
Abstract
Development of mature blood cell progenies from hematopoietic stem cells involves the transition through lineage-restricted progenitors. The first branching point along this developmental process is thought to separate the erythro-myeloid and lymphoid lineage fate by yielding two intermediate progenitors, the common myeloid and the common lymphoid progenitors (CMPs and CLPs). Here, we use single-cell lineage tracing to demonstrate that so-called CMPs are highly heterogeneous with respect to cellular output, with most individual CMPs yielding either only erythrocytes or only myeloid cells after transplantation. Furthermore, based on the labeling of earlier progenitors, we show that the divergence between the myeloid and erythroid lineage develops within multipotent progenitors (MPP). These data provide evidence for a model of hematopoietic branching in which multiple distinct lineage commitments occur in parallel within the MPP pool.
Collapse
Affiliation(s)
- Leïla Perié
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Institut Curie, PSL Research University, CNRS UMR168, 26 rue d'Ulm, 75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France.
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Co Kildare, Ireland
| | - Lianne Kok
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| |
Collapse
|
20
|
Kokkaliaris KD, Lucas D, Beerman I, Kent DG, Perié L. Understanding hematopoiesis from a single-cell standpoint. Exp Hematol 2016; 44:447-50. [PMID: 26997547 DOI: 10.1016/j.exphem.2016.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/04/2016] [Indexed: 12/11/2022]
Abstract
The cellular diversity of the hematopoietic system has been extensively studied, and a plethora of cell surface markers have been used to discriminate and prospectively purify different blood cell types. However, even within phenotypically identical fractions of hematopoietic stem and progenitor cells or lineage-restricted progenitors, significant functional heterogeneity is observed when single cells are analyzed. To address these challenges, researchers are now using techniques to follow single cells and their progeny to improve our understanding of the underlying functional heterogeneity. On November 19, 2015, Dr. David Kent and Dr. Leïla Perié, two emerging young group leaders, presented their recent efforts to dissect the functional properties of individual cells with a webinar series organized by the International Society for Experimental Hematology. Here, we provide a summary of the presented methods for cell labeling and clonal tracking and discuss how these different techniques have been employed to study hematopoiesis.
Collapse
Affiliation(s)
- Konstantinos D Kokkaliaris
- Cell Systems Dynamics Research Group, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Daniel Lucas
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Isabel Beerman
- Program of Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - David G Kent
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge University, Cambridge, UK
| | - Leïla Perié
- Institut Curie, PSL Research University, Paris, France
| |
Collapse
|
21
|
Abstract
For proliferating cells subject to both division and death, how can one estimate the average generation number of the living population without continuous observation or a division-diluting dye? In this paper we provide a method for cell systems such that at each division there is an unlikely, heritable one-way label change that has no impact other than to serve as a distinguishing marker. If the probability of label change per cell generation can be determined and the proportion of labeled cells at a given time point can be measured, we establish that the average generation number of living cells can be estimated. Crucially, the estimator does not depend on knowledge of the statistics of cell cycle, death rates or total cell numbers. We explore the estimator's features through comparison with physiologically parameterized stochastic simulations and extrapolations from published data, using it to suggest new experimental designs.
Collapse
Affiliation(s)
- Tom S Weber
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Leïla Perié
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland.
| |
Collapse
|
22
|
Perié L, Riboli-Sasco L, Ribrault C, Zlotek-Zlotkiewicz E. Outside the Tower. Kids' questions transcend conflict. Science 2014; 345:740. [PMID: 25124421 DOI: 10.1126/science.345.6198.740-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Leïla Perié
- Netherlands Cancer Institute, Amsterdam, 1066CX, Netherlands. Utrecht University, 3584 CH Utrecht, Netherlands.
| | | | | | | |
Collapse
|
23
|
Naik SH, Schumacher TN, Perié L. Cellular barcoding: a technical appraisal. Exp Hematol 2014; 42:598-608. [PMID: 24996012 DOI: 10.1016/j.exphem.2014.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 12/29/2022]
Abstract
Cellular barcoding involves the tagging of individual cells of interest with unique genetic heritable identifiers or barcodes and is emerging as a powerful tool to address individual cell fates on a large scale. However, as with many new technologies, diverse technical and analytical challenges have emerged. Here, we review those challenges and highlight both the power and limitations of cellular barcoding. We then illustrate the contribution of cellular barcoding to the understanding of hematopoiesis and outline the future potential of this technology.
Collapse
Affiliation(s)
- Shalin H Naik
- Molecular Medicine Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Ton N Schumacher
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Leïla Perié
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
24
|
Gerlach C, Rohr JC, Perié L, van Rooij N, van Heijst JWJ, Velds A, Urbanus J, Naik SH, Jacobs H, Beltman JB, de Boer RJ, Schumacher TNM. Heterogeneous differentiation patterns of individual CD8+ T cells. Science 2013; 340:635-9. [PMID: 23493421 DOI: 10.1126/science.1235487] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Upon infection, antigen-specific CD8(+) T lymphocyte responses display a highly reproducible pattern of expansion and contraction that is thought to reflect a uniform behavior of individual cells. We tracked the progeny of individual mouse CD8(+) T cells by in vivo lineage tracing and demonstrated that, even for T cells bearing identical T cell receptors, both clonal expansion and differentiation patterns are heterogeneous. As a consequence, individual naïve T lymphocytes contributed differentially to short- and long-term protection, as revealed by participation of their progeny during primary versus recall infections. The discordance in fate of individual naïve T cells argues against asymmetric division as a singular driver of CD8(+) T cell heterogeneity and demonstrates that reproducibility of CD8(+) T cell responses is achieved through population averaging.
Collapse
Affiliation(s)
- Carmen Gerlach
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Perié L, Aru J, Kourilsky P, Slotine JJ. Does a quorum sensing mechanism direct the behavior of immune cells? C R Biol 2013; 336:13-6. [PMID: 23537765 DOI: 10.1016/j.crvi.2013.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 10/27/2022]
Abstract
Quorum sensing is a decision-making process used by decentralized groups such as colonies of bacteria to trigger a coordinated behavior. The existence of decentralized coordinated behavior has also been suggested in the immune system. In this paper, we explore the possibility for quorum sensing mechanisms in the immune response. Cytokines are good candidates as inducer of quorum sensing effects on migration, proliferation and differentiation of immune cells. The existence of a quorum sensing mechanism should be explored experimentally. It may provide new perspectives into immune responses and could lead to new therapeutic strategies.
Collapse
Affiliation(s)
- Leïla Perié
- Collège de France, Chair of molecular immunology, 11, place Marcelin-Berthelot, 75005 Paris, France.
| | | | | | | |
Collapse
|