1
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Chen DW, Fan JM, Schrey JM, Mitchell DV, Jung SK, Hurwitz SN, Perez EB, Muraro MJ, Carroll M, Taylor DM, Kurre P. Inflammatory recruitment of healthy hematopoietic stem and progenitor cells in the acute myeloid leukemia niche. Leukemia 2024; 38:741-750. [PMID: 38228679 PMCID: PMC10997516 DOI: 10.1038/s41375-024-02136-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
Inflammation in the bone marrow (BM) microenvironment is a constitutive component of leukemogenesis in acute myeloid leukemia (AML). Current evidence suggests that both leukemic blasts and stroma secrete proinflammatory factors that actively suppress the function of healthy hematopoietic stem and progenitor cells (HSPCs). HSPCs are also cellular components of the innate immune system, and we reasoned that they may actively propagate the inflammation in the leukemic niche. In two separate congenic models of AML we confirm by evaluation of the BM plasma secretome and HSPC-selective single-cell RNA sequencing (scRNA-Seq) that multipotent progenitors and long-lived stem cells adopt inflammatory gene expression programs, even at low leukemic infiltration of the BM. In particular, we observe interferon gamma (IFN-γ) pathway activation, along with secretion of its chemokine target, CXCL10. We show that AML-derived nanometer-sized extracellular vesicles (EVAML) are sufficient to trigger this inflammatory HSPC response, both in vitro and in vivo. Altogether, our studies indicate that HSPCs are an unrecognized component of the inflammatory adaptation of the BM by leukemic cells. The pro-inflammatory conversion and long-lived presence of HSPCs in the BM along with their regenerative re-expansion during remission may impact clonal selection and disease evolution.
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Affiliation(s)
- Ding-Wen Chen
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jian-Meng Fan
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julie M Schrey
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dana V Mitchell
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Seul K Jung
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephanie N Hurwitz
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Martin Carroll
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deanne M Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter Kurre
- Comprehensive Bone Marrow Failure Center, Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Groen N, Leenders F, Mahfouz A, Munoz-Garcia A, Muraro MJ, de Graaf N, Rabelink TJ, Hoeben R, van Oudenaarden A, Zaldumbide A, Reinders MJT, de Koning EJP, Carlotti F. Single-Cell Transcriptomics Links Loss of Human Pancreatic β-Cell Identity to ER Stress. Cells 2021; 10:3585. [PMID: 34944092 PMCID: PMC8700697 DOI: 10.3390/cells10123585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022] Open
Abstract
The maintenance of pancreatic islet architecture is crucial for proper β-cell function. We previously reported that disruption of human islet integrity could result in altered β-cell identity. Here we combine β-cell lineage tracing and single-cell transcriptomics to investigate the mechanisms underlying this process in primary human islet cells. Using drug-induced ER stress and cytoskeleton modification models, we demonstrate that altering the islet structure triggers an unfolding protein response that causes the downregulation of β-cell maturity genes. Collectively, our findings illustrate the close relationship between endoplasmic reticulum homeostasis and β-cell phenotype, and strengthen the concept of altered β-cell identity as a mechanism underlying the loss of functional β-cell mass.
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Affiliation(s)
- Nathalie Groen
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
| | - Floris Leenders
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
| | - Ahmed Mahfouz
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (A.M.); (M.J.T.R.)
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Amadeo Munoz-Garcia
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
| | - Mauro J. Muraro
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), 3584 CT Utrecht, The Netherlands; (M.J.M.); (A.v.O.)
| | - Natascha de Graaf
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
| | - Ton. J. Rabelink
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
| | - Rob Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.H.); (A.Z.)
| | - Alexander van Oudenaarden
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), 3584 CT Utrecht, The Netherlands; (M.J.M.); (A.v.O.)
- Molecular Cancer Research, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Arnaud Zaldumbide
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.H.); (A.Z.)
| | - Marcel J. T. Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (A.M.); (M.J.T.R.)
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Eelco J. P. de Koning
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), 3584 CT Utrecht, The Netherlands; (M.J.M.); (A.v.O.)
| | - Françoise Carlotti
- Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (N.G.); (F.L.); (A.M.-G.); (N.d.G.); (T.J.R.); (E.J.P.d.K.)
