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Yang Y, Li S, Luo L. Responses of organ precursors to correct and incorrect inductive signals. Trends Cell Biol 2024; 34:484-495. [PMID: 37739814 DOI: 10.1016/j.tcb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
During embryonic development, the inductive molecules produced by local origins normally arrive at their target tissues in a nondirectional, diffusion manner. The target organ precursor cells must correctly interpret these inductive signals to ensure proper specification/differentiation, which is dependent on two prerequisites: (i) obtaining cell-intrinsic competence; and (ii) receiving correct inductive signals while resisting incorrect ones. Gain of intrinsic competence could avoid a large number of misinductions because the incompetent cells are nonresponsive to inductive signals. However, in cases of different precursor cells with similar competence and located in close proximity, resistance to incorrect inductive signals is essential for accurate determination of cell fate. Here we outline the mechanisms of how organ precursors respond to correct and incorrect inductive signals.
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Affiliation(s)
- Yun Yang
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Shuang Li
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Lingfei Luo
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China; School of Life Sciences, Fudan University, Shanghai, China.
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2
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Bhuria V, Franz T, Baldauf C, Böttcher M, Chatain N, Koschmieder S, Brümmendorf TH, Mougiakakos D, Schraven B, Kahlfuß S, Fischer T. Activating mutations in JAK2 and CALR differentially affect intracellular calcium flux in store operated calcium entry. Cell Commun Signal 2024; 22:186. [PMID: 38509561 PMCID: PMC10956330 DOI: 10.1186/s12964-024-01530-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Calcium (Ca2+) signaling regulates various vital cellular functions, including integrin activation and cell migration. Store-operated calcium entry (SOCE) via calcium release-activated calcium (CRAC) channels represents a major pathway for Ca2+ influx from the extracellular space in multiple cell types. The impact of JAK2-V617F and CALR mutations which are disease initiating in myeloproliferative neoplasms (MPN) on SOCE, calcium flux from the endoplasmic reticulum (ER) to the cytosol, and related key signaling pathways in the presence or absence of erythropoietin (EPO) or thrombopoietin (TPO) is poorly understood. Thus, this study aimed to elucidate the effects of these mutations on the aforementioned calcium dynamics, in cellular models of MPN. METHODS Intracellular Ca2+ levels were measured over a time frame of 0-1080 s in Fura-2 AM labeled myeloid progenitor 32D cells expressing various mutations (JAK2-WT/EpoR, JAK2-V617F/EpoR; CALR-WT/MPL, CALR-ins5/MPL, and del52/MPL). Basal Ca2+ concentrations were assessed from 0-108 s. Subsequently, cells were stimulated with EPO/TPO in Ca2+-free Ringer solution, measuring Ca2+ levels from 109-594 s (store depletion). Then, 2 mM of Ca2+ buffer resembling physiological concentrations was added to induce SOCE, and Ca2+ levels were measured from 595-1080 s. Fura-2 AM emission ratios (F340/380) were used to quantify the integrated Ca2+ signal. Statistical significance was assessed by unpaired Student's t-test or Mann-Whitney-U-test, one-way or two-way ANOVA followed by Tukey's multiple comparison test. RESULTS Following EPO stimulation, the area under the curve (AUC) representing SOCE significantly increased in 32D-JAK2-V617F cells compared to JAK2-WT cells. In TPO-stimulated CALR cells, we observed elevated Ca2+ levels during store depletion and SOCE in CALR-WT cells compared to CALR-ins5 and del52 cells. Notably, upon stimulation, key components of the Ca2+ signaling pathways, including PLCγ-1 and IP3R, were differentially affected in these cell lines. Hyper-activated PLCγ-1 and IP3R were observed in JAK2-V617F but not in CALR mutated cells. Inhibition of calcium regulatory mechanisms suppressed cellular growth and induced apoptosis in JAK2-V617F cells. CONCLUSIONS This report highlights the impact of JAK2 and CALR mutations on Ca2+ flux (store depletion and SOCE) in response to stimulation with EPO and TPO. The study shows that the JAK2-V617F mutation strongly alters the regulatory mechanism of EpoR/JAK2-dependent intracellular calcium balance, affecting baseline calcium levels, EPO-induced calcium entry, and PLCγ-1 signaling pathways. Our results reveal an important role of calcium flux in the homeostasis of JAK2-V617F positive cells.
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Affiliation(s)
- Vikas Bhuria
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany.
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany.
| | - Tobias Franz
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Conny Baldauf
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Martin Böttcher
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Department of Hematology and Oncology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center of Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center of Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center of Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Dimitrios Mougiakakos
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Department of Hematology and Oncology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Burkhart Schraven
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany
| | - Sascha Kahlfuß
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Thomas Fischer
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.
- Health-Campus Immunology, Infectiology, and Inflammation (GC-I3), Medical Center, Otto-von-Guericke University, Magdeburg, Germany.
- Center for Health and Medical Prevention - CHaMP, Otto-von-Guericke University, Magdeburg, Germany.
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3
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Urman MA, John NS, Jung T, Lee C. Aging disrupts spatiotemporal regulation of germline stem cells and niche integrity. Biol Open 2024; 13:bio060261. [PMID: 38156664 PMCID: PMC10810562 DOI: 10.1242/bio.060261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
A major factor driving stem cell decline is stem cell niche aging, but its molecular mechanism remains elusive. We use the Caenorhabditis elegans distal tip cell (DTC), the mesenchymal niche that employs Notch signaling to regulate germline stem cells (GSCs), as an in vivo niche aging model and delineate the molecular details of the DTC/niche aging process. Here, we demonstrate that a drastic decrease in C. elegans germline fecundity, which begins even in early adulthood, is mainly due to an age-induced disruption in spatial regulation of Notch-dependent transcription in the germline combined with a moderate reduction in Notch transcription at both tissue and cellular levels. Consequently, the Notch-responsive GSC pool shifts from the distal end of the gonad to a more proximal region, disrupting the distal-to-proximal germline polarity. We find that this GSC pool shift is due to a dislocation of the DTC/niche nucleus, which is associated with age-induced changes in the structure and morphology of the DTC/niche. Our findings reveal a critical link between physiological changes in the aging niche, their consequences in stem cell regulation, and germline tissue functions.
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Affiliation(s)
- Michelle A. Urman
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Nimmy S. John
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Tyler Jung
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - ChangHwan Lee
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
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4
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Kreller T, Zimmermann J, van Rienen U, Boccaccini AR, Jonitz-Heincke A, Detsch R. Alternating electric field stimulation: Phenotype analysis and osteoclast activity of differentiated RAW 264.7 macrophages on hydroxyapatite-coated Ti6Al4V surfaces and their crosstalk with MC3T3-E1 pre-osteoblasts. BIOMATERIALS ADVANCES 2023; 146:213285. [PMID: 36640524 DOI: 10.1016/j.bioadv.2023.213285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Affiliation(s)
- T Kreller
- Institute of Biomaterials, Department of Materials Science and Engineering, Friedrich Alexander-University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - J Zimmermann
- Institute of General Electrical Engineering, University of Rostock, 18051 Rostock, Germany
| | - U van Rienen
- Institute of General Electrical Engineering, University of Rostock, 18051 Rostock, Germany; Department Life, Light and Matter, University of Rostock, 18051 Rostock, Germany; Department Ageing of Individuals and Society, University of Rostock, 18051 Rostock, Germany
| | - A R Boccaccini
- Institute of Biomaterials, Department of Materials Science and Engineering, Friedrich Alexander-University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - A Jonitz-Heincke
- Research Laboratory for Biomechanics and Implant Technology, Department of Orthopedics, Rostock University Medical Center, 18057 Rostock, Germany
| | - R Detsch
- Institute of Biomaterials, Department of Materials Science and Engineering, Friedrich Alexander-University Erlangen-Nuremberg, 91058 Erlangen, Germany.
