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Ramkumar N, Richardson C, O'Brien M, Butt FA, Park J, Chao AT, Bagnat M, Poss K, Di Talia S. Phased ERK-responsiveness and developmental robustness regulate teleost skin morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593750. [PMID: 38798380 PMCID: PMC11118522 DOI: 10.1101/2024.05.13.593750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Elongation of the vertebrate embryonic axis necessitates rapid expansion of the epidermis to accommodate the growth of underlying tissues. Here, we generated a toolkit to visualize and quantify signaling in entire cell populations of periderm, the outermost layer of the epidermis, in live developing zebrafish. We find that oriented cell divisions facilitate growth of the early periderm during axial elongation rather than cell addition from the basal layer. Activity levels of ERK, a downstream effector of MAPK pathway, gauged by a live biosensor, predicts cell cycle entry, and optogenetic ERK activation controls proliferation dynamics. As development proceeds, rates of peridermal cell proliferation decrease, ERK activity becomes more pulsatile and functionally transitions to promote hypertrophic cell growth. Targeted genetic blockade of cell division generates animals with oversized periderm cells, yet, unexpectedly, development to adulthood is not impaired. Our findings reveal stage-dependent differential responsiveness to ERK signaling and marked developmental robustness in growing teleost skin.
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2
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Kirchberger S, Shoeb MR, Lazic D, Wenninger-Weinzierl A, Fischer K, Shaw LE, Nogueira F, Rifatbegovic F, Bozsaky E, Ladenstein R, Bodenmiller B, Lion T, Traver D, Farlik M, Schöfer C, Taschner-Mandl S, Halbritter F, Distel M. Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation. Nat Commun 2024; 15:1792. [PMID: 38413586 PMCID: PMC10899643 DOI: 10.1038/s41467-024-45802-1] [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: 07/03/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Neutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defense. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized, which limits their applicability to studying human disease. Here we show, by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages, a high-resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors, including C/ebp-β, which is important for late neutrophil maturation. Cross-species comparison of zebrafish, mouse, and human samples confirms high molecular similarity of immature stages and discriminates zebrafish-specific from pan-species gene signatures. Applying the pan-species neutrophil maturation signature to RNA-sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease.
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Grants
- St. Anna Kinderkrebsforschung (to S.T.M., R.L., F.H., and M.D.), the Austrian Research Promotion Agency (FFG) (project 7940628, Danio4Can to M.D.), a German Academic Exchange Service postdoctoral fellowship and an EMBO fellowship (to M.D.), the Austrian Science Fund (FWF) through grants TAI454 (to F.H. and M.D.), TAI732 (to F.H.), I4162 (ERA-NET/Transcan-2 LIQUIDHOPE; to S.T.M.), P35841 (MAPMET; to S.T.M.), P34152 (to T.L.), P 30642 (to C.S.) and the Alex’s Lemonade Stand Foundation for Childhood Cancer 20-17258 (to F.H. and M.D.), and the Swiss Government Excellence Scholarship (to D.L.), and the EC H2020 grant no. 826494 (PRIMAGE; to R.L.), and by the European Commission within the FP7 Framework program (Fungitect-Grant No 602125 to T.L.).
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Affiliation(s)
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Daria Lazic
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Kristin Fischer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Lisa E Shaw
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Filomena Nogueira
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia - Labordiagnostik GmbH, Vienna, Austria
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Vienna, Austria
| | | | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Thomas Lion
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia - Labordiagnostik GmbH, Vienna, Austria
- Medical University of Vienna, Department of Pediatrics, Vienna, Austria
| | - David Traver
- Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - Matthias Farlik
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Christian Schöfer
- Medical University of Vienna, Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Vienna, Austria
| | | | | | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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3
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Becker CJ, Cigliola V, Gillotay P, Rich A, De Simone A, Han Y, Di Talia S, Poss KD. In toto imaging of glial JNK signaling during larval zebrafish spinal cord regeneration. Development 2023; 150:dev202076. [PMID: 37997694 PMCID: PMC10753585 DOI: 10.1242/dev.202076] [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: 06/12/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Identification of signaling events that contribute to innate spinal cord regeneration in zebrafish can uncover new targets for modulating injury responses of the mammalian central nervous system. Using a chemical screen, we identify JNK signaling as a necessary regulator of glial cell cycling and tissue bridging during spinal cord regeneration in larval zebrafish. With a kinase translocation reporter, we visualize and quantify JNK signaling dynamics at single-cell resolution in glial cell populations in developing larvae and during injury-induced regeneration. Glial JNK signaling is patterned in time and space during development and regeneration, decreasing globally as the tissue matures and increasing in the rostral cord stump upon transection injury. Thus, dynamic and regional regulation of JNK signaling help to direct glial cell behaviors during innate spinal cord regeneration.