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3
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Siefert JC, Cioni B, Muraro MJ, Alshalalfa M, Vivié J, van der Poel HG, Schoots IG, Bekers E, Feng FY, Wessels LFA, Zwart W, Bergman AM. The Prognostic Potential of Human Prostate Cancer-Associated Macrophage Subtypes as Revealed by Single-Cell Transcriptomics. Mol Cancer Res 2021; 19:1778-1791. [PMID: 34131070 PMCID: PMC9398107 DOI: 10.1158/1541-7786.mcr-20-0740] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 08/26/2020] [Revised: 12/18/2020] [Accepted: 06/07/2021] [Indexed: 01/07/2023]
Abstract
Macrophages in the tumor microenvironment are causally linked with prostate cancer development and progression, yet little is known about their composition in neoplastic human tissue. By performing single cell transcriptomic analysis of human prostate cancer resident macrophages, three distinct populations were identified in the diseased prostate. Unexpectedly, no differences were observed between macrophages isolated from the tumorous and nontumorous portions of the prostatectomy specimens. Markers associated with canonical M1 and M2 macrophage phenotypes were identifiable, however these were not the main factors defining unique subtypes. The genes selectively associated with each macrophage cluster were used to develop a gene signature which was highly associated with both recurrence-free and metastasis-free survival. These results highlight the relevance of tissue-specific macrophage subtypes in the tumor microenvironment for prostate cancer progression and demonstrates the utility of profiling single-cell transcriptomics in human tumor samples as a strategy to design gene classifiers for patient prognostication. IMPLICATIONS: The specific macrophage subtypes present in a diseased human prostate have prognostic value, suggesting that the relative proportions of these populations are related to patient outcome. Understanding the relative contributions of these subtypes will not only inform patient prognostication, but will enable personalized immunotherapeutic strategies to increase beneficial populations or reduce detrimental populations.
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Affiliation(s)
- Joseph C Siefert
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bianca Cioni
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mauro J Muraro
- Single Cell Discoveries B.V., the Netherlands.,Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Judith Vivié
- Single Cell Discoveries B.V., the Netherlands.,Hubrecht Institute-KNAW and University Medical Center Utrecht, the Netherlands
| | - Henk G van der Poel
- Division of Urology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ivo G Schoots
- Department of Radiology and Nuclear Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elise Bekers
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Felix Y Feng
- Department of Radiation Oncology, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Oncode Institute, the Netherlands
| | - Andries M Bergman
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands. .,Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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4
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Lamers MM, van der Vaart J, Knoops K, Riesebosch S, Breugem TI, Mykytyn AZ, Beumer J, Schipper D, Bezstarosti K, Koopman CD, Groen N, Ravelli RBG, Duimel HQ, Demmers JAA, Verjans GMGM, Koopmans MPG, Muraro MJ, Peters PJ, Clevers H, Haagmans BL. An organoid-derived bronchioalveolar model for SARS-CoV-2 infection of human alveolar type II-like cells. EMBO J 2021; 40:e105912. [PMID: 33283287 PMCID: PMC7883112 DOI: 10.15252/embj.2020105912] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [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: 06/12/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes coronavirus disease 2019 (COVID‐19), which may result in acute respiratory distress syndrome (ARDS), multiorgan failure, and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. Here, we describe a human 2D air–liquid interface culture system which was characterized by confocal and electron microscopy and single‐cell mRNA expression analysis. In this model, alveolar cells, but also basal cells and rare neuroendocrine cells, are grown from 3D self‐renewing fetal lung bud tip organoids. These cultures were readily infected by SARS‐CoV‐2 with mainly surfactant protein C‐positive alveolar type II‐like cells being targeted. Consequently, significant viral titers were detected and mRNA expression analysis revealed induction of type I/III interferon response program. Treatment of these cultures with a low dose of interferon lambda 1 reduced viral replication. Hence, these cultures represent an experimental model for SARS‐CoV‐2 infection and can be applied for drug screens.