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Miles J, Townend S, Milonaitytė D, Smith W, Hodge F, Westhead DR, van Oosten-Hawle P. Transcellular chaperone signaling is an intercellular stress-response distinct from the HSF-1-mediated heat shock response. PLoS Biol 2023; 21:e3001605. [PMID: 36780563 PMCID: PMC9956597 DOI: 10.1371/journal.pbio.3001605] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 02/24/2023] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
Organismal proteostasis is maintained by intercellular signaling processes including cell nonautonomous stress responses such as transcellular chaperone signaling (TCS). When TCS is activated upon tissue-specific knockdown of hsp-90 in the Caenorhabditis elegans intestine, heat-inducible hsp-70 is induced in muscle cells at the permissive temperature resulting in increased heat stress resistance and lifespan extension. However, our understanding of the molecular mechanism and signaling factors mediating transcellular activation of hsp-70 expression from one tissue to another is still in its infancy. Here, we conducted a combinatorial approach using transcriptome RNA-Seq profiling and a forward genetic mutagenesis screen to elucidate how stress signaling from the intestine to the muscle is regulated. We find that the TCS-mediated "gut-to-muscle" induction of hsp-70 expression is suppressed by HSF-1 and instead relies on transcellular-X-cross-tissue (txt) genes. We identify a key role for the PDZ-domain guanylate cyclase txt-1 and the homeobox transcription factor ceh-58 as signaling hubs in the stress receiving muscle cells to initiate hsp-70 expression and facilitate TCS-mediated heat stress resistance and lifespan extension. Our results provide a new view on cell-nonautonomous regulation of "inter-tissue" stress responses in an organism that highlight a key role for the gut. Our data suggest that the HSF-1-mediated heat shock response is switched off upon TCS activation, in favor of an intercellular stress-signaling route to safeguard survival.
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Affiliation(s)
- Jay Miles
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sarah Townend
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Dovilė Milonaitytė
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - William Smith
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Francesca Hodge
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David R. Westhead
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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6
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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7
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Du L, Sohr A, Li Y, Roy S. GPI-anchored FGF directs cytoneme-mediated bidirectional contacts to regulate its tissue-specific dispersion. Nat Commun 2022; 13:3482. [PMID: 35710780 PMCID: PMC9203819 DOI: 10.1038/s41467-022-30417-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/20/2022] [Indexed: 01/03/2023] Open
Abstract
How signaling proteins generate a multitude of information to organize tissue patterns is critical to understanding morphogenesis. In Drosophila, FGF produced in wing-disc cells regulates the development of the disc-associated air-sac-primordium (ASP). Here, we show that FGF is Glycosylphosphatidylinositol-anchored to the producing cell surface and that this modification both inhibits free FGF secretion and promotes target-specific cytoneme contacts and contact-dependent FGF release. FGF-source and ASP cells extend cytonemes that present FGF and FGFR on their surfaces and reciprocally recognize each other over distance by contacting through cell-adhesion-molecule (CAM)-like FGF-FGFR binding. Contact-mediated FGF-FGFR interactions induce bidirectional responses in ASP and source cells that, in turn, polarize FGF-sending and FGF-receiving cytonemes toward each other to reinforce signaling contacts. Subsequent un-anchoring of FGFR-bound-FGF from the source membrane dissociates cytoneme contacts and delivers FGF target-specifically to ASP cytonemes for paracrine functions. Thus, GPI-anchored FGF organizes both source and recipient cells and self-regulates its cytoneme-mediated tissue-specific dispersion. Cytonemes are signaling filopodia that mediate target-specific long-distance communications of signals like FGFs. Du et al. show that a Drosophila FGF is anchored to the FGF-producing cell surface, inhibiting free FGF secretion and activating contact-dependent bidirectional FGF-FGFR interactions, controlling target-specific cytoneme contacts and contact-dependent FGF release.
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Affiliation(s)
- Lijuan Du
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Alex Sohr
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.,Division of Cell and Gene Therapy, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Yujia Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Sougata Roy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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8
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Greenspan LJ, de Cuevas M, Le KH, Viveiros JM, Matunis EL. Activation of the EGFR/MAPK pathway drives transdifferentiation of quiescent niche cells to stem cells in the Drosophila testis niche. eLife 2022; 11:e70810. [PMID: 35468055 PMCID: PMC9038189 DOI: 10.7554/elife.70810] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 03/31/2022] [Indexed: 12/28/2022] Open
Abstract
Adult stem cells are maintained in niches, specialized microenvironments that regulate their self-renewal and differentiation. In the adult Drosophila testis stem cell niche, somatic hub cells produce signals that regulate adjacent germline stem cells (GSCs) and somatic cyst stem cells (CySCs). Hub cells are normally quiescent, but after complete genetic ablation of CySCs, they can proliferate and transdifferentiate into new CySCs. Here we find that Epidermal growth factor receptor (EGFR) signaling is upregulated in hub cells after CySC ablation and that the ability of testes to recover from ablation is inhibited by reduced EGFR signaling. In addition, activation of the EGFR pathway in hub cells is sufficient to induce their proliferation and transdifferentiation into CySCs. We propose that EGFR signaling, which is normally required in adult cyst cells, is actively inhibited in adult hub cells to maintain their fate but is repurposed to drive stem cell regeneration after CySC ablation.
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Affiliation(s)
- Leah J Greenspan
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Margaret de Cuevas
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Kathy H Le
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Graduate Program in Biophysics, Stanford UniversityStanfordUnited States
| | - Jennifer M Viveiros
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Erika L Matunis
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
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9
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Zeng T, Yuan P, Liang L, Zhang X, Zhang H, Wu W. Cartilaginous Extracellular Matrix Enriched with Human Gingival Mesenchymal Stem Cells Derived "Matrix Bound Extracellular Vesicles" Enabled Functional Reconstruction of Tracheal Defect. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2102735. [PMID: 34841733 PMCID: PMC8805569 DOI: 10.1002/advs.202102735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 10/14/2021] [Indexed: 05/27/2023]
Abstract
Stem cells derived extracellular vesicles (EVs) conceive cues essential for tissue repair. Mammalian cartilaginous extracellular matrix (cECM) may not be optimally inductive for tracheal regeneration because of the granulomatous, instead of regenerative, responses in injured adult mammalian tracheas. Given the high regenerative capacity of gingiva, it is hypothesized human gingival mesenchymal stem cells derived EVs (gEVs) can induce mammalian tracheal epithelia regeneration. Coculturing chondrocytes with GMSCs produce abundant "matrix bound gEVs (gMVs)" in forming cartilaginous ECM, which are further preserved in acellular cECM (cACM) following mild, short-period decellularization. The results show that gMVs-cACM could be well anchored on polyglycerol sebacate microporous patch thus enforce the surgical suturability and mechanical strength. In rabbit tracheal defect, the gMVs-cACM patch induces rapid regeneration of vascularized ciliated columnar epithelium, which supports long-term survival of animals. gMVs-cACM treated groups exhibit proliferation of tracheal progenitors-basal epithelial cells, as well as, activation of JAK2/STAT1 pathway in reparative cells. This study departs from conventional focuses on tissue derived ECM and introduces a new approach for tracheal tissue regeneration.