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Affiliation(s)
- Clayton J. Becker
- Duke Regeneration Center and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Valentina Cigliola
- Duke Regeneration Center and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose, 06100 Nice, France
| | - Pierre Gillotay
- Duke Regeneration Center and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashley Rich
- Duke Regeneration Center and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Alessandro De Simone
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Yanchao Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Suzhou Medical College, Soochow University, Suzhou, 215006 Jiangsu, China
| | - Stefano Di Talia
- Duke Regeneration Center and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Duke Regeneration Center and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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4
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Wilcockson SG, Guglielmi L, Araguas Rodriguez P, Amoyel M, Hill CS. An improved Erk biosensor detects oscillatory Erk dynamics driven by mitotic erasure during early development. Dev Cell 2023; 58:2802-2818.e5. [PMID: 37714159 PMCID: PMC7615346 DOI: 10.1016/j.devcel.2023.08.021] [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: 11/01/2022] [Revised: 06/02/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
Extracellular signal-regulated kinase (Erk) signaling dynamics elicit distinct cellular responses in a variety of contexts. The early zebrafish embryo is an ideal model to explore the role of Erk signaling dynamics in vivo, as a gradient of activated diphosphorylated Erk (P-Erk) is induced by fibroblast growth factor (Fgf) signaling at the blastula margin. Here, we describe an improved Erk-specific biosensor, which we term modified Erk kinase translocation reporter (modErk-KTR). We demonstrate the utility of this biosensor in vitro and in developing zebrafish and Drosophila embryos. Moreover, we show that Fgf/Erk signaling is dynamic and coupled to tissue growth during both early zebrafish and Drosophila development. Erk activity is rapidly extinguished just prior to mitosis, which we refer to as mitotic erasure, inducing periods of inactivity, thus providing a source of heterogeneity in an asynchronously dividing tissue. Our modified reporter and transgenic lines represent an important resource for interrogating the role of Erk signaling dynamics in vivo.
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Affiliation(s)
- Scott G Wilcockson
- Developmental Signalling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Pablo Araguas Rodriguez
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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5
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Dinsmore CJ, Soriano P. Conditional fluorescent mouse translocation reporters for ERK1/2 and AKT signaling. Dev Biol 2023; 503:113-119. [PMID: 37660778 PMCID: PMC10529872 DOI: 10.1016/j.ydbio.2023.08.007] [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: 04/08/2023] [Revised: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Understanding how cells activate intracellular signaling pathways in response to external signals, such as growth factors, is a longstanding goal of cell and developmental biology. Recently, live-cell signaling reporters have greatly expanded our understanding of signaling dynamics in response to wide-ranging stimuli and chemical or genetic perturbation, both ex vivo (cell lines) and in vivo (whole embryos or animals). Among the many varieties of reporter systems, translocation reporters that change sub-cellular localization in response to pathway activation have received considerable attention for their ease of use compared to FRET systems and favorable response times compared to transcriptional reporters. We reasoned that mouse reporter lines expressed in a conditional fashion would be a useful addition to the arsenal of mouse genetic tools, as such lines remain undeveloped despite widespread use of these sensors. We therefore created and validated two novel mouse reporter lines at the ROSA26 locus. One expresses an ERK1/2 pathway reporter and a nuclear marker from a single transcript, while the second additionally expresses an AKT reporter in order to simultaneously interrogate both pathways.