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Affiliation(s)
- Mart M Lamers
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jelte van der Vaart
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands
| | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anna Z Mykytyn
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands
| | - Debby Schipper
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Hans Q Duimel
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Georges M G M Verjans
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P G Koopmans
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus University Medical Center, Rotterdam, The Netherlands
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5
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Cioni B, Zaalberg A, van Beijnum JR, Melis MHM, van Burgsteden J, Muraro MJ, Hooijberg E, Peters D, Hofland I, Lubeck Y, de Jong J, Sanders J, Vivié J, van der Poel HG, de Boer JP, Griffioen AW, Zwart W, Bergman AM. Androgen receptor signalling in macrophages promotes TREM-1-mediated prostate cancer cell line migration and invasion. Nat Commun 2020; 11:4498. [PMID: 32908142 PMCID: PMC7481219 DOI: 10.1038/s41467-020-18313-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [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: 08/10/2018] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
The androgen receptor (AR) is the master regulator of prostate cancer (PCa) development, and inhibition of AR signalling is the most effective PCa treatment. AR is expressed in PCa cells and also in the PCa-associated stroma, including infiltrating macrophages. Macrophages have a decisive function in PCa initiation and progression, but the role of AR in macrophages remains largely unexplored. Here, we show that AR signalling in the macrophage-like THP-1 cell line supports PCa cell line migration and invasion in culture via increased Triggering Receptor Expressed on Myeloid cells-1 (TREM-1) signalling and expression of its downstream cytokines. Moreover, AR signalling in THP-1 and monocyte-derived macrophages upregulates IL-10 and markers of tissue residency. In conclusion, our data suggest that AR signalling in macrophages may support PCa invasiveness, and blocking this process may constitute one mechanism of anti-androgen therapy. Anti-androgen therapy inhibits prostate cancer (PC) progression, and is thought to act directly on cancer cells. Here the authors show that androgen receptor is expressed on normal and PC-associated macrophages, and its stimulation alters macrophage secretome to promote migration of cultured PC cell lines.
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Affiliation(s)
- Bianca Cioni
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Anniek Zaalberg
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Judy R van Beijnum
- Angiogenesis laboratory, Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Monique H M Melis
- Molecular Genetics, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | | | - Mauro J Muraro
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Erik Hooijberg
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Dennis Peters
- Core Facility Molecular Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Ingrid Hofland
- Core Facility Molecular Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Yoni Lubeck
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Jeroen de Jong
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Joyce Sanders
- Division of Pathology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Judith Vivié
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
| | - Henk G van der Poel
- Urology and Medical Oncology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Jan Paul de Boer
- Urology and Medical Oncology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Arjan W Griffioen
- Angiogenesis laboratory, Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. .,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB, Eindhoven, The Netherlands. .,, Oncode Institute, The Netherlands.
| | - Andries M Bergman
- Divisions of Oncogenomics, The Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands. .,Urology and Medical Oncology, NKI, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
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6
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Baron CS, Barve A, Muraro MJ, van der Linden R, Dharmadhikari G, Lyubimova A, de Koning EJP, van Oudenaarden A. Cell Type Purification by Single-Cell Transcriptome-Trained Sorting. Cell 2020; 179:527-542.e19. [PMID: 31585086 PMCID: PMC6863042 DOI: 10.1016/j.cell.2019.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 01/23/2023]
Abstract
Much of current molecular and cell biology research relies on the ability to purify cell types by fluorescence-activated cell sorting (FACS). FACS typically relies on the ability to label cell types of interest with antibodies or fluorescent transgenic constructs. However, antibody availability is often limited, and genetic manipulation is labor intensive or impossible in the case of primary human tissue. To date, no systematic method exists to enrich for cell types without a priori knowledge of cell-type markers. Here, we propose GateID, a computational method that combines single-cell transcriptomics with FACS index sorting to purify cell types of choice using only native cellular properties such as cell size, granularity, and mitochondrial content. We validate GateID by purifying various cell types from zebrafish kidney marrow and the human pancreas to high purity without resorting to specific antibodies or transgenes.