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Affiliation(s)
- Tian Zeng
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologyDepartment of Anesthesiologyand Department of Oral & Maxillofacial SurgerySchool of Stomatologythe Fourth Military Medical UniversityXi'an710032P. R. China
- Department of Anesthesiologythe 986th Air Force Hospital, Xijing hospitalthe Fourth Military Medical UniversityXi'an710032P. R. China
| | - Pingping Yuan
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologyDepartment of Oral & Maxillofacial SurgerySchool of Stomatologythe Fourth Military Medical UniversityXi'an710032P. R. China
| | - Lirong Liang
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologyDepartment of AnesthesiologySchool of Stomatologythe Fourth Military Medical UniversityXi'an710032P. R. China
| | - Xinchi Zhang
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologyDepartment of Oral & Maxillofacial SurgerySchool of Stomatologythe Fourth Military Medical UniversityXi'an710032P. R. China
| | - Hui Zhang
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologyDepartment of AnesthesiologySchool of Stomatologythe Fourth Military Medical UniversityXi'an710032P. R. China
| | - Wei Wu
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologyDepartment of Oral & Maxillofacial SurgerySchool of Stomatologythe Fourth Military Medical UniversityXi'an710032P. R. China
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10
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Nienałtowski K, Rigby RE, Walczak J, Zakrzewska KE, Głów E, Rehwinkel J, Komorowski M. Fractional response analysis reveals logarithmic cytokine responses in cellular populations. Nat Commun 2021; 12:4175. [PMID: 34234126 PMCID: PMC8263596 DOI: 10.1038/s41467-021-24449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 06/17/2021] [Indexed: 01/10/2023] Open
Abstract
Although we can now measure single-cell signaling responses with multivariate, high-throughput techniques our ability to interpret such measurements is still limited. Even interpretation of dose–response based on single-cell data is not straightforward: signaling responses can differ significantly between cells, encompass multiple signaling effectors, and have dynamic character. Here, we use probabilistic modeling and information-theory to introduce fractional response analysis (FRA), which quantifies changes in fractions of cells with given response levels. FRA can be universally performed for heterogeneous, multivariate, and dynamic measurements and, as we demonstrate, quantifies otherwise hidden patterns in single-cell data. In particular, we show that fractional responses to type I interferon in human peripheral blood mononuclear cells are very similar across different cell types, despite significant differences in mean or median responses and degrees of cell-to-cell heterogeneity. Further, we demonstrate that fractional responses to cytokines scale linearly with the log of the cytokine dose, which uncovers that heterogeneous cellular populations are sensitive to fold-changes in the dose, as opposed to additive changes. Our ability to interpret single-cell multivariate signaling responses is still limited. Here the authors introduce fractional response analysis (FRA), involving fractional cell counting, capable of deconvoluting heterogeneous multivariate responses of cellular populations.
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Affiliation(s)
- Karol Nienałtowski
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Rachel E Rigby
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jarosław Walczak
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina E Zakrzewska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Edyta Głów
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michał Komorowski
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
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11
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Joshi P, Skromne I. A theoretical model of neural maturation in the developing chick spinal cord. PLoS One 2020; 15:e0244219. [PMID: 33338079 PMCID: PMC7748286 DOI: 10.1371/journal.pone.0244219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/04/2020] [Indexed: 11/21/2022] Open
Abstract
Cellular differentiation is a tightly regulated process under the control of intricate signaling and transcription factors interaction network working in coordination. These interactions make the systems dynamic, robust and stable but also difficult to dissect. In the spinal cord, recent work has shown that a network of FGF, WNT and Retinoic Acid (RA) signaling factors regulate neural maturation by directing the activity of a transcription factor network that contains CDX at its core. Here we have used partial and ordinary (Hill) differential equation based models to understand the spatiotemporal dynamics of the FGF/WNT/RA and the CDX/transcription factor networks, alone and in combination. We show that in both networks, the strength of interaction among network partners impacts the dynamics, behavior and output of the system. In the signaling network, interaction strength determine the position and size of discrete regions of cell differentiation and small changes in the strength of the interactions among networking partners can result in a signal overriding, balancing or oscillating with another signal. We also show that the spatiotemporal information generated by the signaling network can be conveyed to the CDX/transcription network to produces a transition zone that separates regions of high cell potency from regions of cell differentiation, in agreement with most in vivo observations. Importantly, one emerging property of the networks is their robustness to extrinsic disturbances, which allows the system to retain or canalize NP cells in developmental trajectories. This analysis provides a model for the interaction conditions underlying spinal cord cell maturation during embryonic axial elongation.
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Affiliation(s)
- Piyush Joshi
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Isaac Skromne
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
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12
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Migliorini E, Guevara-Garcia A, Albiges-Rizo C, Picart C. Learning from BMPs and their biophysical extracellular matrix microenvironment for biomaterial design. Bone 2020; 141:115540. [PMID: 32730925 PMCID: PMC7614069 DOI: 10.1016/j.bone.2020.115540] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 01/19/2023]
Abstract
It is nowadays well-accepted that the extracellular matrix (ECM) is not a simple reservoir for growth factors but is an organization center of their biological activity. In this review, we focus on the ability of the ECM to regulate the biological activity of BMPs. In particular, we survey the role of the ECM components, notably the glycosaminoglycans and fibrillary ECM proteins, which can be promoters or repressors of the biological activities mediated by the BMPs. We examine how a process called mechano-transduction induced by the ECM can affect BMP signaling, including BMP internalization by the cells. We also focus on the spatio-temporal regulation of the BMPs, including their release from the ECM, which enables to modulate their spatial localization as well as their local concentration. We highlight how biomaterials can recapitulate some aspects of the BMPs/ECM interactions and help to answer fundamental questions to reveal previously unknown molecular mechanisms. Finally, the design of new biomaterials inspired by the ECM to better present BMPs is discussed, and their use for a more efficient bone regeneration in vivo is also highlighted.
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Affiliation(s)
- Elisa Migliorini
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble, France; CEA, Institute of Interdisciplinary Research of Grenoble (IRIG), Biomimetism and Regenerative Medicine Lab, ERL 5000, Université Grenoble-Alpes (UGA)/CEA/CNRS, Grenoble France.
| | - Amaris Guevara-Garcia
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble, France; CEA, Institute of Interdisciplinary Research of Grenoble (IRIG), Biomimetism and Regenerative Medicine Lab, ERL 5000, Université Grenoble-Alpes (UGA)/CEA/CNRS, Grenoble France; Université Grenoble Alpes, Institut for Advances Biosciences, Institute Albert Bonniot, INSERM U1209, CNRS 5309, La Tronche, France
| | - Corinne Albiges-Rizo
- Université Grenoble Alpes, Institut for Advances Biosciences, Institute Albert Bonniot, INSERM U1209, CNRS 5309, La Tronche, France
| | - Catherine Picart
- CNRS, Grenoble Institute of Technology, LMGP, UMR 5628, 3 Parvis Louis Néel, 38016 Grenoble, France; CEA, Institute of Interdisciplinary Research of Grenoble (IRIG), Biomimetism and Regenerative Medicine Lab, ERL 5000, Université Grenoble-Alpes (UGA)/CEA/CNRS, Grenoble France.
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13
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Stevens CA, Revaitis NT, Caur R, Yakoby N. The ETS-transcription factor Pointed is sufficient to regulate the posterior fate of the follicular epithelium. Development 2020; 147:dev.189787. [PMID: 33028611 DOI: 10.1242/dev.189787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022]
Abstract
The Janus-kinase/signal transducer and activator of transcription (JAK/STAT) pathway regulates the anterior posterior axis of the Drosophila follicle cells. In the anterior, it activates the bone morphogenetic protein (BMP) signaling pathway through expression of the BMP ligand decapentaplegic (dpp). In the posterior, JAK/STAT works with the epidermal growth factor receptor (EGFR) pathway to express the T-box transcription factor midline (mid). Although MID is necessary for establishing the posterior fate of the egg chamber, we show that it is not sufficient to determine a posterior fate. The ETS-transcription factor pointed (pnt) is expressed in an overlapping domain to mid in the follicle cells. This study shows that pnt is upstream of mid and that it is sufficient to induce a posterior fate in the anterior end, which is characterized by the induction of mid, the prevention of the stretched cells formation and the abrogation of border cell migration. We demonstrate that the anterior BMP signaling is abolished by PNT through dpp repression. However, ectopic DPP cannot rescue the anterior fate formation, suggesting additional targets of PNT participate in the posterior fate determination.