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Affiliation(s)
- Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
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6
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Meng Y, Lv T, Zhang J, Shen W, Li L, Li Y, Liu X, Lei X, Lin X, Xu H, Meng A, Jia S. Temporospatial inhibition of Erk signaling is required for lymphatic valve formation. Signal Transduct Target Ther 2023; 8:342. [PMID: 37691058 PMCID: PMC10493226 DOI: 10.1038/s41392-023-01571-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 09/12/2023] Open
Abstract
Intraluminal lymphatic valves (LVs) and lymphovenous valves (LVVs) are critical to ensure the unidirectional flow of lymphatic fluid. Morphological abnormalities in these valves always cause lymph or blood reflux, and result in lymphedema. However, the underlying molecular mechanism of valve development remains poorly understood. We here report the implication of Efnb2-Ephb4-Rasa1 regulated Erk signaling axis in lymphatic valve development with identification of two new valve structures. Dynamic monitoring of phospho-Erk activity indicated that Erk signaling is spatiotemporally inhibited in some lymphatic endothelial cells (LECs) during the valve cell specification. Inhibition of Erk signaling via simultaneous depletion of zygotic erk1 and erk2 or treatment with MEK inhibitor selumetinib causes lymphatic vessel hypoplasia and lymphatic valve hyperplasia, suggesting opposite roles of Erk signaling during these two processes. ephb4b mutants, efnb2a;efnb2b or rasa1a;rasa1b double mutants all have defective LVs and LVVs and exhibit blood reflux into lymphatic vessels with an edema phenotype. Importantly, the valve defects in ephb4b or rasa1a;rasa1b mutants are mitigated with high-level gata2 expression in the presence of MEK inhibitors. Therefore, Efnb2-Ephb4 signaling acts to suppress Erk activation in valve-forming cells to promote valve specification upstream of Rasa1. Not only do our findings reveal a molecular mechanism of lymphatic valve formation, but also provide a basis for the treatment of lymphatic disorders.
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Affiliation(s)
- Yaping Meng
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tong Lv
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Junfeng Zhang
- Guangzhou Laboratory, Guangzhou, 510320, Guangdong Province, China
| | - Weimin Shen
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lifang Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yaqi Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xin Liu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xing Lei
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuguang Lin
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hanfang Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Guangzhou Laboratory, Guangzhou, 510320, Guangdong Province, China.
| | - Shunji Jia
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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7
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Boezio GLM, Zhao S, Gollin J, Priya R, Mansingh S, Guenther S, Fukuda N, Gunawan F, Stainier DYR. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 2023; 16:dmm049571. [PMID: 36172839 PMCID: PMC9612869 DOI: 10.1242/dmm.049571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/13/2022] [Indexed: 11/20/2022] Open
Abstract
The epicardium, the outermost layer of the heart, is an important regulator of cardiac regeneration. However, a detailed understanding of the crosstalk between the epicardium and myocardium during development requires further investigation. Here, we generated three models of epicardial impairment in zebrafish by mutating the transcription factor genes tcf21 and wt1a, and ablating tcf21+ epicardial cells. Notably, all three epicardial impairment models exhibited smaller ventricles. We identified the initial cause of this phenotype as defective cardiomyocyte growth, resulting in reduced cell surface and volume. This failure of cardiomyocyte growth was followed by decreased proliferation and increased abluminal extrusion. By temporally manipulating its ablation, we show that the epicardium is required to support cardiomyocyte growth mainly during early cardiac morphogenesis. By transcriptomic profiling of sorted epicardial cells, we identified reduced expression of FGF and VEGF ligand genes in tcf21-/- hearts, and pharmacological inhibition of these signaling pathways in wild type partially recapitulated the ventricular growth defects. Taken together, these data reveal distinct roles of the epicardium during cardiac morphogenesis and signaling pathways underlying epicardial-myocardial crosstalk.
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Affiliation(s)
- Giulia L. M. Boezio
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Shengnan Zhao
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Josephine Gollin
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Rashmi Priya
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Shivani Mansingh
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Stefan Guenther
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Nana Fukuda
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Felix Gunawan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
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8
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Liu Y, Yuan G, Hassan MM, Abraham PE, Mitchell JC, Jacobson D, Tuskan GA, Khakhar A, Medford J, Zhao C, Liu CJ, Eckert CA, Doktycz MJ, Tschaplinski TJ, Yang X. Biological and Molecular Components for Genetically Engineering Biosensors in Plants. BIODESIGN RESEARCH 2022; 2022:9863496. [PMID: 37850147 PMCID: PMC10521658 DOI: 10.34133/2022/9863496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/08/2022] [Indexed: 10/19/2023] Open
Abstract
Plants adapt to their changing environments by sensing and responding to physical, biological, and chemical stimuli. Due to their sessile lifestyles, plants experience a vast array of external stimuli and selectively perceive and respond to specific signals. By repurposing the logic circuitry and biological and molecular components used by plants in nature, genetically encoded plant-based biosensors (GEPBs) have been developed by directing signal recognition mechanisms into carefully assembled outcomes that are easily detected. GEPBs allow for in vivo monitoring of biological processes in plants to facilitate basic studies of plant growth and development. GEPBs are also useful for environmental monitoring, plant abiotic and biotic stress management, and accelerating design-build-test-learn cycles of plant bioengineering. With the advent of synthetic biology, biological and molecular components derived from alternate natural organisms (e.g., microbes) and/or de novo parts have been used to build GEPBs. In this review, we summarize the framework for engineering different types of GEPBs. We then highlight representative validated biological components for building plant-based biosensors, along with various applications of plant-based biosensors in basic and applied plant science research. Finally, we discuss challenges and strategies for the identification and design of biological components for plant-based biosensors.