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Affiliation(s)
- Chloé S Baron
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Aditya Barve
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Mauro J Muraro
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Single Cell Discoveries, Utrecht, the Netherlands
| | - Reinier van der Linden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Gitanjali Dharmadhikari
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands
| | - Anna Lyubimova
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Eelco J P de Koning
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Section of Nephrology and Section of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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7
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Honkoop H, de Bakker DE, Aharonov A, Kruse F, Shakked A, Nguyen PD, de Heus C, Garric L, Muraro MJ, Shoffner A, Tessadori F, Peterson JC, Noort W, Bertozzi A, Weidinger G, Posthuma G, Grün D, van der Laarse WJ, Klumperman J, Jaspers RT, Poss KD, van Oudenaarden A, Tzahor E, Bakkers J. Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart. eLife 2019; 8:50163. [PMID: 31868166 PMCID: PMC7000220 DOI: 10.7554/elife.50163] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
While the heart regenerates poorly in mammals, efficient heart regeneration occurs in zebrafish. Studies in zebrafish have resulted in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. To identify which processes occur in proliferating cardiomyocytes we have used a single-cell RNA-sequencing approach. We uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the nonproliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover, these cells have reduced expression of mitochondrial genes and reduced mitochondrial activity, while glycolysis gene expression and glucose uptake are increased, indicative for metabolic reprogramming. Furthermore, we find that the metabolic reprogramming of border zone cardiomyocytes is induced by Nrg1/ErbB2 signaling and is important for their proliferation. This mechanism is conserved in murine hearts in which cardiomyocyte proliferation is induced by activating ErbB2 signaling. Together these results demonstrate that glycolysis regulates cardiomyocyte proliferation during heart regeneration. Heart attacks are a common cause of death in the Western world. During a heart attack, oxygen levels in the affected part of the heart decrease, which causes heart muscle cells to die. In humans the dead cells are replaced by a permanent scar that stabilizes the injury but does not completely heal it. As a result, individuals have a lower quality of life after a heart attack and are more likely to die from a subsequent attack. Unlike humans, zebrafish are able to regenerate their hearts after injury: heart muscle cells close to a wound divide to produce new cells that slowly replace the scar tissue and restore normal function to the area. It remains unclear, however, what stimulates the heart muscle cells of zebrafish to start dividing. To address this question, Honkoop, de Bakker et al. used a technique called single-cell sequencing to study heart muscle cells in wounded zebrafish hearts. The experiments identified a group of heart muscle cells close to the site of the wound that multiplied to repair the damage. This group of cells had altered their metabolism compared to other heart muscle cells so that they relied on a pathway called glycolysis to produce the energy and building blocks they needed to proliferate. Blocking glycolysis impaired the ability of the heart muscle cells to divide, indicating that this switch is necessary for the heart to regenerate. Further experiments showed that a signaling cascade, which includes the molecules Nrg1 and ErbB2, induces heart muscle cells in both zebrafish and mouse hearts to switch to glycolysis and undergo division. These findings indicate that activating glycolysis in heart muscle cells may help to stimulate the heart to regenerate after a heart attack or other injury. The next step following on from this work is to develop methods to activate glycolysis and promote cell division in injured hearts.