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Affiliation(s)
- Cody A Stevens
- Center for Computational and Integrative Biology, Rutgers, The State University of NJ, Camden, NJ 08102, USA
| | - Nicole T Revaitis
- Center for Computational and Integrative Biology, Rutgers, The State University of NJ, Camden, NJ 08102, USA
| | - Rumkan Caur
- Department of Biology, Rutgers, The State University of NJ, Camden, NJ 08102, USA
| | - Nir Yakoby
- Center for Computational and Integrative Biology, Rutgers, The State University of NJ, Camden, NJ 08102, USA .,Department of Biology, Rutgers, The State University of NJ, Camden, NJ 08102, USA
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14
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Dhusia K, Su Z, Wu Y. Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method. J Chem Theory Comput 2020; 16:5323-5333. [PMID: 32667783 PMCID: PMC10829009 DOI: 10.1021/acs.jctc.0c00439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes formed among diverse proteins carry out versatile functions in nearly all physiological processes. Association rates which measure how fast proteins form various complexes are of fundamental importance to characterize their functions. The association rates are not only determined by the energetic features at binding interfaces of a protein complex but also influenced by the intrinsic conformational dynamics of each protein in the complex. Unfortunately, how this conformational effect regulates protein association has never been calibrated on a systematic level. To tackle this problem, we developed a multiscale strategy to incorporate the information on protein conformational variations from Langevin dynamic simulations into a kinetic Monte Carlo algorithm of protein-protein association. By systematically testing this approach against a large-scale benchmark set, we found the association of a protein complex with a relatively rigid structure tends to be reduced by its conformational fluctuations. With specific examples, we further show that higher degrees of structural flexibility in various protein complexes can facilitate the searching and formation of intermolecular interactions and thereby accelerate their associations. In general, the integration of conformational dynamics can improve the correlation between experimentally measured association rates and computationally derived association probabilities. Finally, we analyzed the statistical distributions of different secondary structural types on protein-protein binding interfaces and their preference to the change of association rates. Our study, to the best of our knowledge, is the first computational method that systematically estimates the impacts of protein conformational dynamics on protein-protein association. It throws lights on the molecular mechanisms of how protein-protein recognition is kinetically modulated.
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Affiliation(s)
- Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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15
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Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association. Biomolecules 2020; 10:biom10071056. [PMID: 32679892 PMCID: PMC7407674 DOI: 10.3390/biom10071056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022] Open
Abstract
The formation of functionally versatile protein complexes underlies almost every biological process. The estimation of how fast these complexes can be formed has broad implications for unravelling the mechanism of biomolecular recognition. This kinetic property is traditionally quantified by association rates, which can be measured through various experimental techniques. To complement these time-consuming and labor-intensive approaches, we developed a coarse-grained simulation approach to study the physical processes of protein–protein association. We systematically calibrated our simulation method against a large-scale benchmark set. By combining a physics-based force field with a statistically-derived potential in the simulation, we found that the association rates of more than 80% of protein complexes can be correctly predicted within one order of magnitude relative to their experimental measurements. We further showed that a mixture of force fields derived from complementary sources was able to describe the process of protein–protein association with mechanistic details. For instance, we show that association of a protein complex contains multiple steps in which proteins continuously search their local binding orientations and form non-native-like intermediates through repeated dissociation and re-association. Moreover, with an ensemble of loosely bound encounter complexes observed around their native conformation, we suggest that the transition states of protein–protein association could be highly diverse on the structural level. Our study also supports the idea in which the association of a protein complex is driven by a “funnel-like” energy landscape. In summary, these results shed light on our understanding of how protein–protein recognition is kinetically modulated, and our coarse-grained simulation approach can serve as a useful addition to the existing experimental approaches that measure protein–protein association rates.
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16
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Herrera SC, Bach EA. JAK/STAT signaling in stem cells and regeneration: from Drosophila to vertebrates. Development 2019; 146:dev167643. [PMID: 30696713 PMCID: PMC6361132 DOI: 10.1242/dev.167643] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022]
Abstract
The JAK/STAT pathway is a conserved metazoan signaling system that transduces cues from extracellular cytokines into transcriptional changes in the nucleus. JAK/STAT signaling is best known for its roles in immunity. However, recent work has demonstrated that it also regulates critical homeostatic processes in germline and somatic stem cells, as well as regenerative processes in several tissues, including the gonad, intestine and appendages. Here, we provide an overview of JAK/STAT signaling in stem cells and regeneration, focusing on Drosophila and highlighting JAK/STAT pathway functions in proliferation, survival and cell competition that are conserved between Drosophila and vertebrates.
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Affiliation(s)
- Salvador C Herrera
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Erika A Bach
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Helen L. and Martin S. Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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17
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Komorowski M, Tawfik DS. The Limited Information Capacity of Cross-Reactive Sensors Drives the Evolutionary Expansion of Signaling. Cell Syst 2019; 8:76-85.e6. [PMID: 30660612 DOI: 10.1016/j.cels.2018.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/15/2018] [Accepted: 12/10/2018] [Indexed: 01/10/2023]
Abstract
Signaling systems expand by duplications of various components, be it receptors or downstream effectors. However, whether and how duplicated components contribute to higher signaling capacity is unclear, especially because in most cases, their specificities overlap. Using information theory, we found that augmentation of capacity by an increase in the copy number is strongly limited by logarithmic diminishing returns. Moreover, counter to conventional biochemical wisdom, refinements of the response mechanism, e.g., by cooperativity or allostery, do not increase the overall signaling capacity. However, signaling capacity nearly doubles when a promiscuous, non-cognate ligand becomes explicitly recognized via duplication and partial divergence of signaling components. Our findings suggest that expansion of signaling components via duplication and enlistment of promiscuously acting cues is virtually the only accessible evolutionary strategy to achieve overall high-signaling capacity despite overlapping specificities and molecular noise. This mode of expansion also explains the highly cross-wired architecture of signaling pathways.
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Affiliation(s)
- Michał Komorowski
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw 02-106, Poland.
| | - Dan S Tawfik
- Weizmann Institute of Science, The Department of Biomolecular Sciences, Rehovot 7610001, Israel
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18
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Ahaley SS. Synaptojanin regulates Hedgehog signalling by modulating phosphatidylinositol 4-phosphate levels. J Biosci 2018; 43:867-876. [PMID: 30541947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Hedgehog (Hh) signalling, Hh ligand concentration gradient is effectively translated into a spatially distinct transcriptional program to give precisely controlled context dependent developmental outcomes. In the absence of Hh, the receptor Patched (Ptc) inhibits the signal transducer Smoothened (Smo) by maintaining low phosphatidylinositol 4-phosphate (PI(4)P) levels. Binding of Hh to its receptor Ptc promotes PI(4)P production, which in turn activates Smo. Using wingdiscs of Drosophila melanogaster, this study shows that Synaptojanin (Synj), a dual phosphatase, modulates PI(4)P levels and affects Smo activation, and thereby functions as an additional regulatory step in the Hh pathway. Reducing the levels of Synj in the wing-discs caused enhancement of a Hh dominant gain-of-function Moonrat phenotype in the adult wings. Synj downregulation augmented Hh signalling, which was associated with elevated PI(4)P levels and Smo activation. Synj did not control the absolute pathway activity but rather fine-tuned the response since its downregulation increased expression of decapentaplegic (dpp), a low-threshold target of the pathway while the high-threshold targets remained unaffected. This is the first report that identifies Synj as a negative regulator of Hh signalling, implying its importance and an additional regulatory step in Hh signal transduction.
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Affiliation(s)
- Shital Sarah Ahaley
- Biology Department, Indian Institute of Science Education and Research, Pune 411 008, India,
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19
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Yin J, Lee R, Ono Y, Ingham PW, Saunders TE. Spatiotemporal Coordination of FGF and Shh Signaling Underlies the Specification of Myoblasts in the Zebrafish Embryo. Dev Cell 2018; 46:735-750.e4. [PMID: 30253169 DOI: 10.1016/j.devcel.2018.08.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/11/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
Abstract
Somitic cells give rise to a variety of cell types in response to Hh, BMP, and FGF signaling. Cell position within the developing zebrafish somite is highly dynamic: how, when, and where these signals specify cell fate is largely unknown. Combining four-dimensional imaging with pathway perturbations, we characterize the spatiotemporal specification and localization of somitic cells. Muscle formation is guided by highly orchestrated waves of cell specification. We find that FGF directly and indirectly controls the differentiation of fast and slow-twitch muscle lineages, respectively. FGF signaling imposes tight temporal control on Shh induction of slow muscles by regulating the time at which fast-twitch progenitors displace slow-twitch progenitors from contacting the Shh-secreting notochord. Further, we find a reciprocal regulation of fast and slow muscle differentiation, morphogenesis, and migration. In conclusion, robust cell fate determination in the developing somite requires precise spatiotemporal coordination between distinct cell lineages and signaling pathways.
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Affiliation(s)
- Jianmin Yin
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Raymond Lee
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore, Singapore
| | - Yosuke Ono
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Living Systems Institute, University of Exeter, Exeter, UK
| | - Philip W Ingham
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore, Singapore; Living Systems Institute, University of Exeter, Exeter, UK.
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore, Singapore; Living Systems Institute, University of Exeter, Exeter, UK.