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Affiliation(s)
- Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - June Medford
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Cheng Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Carrie A. Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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9
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Yuen AC, Prasad AR, Fernandes VM, Amoyel M. A kinase translocation reporter reveals real-time dynamics of ERK activity in Drosophila. Biol Open 2022; 11:bio059364. [PMID: 35608229 PMCID: PMC9167624 DOI: 10.1242/bio.059364] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Extracellular signal-regulated kinase (ERK) lies downstream of a core signalling cascade that controls all aspects of development and adult homeostasis. Recent developments have led to new tools to image and manipulate the pathway. However, visualising ERK activity in vivo with high temporal resolution remains a challenge in Drosophila. We adapted a kinase translocation reporter (KTR) for use in Drosophila, which shuttles out of the nucleus when phosphorylated by ERK. We show that ERK-KTR faithfully reports endogenous ERK signalling activity in developing and adult tissues, and that it responds to genetic perturbations upstream of ERK. Using ERK-KTR in time-lapse imaging, we made two novel observations: firstly, sustained hyperactivation of ERK by expression of dominant-active epidermal growth factor receptor raised the overall level but did not alter the kinetics of ERK activity; secondly, the direction of migration of retinal basal glia correlated with their ERK activity levels, suggesting an explanation for the heterogeneity in ERK activity observed in fixed tissue. Our results show that KTR technology can be applied in Drosophila to monitor ERK activity in real-time and suggest that this modular tool can be further adapted to study other kinases. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | | | | | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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10
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A synthetic gene circuit for imaging-free detection of signaling pulses. Cell Syst 2022; 13:131-142.e13. [PMID: 34739875 PMCID: PMC8857027 DOI: 10.1016/j.cels.2021.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022]
Abstract
Cells employ intracellular signaling pathways to sense and respond to changes in their external environment. In recent years, live-cell biosensors have revealed complex pulsatile dynamics in many pathways, but studies of these signaling dynamics are limited by the necessity of live-cell imaging at high spatiotemporal resolution. Here, we describe an approach to infer pulsatile signaling dynamics from a single measurement in fixed cells using a pulse-detecting gene circuit. We computationally screened for circuits with the capability to selectively detect signaling pulses, revealing an incoherent feedforward topology that robustly performs this computation. We implemented the motif experimentally for the Erk signaling pathway using a single engineered transcription factor and fluorescent protein reporter. Our "recorder of Erk activity dynamics" (READer) responds sensitively to spontaneous and stimulus-driven Erk pulses. READer circuits open the door to permanently labeling transient, dynamic cell populations to elucidate the mechanistic underpinnings and biological consequences of signaling dynamics.
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11
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Raina D, Fabris F, Morelli LG, Schröter C. Intermittent ERK oscillations downstream of FGF in mouse embryonic stem cells. Development 2022; 149:dev199710. [PMID: 35175328 PMCID: PMC8918804 DOI: 10.1242/dev.199710] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/31/2021] [Indexed: 01/20/2023]
Abstract
Signal transduction networks generate characteristic dynamic activities to process extracellular signals and guide cell fate decisions such as to divide or differentiate. The differentiation of pluripotent cells is controlled by FGF/ERK signaling. However, only a few studies have addressed the dynamic activity of the FGF/ERK signaling network in pluripotent cells at high time resolution. Here, we use live cell sensors in wild-type and Fgf4-mutant mouse embryonic stem cells to measure dynamic ERK activity in single cells, for defined ligand concentrations and differentiation states. These sensors reveal pulses of ERK activity. Pulsing patterns are heterogeneous between individual cells. Consecutive pulse sequences occur more frequently than expected from simple stochastic models. Sequences become more prevalent with higher ligand concentration, but are rarer in more differentiated cells. Our results suggest that FGF/ERK signaling operates in the vicinity of a transition point between oscillatory and non-oscillatory dynamics in embryonic stem cells. The resulting heterogeneous dynamic signaling activities add a new dimension to cellular heterogeneity that may be linked to divergent fate decisions in stem cell cultures.