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Affiliation(s)
- Hessel Honkoop
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Dennis Em de Bakker
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Alla Aharonov
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Fabian Kruse
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Avraham Shakked
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Phong D Nguyen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Laurence Garric
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Mauro J Muraro
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Adam Shoffner
- Regeneration Next, Department of Cell Biology, Duke University Medical Center, Durham, United States
| | - Federico Tessadori
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands
| | - Joshua Craiger Peterson
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Wendy Noort
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Alberto Bertozzi
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
| | - George Posthuma
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Dominic Grün
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Willem J van der Laarse
- Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Richard T Jaspers
- Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Kenneth D Poss
- Regeneration Next, Department of Cell Biology, Duke University Medical Center, Durham, United States
| | | | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, Netherlands.,Department of Medical Physiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
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8
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Driehuis E, Kolders S, Spelier S, Lõhmussaar K, Willems SM, Devriese LA, de Bree R, de Ruiter EJ, Korving J, Begthel H, van Es JH, Geurts V, He GW, van Jaarsveld RH, Oka R, Muraro MJ, Vivié J, Zandvliet MMJM, Hendrickx APA, Iakobachvili N, Sridevi P, Kranenburg O, van Boxtel R, Kops GJPL, Tuveson DA, Peters PJ, van Oudenaarden A, Clevers H. Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy. Cancer Discov 2019; 9:852-871. [PMID: 31053628 DOI: 10.1158/2159-8290.cd-18-1522] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Previous studies have described that tumor organoids can capture the diversity of defined human carcinoma types. Here, we describe conditions for long-term culture of human mucosal organoids. Using this protocol, a panel of 31 head and neck squamous cell carcinoma (HNSCC)-derived organoid lines was established. This panel recapitulates genetic and molecular characteristics previously described for HNSCC. Organoids retain their tumorigenic potential upon xenotransplantation. We observe differential responses to a panel of drugs including cisplatin, carboplatin, cetuximab, and radiotherapy in vitro. Additionally, drug screens reveal selective sensitivity to targeted drugs that are not normally used in the treatment of patients with HNSCC. These observations may inspire a personalized approach to the management of HNSCC and expand the repertoire of HNSCC drugs. SIGNIFICANCE: This work describes the culture of organoids derived from HNSCC and corresponding normal epithelium. These tumoroids recapitulate the disease genetically, histologically, and functionally. In vitro drug screening of tumoroids reveals responses to therapies both currently used in the treatment of HNSCC and those not (yet) used in clinical practice.See related commentary by Hill and D'Andrea, p. 828.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sigrid Kolders
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sacha Spelier
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kadi Lõhmussaar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lot A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emma J de Ruiter
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeroen Korving
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Johan H van Es
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Veerle Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gui-Wei He
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, Utrecht, the Netherlands
| | - Mauro J Muraro
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Judith Vivié
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Maurice M J M Zandvliet
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nino Iakobachvili
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Priya Sridevi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Onno Kranenburg
- Utrecht Platform for Organoid Technology (U-PORT), Utrecht Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Peter J Peters
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands. .,Princess Maxima Center, Utrecht, the Netherlands
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9
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van Gurp L, Muraro MJ, Dielen T, Seneby L, Dharmadhikari G, Gradwohl G, van Oudenaarden A, de Koning EJP. A transcriptomic roadmap to alpha- and beta cell differentiation in the embryonic pancreas. Development 2019; 146:dev.173716. [DOI: 10.1242/dev.173716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
During pancreatic development, endocrine cells appear from the pancreatic epithelium when Neurog3 positive cells delaminate and differentiate into alpha, beta, gamma and delta cells. The mechanisms involved in this process are still incompletely understood. We characterized the temporal, lineage-specific developmental programs during pancreatic development by sequencing the transcriptome of thousands of individual pancreatic cells from embryonic day E12.5 to E18.5 in mice, and identified all known cell types that are present in the embryonic pancreas, but focused specifically on alpha and beta cell differentiation by enrichment of a MIP-GFP reporter. We characterized transcriptomic heterogeneity in the tip domain based on proliferation, and characterized two endocrine precursor clusters marked by expression of Neurog3 and Fev. Pseudotime analysis revealed specific branches for developing alpha- and beta cells, which allowed identification of specific gene regulation patterns. These include some known and many previously unreported genes that appear to define pancreatic cell fate transitions. This resource allows dynamic profiling of embryonic pancreas development at single cell resolution and reveals novel gene signatures during pancreatic differentiation into alpha and beta cells.