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20
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Synaptojanin regulates Hedgehog signalling by modulating phosphatidylinositol 4-phosphate levels. J Biosci 2018. [DOI: 10.1007/s12038-018-9799-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Hu P, Nebreda AR, Hanenberg H, Kinnebrew GH, Ivan M, Yoder MC, Filippi MD, Broxmeyer HE, Kapur R. P38α/JNK signaling restrains erythropoiesis by suppressing Ezh2-mediated epigenetic silencing of Bim. Nat Commun 2018; 9:3518. [PMID: 30158520 PMCID: PMC6115418 DOI: 10.1038/s41467-018-05955-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 05/29/2018] [Indexed: 01/05/2023] Open
Abstract
While erythropoietin (EPO) constitutes the major treatment for anemia, a range of anemic disorders remain resistant to EPO treatment. The need for alternative therapeutic strategies requires the identification of mechanisms that physiologically restrain erythropoiesis. Here we show that P38α restrains erythropoiesis in mouse and human erythroblasts independently of EPO by integrating apoptotic signals during recovery from anemia. P38α deficiency promotes JNK activation through increased expression of Map3k4 via a negative feedback mechanism. JNK prevents Cdk1-mediated phosphorylation and subsequent degradation by Smurf2 of the epigenetic silencer Ezh2. Stabilized Ezh2 silences Bim expression and protects erythroblasts from apoptosis. Thus, we identify P38α/JNK signaling as a molecular brake modulating erythropoiesis through epigenetic silencing of Bim. We propose that inhibition of P38α, by enhancing erythropoiesis in an EPO-independent fashion, may provide an alternative strategy for the treatment of anemia. Erythropoietin (EPO) stimulates erythropoiesis and is commonly used to treat anemia. Here Hu et al. find that P38α/JNK signaling restrains erythropoiesis independently of EPO by regulating epigenetic silencing of the proapoptotic protein Bim, and thus identify putative targets for the treatment of anemic disorders resistant to EPO.
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Affiliation(s)
- Ping Hu
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona). Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122, Essen, Germany
| | - Garrett H Kinnebrew
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Mircea Ivan
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Mervin C Yoder
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Marie-Dominique Filippi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Hal E Broxmeyer
- Department of Microbiology/Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Reuben Kapur
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA.
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22
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Matrix Signaling Subsequent to a Myocardial Infarction: A Proteomic Profile of Tissue Factor Microparticles. JACC Basic Transl Sci 2018; 2:529-542. [PMID: 30062169 PMCID: PMC6058924 DOI: 10.1016/j.jacbts.2017.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/27/2017] [Accepted: 04/04/2017] [Indexed: 11/24/2022]
Abstract
The occurrence of an MI activates production of TFMPs. We induced an MI in Yucatan miniswine and collected plasma samples over a 6-month period post-MI. Experimental groups consisted of infarcted but untreated animals and infarcted animals treated with CRT plus β-blocker. Using proteomic profiling, we confirm the heterogeneity of TFMP protein content with respect to physiological status of the host temporally. Spatially, the contents of the TFMPs provided information about multiple entities supplemental to what we obtained from assessing a set of 8 currently used cardiac biomarkers. The results from this study support recommending TFMP protein content profiling be used prospectively as a viable investigative methodology for chronic ischemic cardiomyopathy to help improve our understanding of β-adrenergic receptor signaling after an MI.
This study investigated the release and proteomic profile of tissue factor microparticles (TFMPs) prospectively (up to 6 months) following a myocardial infarction (MI) in a chronic porcine model to establish their utility in tracking cellular level activities that predict physiologic outcomes. Our animal groups (n = 6 to 8 each) consisted of control, noninfarcted (negative control); infarcted only (positive control); and infarcted animals treated with cardiac resynchronization therapy (CRT) and a β-blocker (BB) (metoprolol succinate). The authors found different protein profiles in TFMPs between the control, infarcted only group, and the CRT + BB treated group with predictive impact on the outward phenotype of pathological remodeling after an MI within and between groups. This novel approach of monitoring cellular level activities by profiling the content of TFMPs has the potential of addressing a shortfall of the current crop of cardiac biomarkers, which is the inability to capture composite molecular changes associated with chronic maladaptive signaling in a spatial and temporal manner.
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Key Words
- ADRB1, β1-adrenergic receptor
- ADRB2, β2-adrenergic receptor
- AR, adrenergic receptor
- ARRB1, β1-arrestin
- BB, β-blocker
- CRT, cardiac resynchronization therapy
- EDV, end-diastolic volume
- EF, ejection fraction
- ELISA, enzyme-linked immunosorbent assay
- ESV, end-systolic volume
- FACS, fluorescence-activated cell sorting
- GRK, G-protein receptor kinase
- HSP, heat shock protein
- HUVEC, human umbilical vein endothelial cell
- LVAd MV, left ventricular area around the mitral valve at diastole
- LVAd PM, left ventricular area around the papillary muscle at diastole
- LVAs MV, left ventricular area around the mitral valve at systole
- LVAs PM, left ventricular area around the papillary muscle at systole
- MI, myocardial infarction
- MP, microparticle
- PCR, polymerase chain reaction
- TF, tissue factor
- TFMP, tissue factor–bearing microparticle
- TnT, troponin T
- Yucatan mini swine
- cAMP, cyclic adenosine monophosphate
- chronic ischemic cardiomyopathy
- matrix signaling
- myocardial infarction
- tissue factor-bearing microparticles
- βAR signaling
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23
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Abstract
The extracellular signal-regulated kinase (ERK) pathway leads to activation of the effector molecule ERK, which controls downstream responses by phosphorylating a variety of substrates, including transcription factors. Crucial insights into the regulation and function of this pathway came from studying embryos in which specific phenotypes arise from aberrant ERK activation. Despite decades of research, several important questions remain to be addressed for deeper understanding of this highly conserved signaling system and its function. Answering these questions will require quantifying the first steps of pathway activation, elucidating the mechanisms of transcriptional interpretation and measuring the quantitative limits of ERK signaling within which the system must operate to avoid developmental defects.
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Affiliation(s)
- Aleena L Patel
- Lewis Sigler Institute for Integrative Genomics, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- Lewis Sigler Institute for Integrative Genomics, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
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24
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Kubota H, Uda S, Matsuzaki F, Yamauchi Y, Kuroda S. In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver. Cell Syst 2018; 7:118-128.e3. [PMID: 29960883 DOI: 10.1016/j.cels.2018.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/06/2018] [Accepted: 05/18/2018] [Indexed: 10/28/2022]
Abstract
Cells respond to various extracellular stimuli through a limited number of signaling pathways. One strategy to process such stimuli is to code the information into the temporal patterns of molecules. Although we showed that insulin selectively regulated molecules depending on its temporal patterns using Fao cells, the in vivo mechanism remains unknown. Here, we show how the insulin-AKT pathway processes the information encoded into the temporal patterns of blood insulin. We performed hyperinsulinemic-euglycemic clamp experiments and found that, in the liver, all temporal patterns of insulin are encoded into the insulin receptor, and downstream molecules selectively decode them through AKT. S6K selectively decodes the additional secretion information. G6Pase interprets the basal secretion information through FoxO1, while GSK3β decodes all secretion pattern information. Mathematical modeling revealed the mechanism via differences in network structures and from sensitivity and time constants. Given that almost all hormones exhibit distinct temporal patterns, temporal coding may be a general principle of system homeostasis by hormones.
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Affiliation(s)
- Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Agency, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
| | - Shinsuke Uda
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Fumiko Matsuzaki
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yukiyo Yamauchi
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Corporation, Bunkyo-ku, Tokyo 113-0033, Japan.