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Affiliation(s)
- Dhruv Raina
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Fiorella Fabris
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Polo Científico Tecnológico, Godoy Cruz 2390, C1425FQD Buenos Aires, Argentina
| | - Luis G. Morelli
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)–CONICET–Partner Institute of the Max Planck Society, Polo Científico Tecnológico, Godoy Cruz 2390, C1425FQD Buenos Aires, Argentina
- Departamento de Física, FCEyN UBA, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Christian Schröter
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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12
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Fgf8 dynamics and critical slowing down may account for the temperature independence of somitogenesis. Commun Biol 2022; 5:113. [PMID: 35132142 PMCID: PMC8821593 DOI: 10.1038/s42003-022-03053-0] [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: 08/01/2020] [Accepted: 12/29/2021] [Indexed: 12/17/2022] Open
Abstract
Somitogenesis, the segmentation of the antero-posterior axis in vertebrates, is thought to result from the interactions between a genetic oscillator and a posterior-moving determination wavefront. The segment (somite) size is set by the product of the oscillator period and the velocity of the determination wavefront. Surprisingly, while the segmentation period can vary by a factor three between 20 °C and 32 °C, the somite size is constant. How this temperature independence is achieved is a mystery that we address in this study. Using RT-qPCR we show that the endogenous fgf8 mRNA concentration decreases during somitogenesis and correlates with the exponent of the shrinking pre-somitic mesoderm (PSM) size. As the temperature decreases, the dynamics of fgf8 and many other gene transcripts, as well as the segmentation frequency and the PSM shortening and tail growth rates slows down as T-Tc (with Tc = 14.4 °C). This behavior characteristic of a system near a critical point may account for the temperature independence of somitogenesis in zebrafish.
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13
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Temperature-responsive optogenetic probes of cell signaling. Nat Chem Biol 2022; 18:152-160. [PMID: 34937907 PMCID: PMC9252025 DOI: 10.1038/s41589-021-00917-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/06/2021] [Indexed: 12/18/2022]
Abstract
We describe single-component optogenetic probes whose activation dynamics depend on both light and temperature. We used the BcLOV4 photoreceptor to stimulate Ras and phosphatidyl inositol-3-kinase signaling in mammalian cells, allowing activation over a large dynamic range with low basal levels. Surprisingly, we found that BcLOV4 membrane translocation dynamics could be tuned by both light and temperature such that membrane localization spontaneously decayed at elevated temperatures despite constant illumination. Quantitative modeling predicted BcLOV4 activation dynamics across a range of light and temperature inputs and thus provides an experimental roadmap for BcLOV4-based probes. BcLOV4 drove strong and stable signal activation in both zebrafish and fly cells, and thermal inactivation provided a means to multiplex distinct blue-light sensitive tools in individual mammalian cells. BcLOV4 is thus a versatile photosensor with unique light and temperature sensitivity that enables straightforward generation of broadly applicable optogenetic tools.
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14
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Nakamura A, Goto Y, Kondo Y, Aoki K. Shedding light on developmental ERK signaling with genetically encoded biosensors. Development 2021; 148:271153. [PMID: 34338283 DOI: 10.1242/dev.199767] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The extracellular signal-regulated kinase (ERK) pathway governs cell proliferation, differentiation and migration, and therefore plays key roles in various developmental and regenerative processes. Recent advances in genetically encoded fluorescent biosensors have unveiled hitherto unrecognized ERK activation dynamics in space and time and their functional importance mainly in cultured cells. However, ERK dynamics during embryonic development have still only been visualized in limited numbers of model organisms, and we are far from a sufficient understanding of the roles played by developmental ERK dynamics. In this Review, we first provide an overview of the biosensors used for visualization of ERK activity in live cells. Second, we highlight the applications of the biosensors to developmental studies of model organisms and discuss the current understanding of how ERK dynamics are encoded and decoded for cell fate decision-making.