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Affiliation(s)
- Léon van Gurp
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Mauro J. Muraro
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Single Cell Discoveries, Utrecht, the Netherlands
| | - Tim Dielen
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Lina Seneby
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Gitanjali Dharmadhikari
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Gerard Gradwohl
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexander van Oudenaarden
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Single Cell Discoveries, Utrecht, the Netherlands
- Oncode Institute, the Netherlands
| | - Eelco J. P. de Koning
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
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10
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Mok KW, Saxena N, Heitman N, Grisanti L, Srivastava D, Muraro MJ, Jacob T, Sennett R, Wang Z, Su Y, Yang LM, Ma'ayan A, Ornitz DM, Kasper M, Rendl M. Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. Dev Cell 2018; 48:32-48.e5. [PMID: 30595537 DOI: 10.1016/j.devcel.2018.11.034] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 12/29/2022]
Abstract
Cell fate transitions are essential for specification of stem cells and their niches, but the precise timing and sequence of molecular events during embryonic development are largely unknown. Here, we identify, with 3D and 4D microscopy, unclustered precursors of dermal condensates (DC), signaling niches for epithelial progenitors in hair placodes. With population-based and single-cell transcriptomics, we define a molecular time-lapse from pre-DC fate specification through DC niche formation and establish the developmental trajectory as the DC lineage emerges from fibroblasts. Co-expression of downregulated fibroblast and upregulated DC genes in niche precursors reveals a transitory molecular state following a proliferation shutdown. Waves of transcription factor and signaling molecule expression then coincide with DC formation. Finally, ablation of epidermal Wnt signaling and placode-derived FGF20 demonstrates their requirement for pre-DC specification. These findings uncover a progenitor-dependent niche precursor fate and the transitory molecular events controlling niche formation and function.
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Affiliation(s)
- Ka-Wai Mok
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA
| | - Nivedita Saxena
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA
| | - Nicholas Heitman
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA
| | - Laura Grisanti
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA
| | - Devika Srivastava
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA
| | - Mauro J Muraro
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), and University Medical Center Utrecht, Utrecht 3584 CT, the Netherlands
| | - Tina Jacob
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Rachel Sennett
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center, Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yutao Su
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lu M Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center, Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Maria Kasper
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden
| | - Michael Rendl
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, Atran Building AB7-10C, Box 1020, New York, NY 10029, USA.
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11
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Basak O, Krieger TG, Muraro MJ, Wiebrands K, Stange DE, Frias-Aldeguer J, Rivron NC, van de Wetering M, van Es JH, van Oudenaarden A, Simons BD, Clevers H. Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy. Proc Natl Acad Sci U S A 2018; 115:E610-E619. [PMID: 29311336 PMCID: PMC5789932 DOI: 10.1073/pnas.1715911114] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The adult mouse subependymal zone provides a niche for mammalian neural stem cells (NSCs). However, the molecular signature, self-renewal potential, and fate behavior of NSCs remain poorly defined. Here we propose a model in which the fate of active NSCs is coupled to the total number of neighboring NSCs in a shared niche. Using knock-in reporter alleles and single-cell RNA sequencing, we show that the Wnt target Tnfrsf19/Troy identifies both active and quiescent NSCs. Quantitative analysis of genetic lineage tracing of individual NSCs under homeostasis or in response to injury reveals rapid expansion of stem-cell number before some return to quiescence. This behavior is best explained by stochastic fate decisions, where stem-cell number within a shared niche fluctuates over time. Fate mapping proliferating cells using a Ki67iresCreER allele confirms that active NSCs reversibly return to quiescence, achieving long-term self-renewal. Our findings suggest a niche-based mechanism for the regulation of NSC fate and number.