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25
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Kleczko EK, Heasley LE. Mechanisms of rapid cancer cell reprogramming initiated by targeted receptor tyrosine kinase inhibitors and inherent therapeutic vulnerabilities. Mol Cancer 2018; 17:60. [PMID: 29458371 PMCID: PMC5817864 DOI: 10.1186/s12943-018-0816-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/13/2018] [Indexed: 01/06/2023] Open
Abstract
Receptor tyrosine kinase (RTK) pathways serve as frequent oncogene drivers in solid cancers and small molecule and antibody-based inhibitors have been developed as targeted therapeutics for many of these oncogenic RTKs. In general, these drugs, when delivered as single agents in a manner consistent with the principles of precision medicine, induce tumor shrinkage but rarely complete tumor elimination. Moreover, acquired resistance of treated tumors is nearly invariant such that monotherapy strategies with targeted RTK drugs fail to provide long-term control or cures. The mechanisms mediating acquired resistance in tumors at progression treated with RTK inhibitors are relatively well defined compared to the molecular and cellular understanding of the cancer cells that persist early on therapy. We and others propose that these persisting cancer cells, termed "residual disease", provide the reservoir from which acquired resistance eventually emerges. Herein, we will review the literature that describes rapid reprogramming induced upon inhibition of oncogenic RTKs in cancer cells as a mechanism by which cancer cells persist to yield residual disease and consider strategies for disrupting these intrinsic responses for future therapeutic gain.
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Affiliation(s)
- Emily K. Kleczko
- Division of Renal Diseases and Hypertension, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Lynn E. Heasley
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 USA
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26
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Katiyar A, Sharma S, Singh TP, Kaur P. Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. Front Genet 2018; 9:42. [PMID: 29503661 PMCID: PMC5820528 DOI: 10.3389/fgene.2018.00042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/30/2018] [Indexed: 01/21/2023] Open
Abstract
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis unveiled six interaction networks/crosstalks through overlapping edges between commonly dysregulated pathways of EMS and MS. The PTPN1, ERBB3, and CDH1 were observed to be the highly ranked hub genes connected with disease-related genes of both EMS and MS. Androgen receptor (AR) and nuclear factor-kB p65 (RelA) were observed to be the most enriched transcription factor in the upstream of shared down-regulated and up-regulated genes, respectively. The two disease sample sets compared through crosstalk interactions between shared pathways revealed commonly up- and down-regulated expressions of 10 immunomodulatory proteins as probable linkers between EMS and MS. This study pinpoints the number of shared genes, pathways, protein kinases, and upstream regulators that may help in the development of biomarkers for diagnosis of MS and endometriosis at the same time through improved understanding of shared molecular signatures and crosstalk.
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Affiliation(s)
- Amit Katiyar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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27
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Billmann M, Chaudhary V, ElMaghraby MF, Fischer B, Boutros M. Widespread Rewiring of Genetic Networks upon Cancer Signaling Pathway Activation. Cell Syst 2017; 6:52-64.e4. [PMID: 29199019 PMCID: PMC5791663 DOI: 10.1016/j.cels.2017.10.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/30/2017] [Accepted: 10/25/2017] [Indexed: 12/14/2022]
Abstract
Cellular signaling networks coordinate physiological processes in all multicellular organisms. Within networks, modules switch their function to control signaling activity in response to the cellular context. However, systematic approaches to map the interplay of such modules have been lacking. Here, we generated a context-dependent genetic interaction network of a metazoan's signaling pathway. Using Wnt signaling in Drosophila as a model, we measured >290,000 double perturbations of the pathway in a baseline state, after activation by Wnt ligand or after loss of the tumor suppressor APC. We found that genetic interactions within the Wnt network globally rewired after pathway activation. We derived between-state networks that showed how genes changed their function between state-specific networks. This related pathway inhibitors across states and identified genes required for pathway activation. For instance, we predicted and confirmed the ER-resident protein Catsup to be required for ligand-mediated Wnt signaling activation. Together, state-dependent and between-state genetic interaction networks identify responsive functional modules that control cellular pathways. Genetic interaction networks of Wnt signaling in three cellular states Networks rewire upon activation of Wnt pathway by ligand or by loss of APC Interaction profiles identify known and novel state-dependent pathway modules State-specific and between-state profile similarity identify signaling regulators
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Affiliation(s)
- Maximilian Billmann
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Varun Chaudhary
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Mostafa F ElMaghraby
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Bernd Fischer
- German Cancer Research Center (DKFZ), Computational Genome Biology Group, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, Department of Cell and Molecular Biology, Faculty of Medicine Mannheim, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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28
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Mutations that impair Eyes absent tyrosine phosphatase activity in vitro reduce robustness of retinal determination gene network output in Drosophila. PLoS One 2017; 12:e0187546. [PMID: 29108015 PMCID: PMC5673202 DOI: 10.1371/journal.pone.0187546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/20/2017] [Indexed: 12/01/2022] Open
Abstract
A limited collection of signaling networks and transcriptional effectors directs the full spectrum of cellular behaviors that comprise development. One mechanism to diversify regulatory potential is to combine multiple biochemical activities into the same protein. Exemplifying this principle of modularity, Eyes absent (Eya), originally identified as a transcriptional co-activator within the retinal determination gene network (RDGN), also harbors tyrosine and threonine phosphatase activities. Although mounting evidence argues for the importance of Eya’s phosphatase activities to mammalian biology, genetic rescue experiments in Drosophila have shown that the tyrosine phosphatase function is dispensable for normal development. In this study, we repeated these rescue experiments in genetically sensitized backgrounds in which the dose of one or more RDGN factor was reduced. Heterozygosity for sine oculis or dachshund, both core RDGN members, compromised the ability of phosphatase-dead eya, but not of the control wild type eya transgene, to rescue the retinal defects and reduced viability associated with eya loss. We speculate that Eya’s tyrosine phosphatase activity, although non-essential, confers robustness to RDGN output.
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29
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Rogers WA, Goyal Y, Yamaya K, Shvartsman SY, Levine MS. Uncoupling neurogenic gene networks in the Drosophila embryo. Genes Dev 2017; 31:634-638. [PMID: 28428262 PMCID: PMC5411704 DOI: 10.1101/gad.297150.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/20/2017] [Indexed: 12/22/2022]
Abstract
The EGF signaling pathway specifies neuronal identities in the Drosophila embryo by regulating developmental patterning genes such as intermediate neuroblasts defective (ind). EGFR is activated in the ventral midline and neurogenic ectoderm by the Spitz ligand, which is processed by the Rhomboid protease. CRISPR/Cas9 was used to delete defined rhomboid enhancers mediating expression at each site of Spitz processing. Surprisingly, the neurogenic ectoderm, not the ventral midline, was found to be the dominant source of EGF patterning activity. We suggest that Drosophila is undergoing an evolutionary transition in central nervous system (CNS)-organizing activity from the ventral midline to the neurogenic ectoderm.
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Affiliation(s)
- William A Rogers
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Yogesh Goyal
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Kei Yamaya
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Stanislav Y Shvartsman
- Department of Chemical and Biological Engineering, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Michael S Levine
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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30
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Abstract
Animal cells use a conserved repertoire of intercellular signaling pathways to communicate with one another. These pathways are well-studied from a molecular point of view. However, we often lack an "operational" understanding that would allow us to use these pathways to rationally control cellular behaviors. This requires knowing what dynamic input features each pathway perceives and how it processes those inputs to control downstream processes. To address these questions, researchers have begun to reconstitute signaling pathways in living cells, analyzing their dynamic responses to stimuli, and developing new functional representations of their behavior. Here we review important insights obtained through these new approaches, and discuss challenges and opportunities in understanding signaling pathways from an operational point of view.
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Affiliation(s)
- Yaron E Antebi
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nagarajan Nandagopal
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.,Howard Hughes Medical Institute, USA
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31
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Lee C, Sorensen EB, Lynch TR, Kimble J. C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool. eLife 2016; 5:e18370. [PMID: 27705743 PMCID: PMC5094854 DOI: 10.7554/elife.18370] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/04/2016] [Indexed: 12/26/2022] Open
Abstract
C. elegans Notch signaling maintains a pool of germline stem cells within their single-celled mesenchymal niche. Here we investigate the Notch transcriptional response in germline stem cells using single-molecule fluorescence in situ hybridization coupled with automated, high-throughput quantitation. This approach allows us to distinguish Notch-dependent nascent transcripts in the nucleus from mature mRNAs in the cytoplasm. We find that Notch-dependent active transcription sites occur in a probabilistic fashion and, unexpectedly, do so in a steep gradient across the stem cell pool. Yet these graded nuclear sites create a nearly uniform field of mRNAs that extends beyond the region of transcriptional activation. Therefore, active transcription sites provide a precise view of where the Notch-dependent transcriptional complex is productively engaged. Our findings offer a new window into the Notch transcriptional response and demonstrate the importance of assaying nascent transcripts at active transcription sites as a readout for canonical signaling.
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Affiliation(s)
- ChangHwan Lee
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Erika B Sorensen
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Tina R Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Judith Kimble
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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32
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Determination of EGFR Signaling Output by Opposing Gradients of BMP and JAK/STAT Activity. Curr Biol 2016; 26:2572-2582. [DOI: 10.1016/j.cub.2016.07.073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 11/24/2022]
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33
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Abstract
During development and homeostasis, cells integrate multiple signals originating either from neighboring cells or systemically. In turn, responding cells can produce signals that act in an autocrine, paracrine, or endocrine manner. Although the nature of the signals and pathways used in cell-cell communication are well characterized, we lack, in most cases, an integrative view of signaling describing the spatial and temporal interactions between pathways (e.g., whether the signals are processed sequentially or concomitantly when two pathways are required for a specific outcome). To address the extent of cross-talk between the major metazoan signaling pathways, we characterized immediate transcriptional responses to either single- or multiple pathway stimulations in homogeneous Drosophila cell lines. Our study, focusing on seven core pathways, epidermal growth factor receptor (EGFR), bone morphogenetic protein (BMP), Jun kinase (JNK), JAK/STAT, Notch, Insulin, and Wnt, revealed that many ligands and receptors are primary targets of signaling pathways, highlighting that transcriptional regulation of genes encoding pathway components is a major level of signaling cross-talk. In addition, we found that ligands and receptors can integrate multiple pathway activities and adjust their transcriptional responses accordingly.
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34
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Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila. Genetics 2016; 203:1283-95. [PMID: 27194748 DOI: 10.1534/genetics.115.185918] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/10/2016] [Indexed: 12/15/2022] Open
Abstract
The transcriptional coactivator and phosphatase eyes absent (Eya) is dynamically compartmentalized between the nucleus and cytoplasm. Although the nuclear transcriptional circuits within which Eya operates have been extensively characterized, understanding of its cytoplasmic functions and interactions remains limited. Our previous work showed that phosphorylation of Drosophila Eya by the Abelson tyrosine kinase can recruit Eya to the cytoplasm and that eya-abelson interactions are required for photoreceptor axons to project to correct layers in the brain. Based on these observations, we postulated that photoreceptor axon targeting might provide a suitable context for identifying the cytoplasmic signaling cascades with which Eya interacts. Using a dose-sensitive eya misexpression background, we performed an RNA interference-based genetic screen to identify suppressors. Included among the top 10 hits were nonreceptor tyrosine kinases and multiple members of the Jak/Stat signaling network (hop, Stat92E, Socs36E, and Socs44A), a pathway not previously implicated in axon targeting. Individual loss-of-function phenotypes combined with analysis of axonal projections in Stat92E null clones confirmed the importance of photoreceptor autonomous Jak/Stat signaling. Experiments in cultured cells detected cytoplasmic complexes between Eya and Hop, Socs36E and Socs44A; the latter interaction required both the Src homology 2 motif in Socs44A and tyrosine phosphorylated Eya, suggesting direct binding and validating the premise of the screen. Taken together, our data provide new insight into the cytoplasmic phosphotyrosine signaling networks that operate during photoreceptor axon guidance and suggest specific points of interaction with Eya.
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35
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Chen J, Xie ZR, Wu Y. Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method. J Comput Biol 2016; 23:566-84. [PMID: 27028148 DOI: 10.1089/cmb.2015.0227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The ligand-binding of membrane receptors on cell surfaces initiates the dynamic process of cross-membrane signal transduction. It is an indispensable part of the signaling network for cells to communicate with external environments. Recent experiments revealed that molecular components in signal transduction are not randomly mixed, but spatially organized into distinctive patterns. These patterns, such as receptor clustering and ligand oligomerization, lead to very different gene expression profiles. However, little is understood about the molecular mechanisms and functional impacts of this spatial-temporal regulation in cross-membrane signal transduction. In order to tackle this problem, we developed a hybrid computational method that decomposes a model of signaling network into two simulation modules. The physical process of binding between receptors and ligands on cell surfaces are simulated by a diffusion-reaction algorithm, while the downstream biochemical reactions are modeled by stochastic simulation of Gillespie algorithm. These two processes are coupled together by a synchronization framework. Using this method, we tested the dynamics of a simple signaling network in which the ligand binding of cell surface receptors triggers the phosphorylation of protein kinases, and in turn regulates the expression of target genes. We found that spatial aggregation of membrane receptors at cellular interfaces is able to either amplify or inhibit downstream signaling outputs, depending on the details of clustering mechanism. Moreover, by providing higher binding avidity, the co-localization of ligands into multi-valence complex modulates signaling in very different ways that are closely related to the binding affinity between ligand and receptor. We also found that the temporal oscillation of the signaling pathway that is derived from genetic feedback loops can be modified by the spatial clustering of membrane receptors. In summary, our method demonstrates the functional importance of spatial organization in cross-membrane signal transduction. The method can be applied to any specific signaling pathway in cells.
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Affiliation(s)
- Jiawen Chen
- Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University , Bronx, New York
| | - Zhong-Ru Xie
- Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University , Bronx, New York
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University , Bronx, New York
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36
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Májer I, Hajihosseini A, Becskei A. Identification of optimal parameter combinations for the emergence of bistability. Phys Biol 2015; 12:066011. [DOI: 10.1088/1478-3975/12/6/066011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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37
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Nussinov R, Tsai CJ, Muratcioglu S, Jang H, Gursoy A, Keskin O. Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Expert Rev Proteomics 2015; 12:669-82. [DOI: 10.1586/14789450.2015.1100079] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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38
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Vinogradov AE. Accelerated pathway evolution in mouse-like rodents involves cell cycle control. Mamm Genome 2015; 26:609-18. [PMID: 26424469 DOI: 10.1007/s00335-015-9605-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/23/2015] [Indexed: 10/23/2022]
Abstract
Rodents include both the cancer-susceptible short-lived mouse and the two unrelated cancer-resistant long-lived mole-rats. In this work, their genomes were analyzed with the goal to reveal pathways enriched in genes, which are more similar between the mole-rats than between the mouse and the naked mole-rat. The pathways related to cell cycle control were prominent. They include external signal transduction and all cell cycle stages. There are several stem cell pathways among them. The other enriched pathways involve ubiquitin-dependent protein degradation, immunity, mRNA splicing, and apoptosis. The ubiquitin-dependent protein degradation is a core of network of enriched pathways. However, this phenomenon is not specific for the mouse and the mole-rats. The other muroid species show features similar to the mouse, whereas the non-muroid rodents and the human show features similar to the mole-rats. The higher ratio of non-synonymous to synonymous nucleotide substitutions (dN/dS) indicates the accelerated evolution of revealed pathways in the muroid rodents (except the blind mole-rat). Paradoxically, the dN/dS averaged over the whole genome is lower in the muroids, i.e., the purifying selection is generally stronger in them. In practical sense, these data suggest caveat for using muroid rodents (mouse, rat, and hamsters) as biomedical models of human conditions involving cell cycle and show the network of pathways where muroid genes are most different (compared with non-muroid) from human genes. The guinea pig is emphasized as a more suitable rodent model for biomedical research involving cell cycle.