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Affiliation(s)
- Onur Basak
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
| | - Teresa G Krieger
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Mauro J Muraro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
| | - Kay Wiebrands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
| | - Daniel E Stange
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
| | - Javier Frias-Aldeguer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229ER, Maastricht, The Netherlands
| | - Nicolas C Rivron
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229ER, Maastricht, The Netherlands
| | - Marc van de Wetering
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
- Princess Máxima Centre, 3584 CT, Utrecht, The Netherlands
| | - Johan H van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
| | - Benjamin D Simons
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom;
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands;
- Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 GC, Utrecht, The Netherlands
- Princess Máxima Centre, 3584 CT, Utrecht, The Netherlands
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12
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Dierickx P, Vermunt MW, Muraro MJ, Creyghton MP, Doevendans PA, van Oudenaarden A, Geijsen N, Van Laake LW. Circadian networks in human embryonic stem cell-derived cardiomyocytes. EMBO Rep 2017; 18:1199-1212. [PMID: 28536247 PMCID: PMC5494509 DOI: 10.15252/embr.201743897] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [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: 01/03/2017] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 11/09/2022] Open
Abstract
Cell-autonomous circadian oscillations strongly influence tissue physiology and pathophysiology of peripheral organs including the heart, in which the circadian clock is known to determine cardiac metabolism and the outcome of for instance ischemic stress. Human pluripotent stem cells represent a powerful tool to study developmental processes in vitro, but the extent to which human embryonic stem (ES) cell-derived cardiomyocytes establish circadian rhythmicity in the absence of a systemic context is unknown. Here we demonstrate that while undifferentiated human ES cells do not possess an intrinsic functional clock, oscillatory expression of known core clock genes emerges spontaneously during directed cardiac differentiation. We identify a set of clock-controlled output genes that contain an oscillatory network of stress-related transcripts. Furthermore, we demonstrate that this network results in a time-dependent functional response to doxorubicin, a frequently used anti-cancer drug with known cardiotoxic side effects. Taken together, our data provide a framework from which the effect of oscillatory gene expression on cardiomyocyte physiology can be modeled in vitro, and demonstrate the influence of a functional clock on experimental outcome.
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Affiliation(s)
- Pieterjan Dierickx
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands .,Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marit W Vermunt
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mauro J Muraro
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno P Creyghton
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Pieter A Doevendans
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Netherlands Heart Institute, Utrecht, The Netherlands
| | | | - Niels Geijsen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Linda W Van Laake
- Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands .,Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht, The Netherlands
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13
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Grün D, Muraro MJ, Boisset JC, Wiebrands K, Lyubimova A, Dharmadhikari G, van den Born M, van Es J, Jansen E, Clevers H, de Koning EJP, van Oudenaarden A. De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data. Cell Stem Cell 2016; 19:266-277. [PMID: 27345837 PMCID: PMC4985539 DOI: 10.1016/j.stem.2016.05.010] [Citation(s) in RCA: 345] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/04/2016] [Accepted: 05/12/2016] [Indexed: 02/07/2023]
Abstract
Adult mitotic tissues like the intestine, skin, and blood undergo constant turnover throughout the life of an organism. Knowing the identity of the stem cell is crucial to understanding tissue homeostasis and its aberrations upon disease. Here we present a computational method for the derivation of a lineage tree from single-cell transcriptome data. By exploiting the tree topology and the transcriptome composition, we establish StemID, an algorithm for identifying stem cells among all detectable cell types within a population. We demonstrate that StemID recovers two known adult stem cell populations, Lgr5+ cells in the small intestine and hematopoietic stem cells in the bone marrow. We apply StemID to predict candidate multipotent cell populations in the human pancreas, a tissue with largely uncharacterized turnover dynamics. We hope that StemID will accelerate the search for novel stem cells by providing concrete markers for biological follow-up and validation. StemID infers the lineage tree and identifies stem cells from single-cell mRNA-seq data Direct links of stem cells to distinct sub-types reflect transcriptome plasticity The permissive stem cell transcriptome is characterized by high entropy StemID infers candidate multipotent cell populations in the human pancreas
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Affiliation(s)
- Dominic Grün
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
| | - Mauro J Muraro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jean-Charles Boisset
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Kay Wiebrands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Anna Lyubimova
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Gitanjali Dharmadhikari
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department of Medicine, Section of Nephrology and Section of Endocrinology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Maaike van den Born
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Johan van Es
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Erik Jansen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3508 AB Utrecht, the Netherlands
| | - Eelco J P de Koning
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department of Medicine, Section of Nephrology and Section of Endocrinology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands.
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14
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Muraro MJ, Kempe H, Verschure PJ. Concise Review: The Dynamics of Induced Pluripotency and Its Behavior Captured in Gene Network Motifs. Stem Cells 2013; 31:838-48. [DOI: 10.1002/stem.1340] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/20/2012] [Indexed: 01/01/2023]
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