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39
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Tegge AN, Sharp N, Murali TM. Xtalk: a path-based approach for identifying crosstalk between signaling pathways. Bioinformatics 2015; 32:242-51. [PMID: 26400040 DOI: 10.1093/bioinformatics/btv549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 09/04/2015] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION Cells communicate with their environment via signal transduction pathways. On occasion, the activation of one pathway can produce an effect downstream of another pathway, a phenomenon known as crosstalk. Existing computational methods to discover such pathway pairs rely on simple overlap statistics. RESULTS We present Xtalk, a path-based approach for identifying pairs of pathways that may crosstalk. Xtalk computes the statistical significance of the average length of multiple short paths that connect receptors in one pathway to the transcription factors in another. By design, Xtalk reports the precise interactions and mechanisms that support the identified crosstalk. We applied Xtalk to signaling pathways in the KEGG and NCI-PID databases. We manually curated a gold standard set of 132 crosstalking pathway pairs and a set of 140 pairs that did not crosstalk, for which Xtalk achieved an area under the receiver operator characteristic curve of 0.65, a 12% improvement over the closest competing approach. The area under the receiver operator characteristic curve varied with the pathway, suggesting that crosstalk should be evaluated on a pathway-by-pathway level. We also analyzed an extended set of 658 pathway pairs in KEGG and to a set of more than 7000 pathway pairs in NCI-PID. For the top-ranking pairs, we found substantial support in the literature (81% for KEGG and 78% for NCI-PID). We provide examples of networks computed by Xtalk that accurately recovered known mechanisms of crosstalk. AVAILABILITY AND IMPLEMENTATION The XTALK software is available at http://bioinformatics.cs.vt.edu/~murali/software. Crosstalk networks are available at http://graphspace.org/graphs?tags=2015-bioinformatics-xtalk. CONTACT ategge@vt.edu, murali@cs.vt.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Allison N Tegge
- Department of Computer Science, Department of Statistics and
| | | | - T M Murali
- Department of Computer Science, ICTAS Center for Systems Biology of Engineered Tissues, Virginia Tech, Blacksburg, VA 24061, USA
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40
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Tsuda K, Somssich IE. Transcriptional networks in plant immunity. THE NEW PHYTOLOGIST 2015; 206:932-947. [PMID: 25623163 DOI: 10.1111/nph.13286] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/09/2014] [Indexed: 05/18/2023]
Abstract
Next to numerous abiotic stresses, plants are constantly exposed to a variety of pathogens within their environment. Thus, their ability to survive and prosper during the course of evolution was strongly dependent on adapting efficient strategies to perceive and to respond to such potential threats. It is therefore not surprising that modern plants have a highly sophisticated immune repertoire consisting of diverse signal perception and intracellular signaling pathways. This signaling network is intricate and deeply interconnected, probably reflecting the diverse lifestyles and infection strategies used by the multitude of invading phytopathogens. Moreover it allows signal communication between developmental and defense programs thereby ensuring that plant growth and fitness are not significantly retarded. How plants integrate and prioritize the incoming signals and how this information is transduced to enable appropriate immune responses is currently a major research area. An important finding has been that pathogen-triggered cellular responses involve massive transcriptional reprogramming within the host. Additional key observations emerging from such studies are that transcription factors (TFs) are often sites of signal convergence and that signal-regulated TFs act in concert with other context-specific TFs and transcriptional co-regulators to establish sensory transcription regulatory networks required for plant immunity.
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Affiliation(s)
- Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, Cologne, 50829, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, Cologne, 50829, Germany
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41
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Chua CY, Liu Y, Granberg KJ, Hu L, Haapasalo H, Annala MJ, Cogdell DE, Verploegen M, Moore LM, Fuller GN, Nykter M, Cavenee WK, Zhang W. IGFBP2 potentiates nuclear EGFR-STAT3 signaling. Oncogene 2015; 35:738-47. [PMID: 25893308 PMCID: PMC4615268 DOI: 10.1038/onc.2015.131] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/17/2015] [Accepted: 03/20/2015] [Indexed: 02/04/2023]
Abstract
Insulin-like growth factor binding protein 2 (IGFBP2) is a pleiotropic oncogenic protein that has both extracellular and intracellular functions. Despite a clear causal role in cancer development, the tumor-promoting mechanisms of IGFBP2 are poorly understood. The contributions of intracellular IGFBP2 to tumor development and progression are also unclear. Here we present evidence that both exogenous IGFBP2 treatment and cellular IGFBP2 overexpression lead to aberrant activation of EGFR, which subsequently activates STAT3 signaling. Furthermore, we demonstrate that IGFBP2 augments the nuclear accumulation of EGFR to potentiate STAT3 transactivation activities, via activation of the nuclear EGFR signaling pathway. Nuclear IGFBP2 directly influences the invasive and migratory capacities of human glioblastoma cells, providing a direct link between intracellular (and particularly nuclear) IGFBP2 and cancer hallmarks. These activities are also consistent with the strong association between IGFBP2 and STAT3-activated genes derived from the TCGA database for human glioma. A high level of all 3 proteins (IGFBP2, EGFR and STAT3) was strongly correlated with poorer survival in an independent patient dataset. These results identify a novel tumor-promoting function for IGFBP2 of activating EGFR/STAT3 signaling and facilitating EGFR accumulation in the nucleus, thereby deregulating EGFR signaling by 2 distinct mechanisms. As targeting EGFR in glioma has been relatively unsuccessful, this study suggests that IGFBP2 may be a novel therapeutic target.
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Affiliation(s)
- C Y Chua
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Y Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,ISB-MDA Genome Data Analysis Center, The Cancer Genome Atlas, Seattle, WA/Houston, TX, USA
| | - K J Granberg
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | - L Hu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Haapasalo
- Department of Pathology, Fimlab Laboratories and University of Tampere, Tampere, Finland
| | - M J Annala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Signal Processing, Tampere University of Technology, Tampere, Finland.,Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | - D E Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Verploegen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L M Moore
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - G N Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA.,ISB-MDA Genome Data Analysis Center, The Cancer Genome Atlas, Seattle, WA/Houston, TX, USA
| | - M Nykter
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | - W K Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA, USA
| | - W Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA.,ISB-MDA Genome Data Analysis Center, The Cancer Genome Atlas, Seattle, WA/Houston, TX, USA
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Manku G, Wang Y, Merkbaoui V, Boisvert A, Ye X, Blonder J, Culty M. Role of retinoic acid and platelet-derived growth factor receptor cross talk in the regulation of neonatal gonocyte and embryonal carcinoma cell differentiation. Endocrinology 2015; 156:346-59. [PMID: 25380237 PMCID: PMC5393322 DOI: 10.1210/en.2014-1524] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Neonatal gonocytes are direct precursors of spermatogonial stem cells, the cell pool that supports spermatogenesis. Although unipotent in vivo, gonocytes express pluripotency genes common with embryonic stem cells. Previously, we found that all-trans retinoic acid (RA) induced the expression of differentiation markers and a truncated form of platelet-derived growth factor receptor (PDGFR)β in rat gonocytes, as well as in F9 mouse embryonal carcinoma cells, an embryonic stem cell-surrogate that expresses somatic lineage markers in response to RA. The present study is focused on identifying the signaling pathways involved in RA-induced gonocyte and F9 cell differentiation. Mitogen-activated protein kinase kinase (MEK) 1/2 activation was required during F9 cell differentiation towards somatic lineage, whereas its inhibition potentiated RA-induced Stra8 expression, suggesting that MEK1/2 acts as a lineage specification switch in F9 cells. In both cell types, RA increased the expression of the spermatogonial/premeiotic marker Stra8, which is in line with F9 cells being at a stage before somatic-germline lineage specification. Inhibiting PDGFR kinase activity reduced RA-induced Stra8 expression. Interestingly, RA increased the expression of PDGFRα variant forms in both cell types. Together, these results suggest a potential cross talk between RA and PDGFR signaling pathways in cell differentiation. RA receptor-α inhibition partially reduced RA effects on Stra8 in gonocytes, indicating that RA acts in part via RA receptor-α. RA-induced gonocyte differentiation was significantly reduced by inhibiting SRC (v-src avian sarcoma [Schmidt-Ruppin A-2] viral oncogene) and JAK2/STAT5 (Janus kinase 2/signal transducer and activator of transcription 5) activities, implying that these signaling molecules play a role in gonocyte differentiation. These results suggest that gonocyte and F9 cell differentiation is regulated via cross talk between RA and PDGFRs using different downstream pathways.
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Affiliation(s)
- Gurpreet Manku
- The Research Institute of the McGill University Health Centre (G.M., V.M., A.B., M.C.), Montreal, Quebec, Canada H3G1A4; Departments of Pharmacology and Therapeutics (G.M., M.C.) Medicine (M.C.), McGill University, Montreal, Quebec, Canada H3G1A4; Department of Biochemistry and Molecular and Cellular Biology (Y.W.), Georgetown University Medical Center, Washington, DC 20057; and Protein Characterization Laboratory (X.Y., J.B.), Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
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