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Affiliation(s)
- Akinobu Nakamura
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Kazuhiro Aoki
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,IRCC International Research Collaboration Center, National Institutes of Natural Sciences, 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
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15
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Lauri A, Fasano G, Venditti M, Dallapiccola B, Tartaglia M. In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale. Front Cell Dev Biol 2021; 9:642235. [PMID: 34124035 PMCID: PMC8194860 DOI: 10.3389/fcell.2021.642235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals' intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
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Affiliation(s)
- Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | | | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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16
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Okuda KS, Keyser MS, Gurevich DB, Sturtzel C, Mason EA, Paterson S, Chen H, Scott M, Condon ND, Martin P, Distel M, Hogan BM. Live-imaging of endothelial Erk activity reveals dynamic and sequential signalling events during regenerative angiogenesis. eLife 2021; 10:62196. [PMID: 34003110 PMCID: PMC8175085 DOI: 10.7554/elife.62196] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
The formation of new blood vessel networks occurs via angiogenesis during development, tissue repair, and disease. Angiogenesis is regulated by intracellular endothelial signalling pathways, induced downstream of vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs). A major challenge in understanding angiogenesis is interpreting how signalling events occur dynamically within endothelial cell populations during sprouting, proliferation, and migration. Extracellular signal-regulated kinase (Erk) is a central downstream effector of Vegf-signalling and reports the signalling that drives angiogenesis. We generated a vascular Erk biosensor transgenic line in zebrafish using a kinase translocation reporter that allows live-imaging of Erk-signalling dynamics. We demonstrate the utility of this line to live-image Erk activity during physiologically relevant angiogenic events. Further, we reveal dynamic and sequential endothelial cell Erk-signalling events following blood vessel wounding. Initial signalling is dependent upon Ca2+ in the earliest responding endothelial cells, but is independent of Vegfr-signalling and local inflammation. The sustained regenerative response, however, involves a Vegfr-dependent mechanism that initiates concomitantly with the wound inflammatory response. This work reveals a highly dynamic sequence of signalling events in regenerative angiogenesis and validates a new resource for the study of vascular Erk-signalling in real-time.
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Affiliation(s)
- Kazuhide S Okuda
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Mikaela S Keyser
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - David B Gurevich
- School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, Bristol, United Kingdom.,Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Caterina Sturtzel
- Innovative Cancer Models, St Anna Kinderkrebsforschung, Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for preclinical drug screening (ZANDR), Vienna, Austria
| | - Elizabeth A Mason
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia
| | - Scott Paterson
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Huijun Chen
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Mark Scott
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Nicholas D Condon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
| | - Paul Martin
- School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, Bristol, United Kingdom
| | - Martin Distel
- Innovative Cancer Models, St Anna Kinderkrebsforschung, Children's Cancer Research Institute, Vienna, Austria.,Zebrafish Platform Austria for preclinical drug screening (ZANDR), Vienna, Austria
| | - Benjamin M Hogan
- Organogenesis and Cancer Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, St Lucia, Australia
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17
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The ERK mitogen-activated protein kinase signaling network: the final frontier in RAS signal transduction. Biochem Soc Trans 2021; 49:253-267. [PMID: 33544118 DOI: 10.1042/bst20200507] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022]
Abstract
The RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade is aberrantly activated in a diverse set of human cancers and the RASopathy group of genetic developmental disorders. This protein kinase cascade is one of the most intensely studied cellular signaling networks and has been frequently targeted by the pharmaceutical industry, with more than 30 inhibitors either approved or under clinical evaluation. The ERK-MAPK cascade was originally depicted as a serial and linear, unidirectional pathway that relays extracellular signals, such as mitogenic stimuli, through the cytoplasm to the nucleus. However, we now appreciate that this three-tiered protein kinase cascade is a central core of a complex network with dynamic signaling inputs and outputs and autoregulatory loops. Despite our considerable advances in understanding the ERK-MAPK network, the ability of cancer cells to adapt to the inhibition of key nodes reveals a level of complexity that remains to be fully understood. In this review, we summarize important developments in our understanding of the ERK-MAPK network and identify unresolved issues for ongoing and future study.
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18
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Studying the Tumor Microenvironment in Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1329:69-92. [PMID: 34664234 DOI: 10.1007/978-3-030-73119-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The tumor microenvironment significantly contributes to tumor initiation, progression, neo-angiogenesis, and metastasis, and a better understanding of the role of the different cellular players would facilitate the development of novel therapeutic strategies for cancer treatment. Towards this goal, intravital imaging is a powerful method to unravel interaction partners of tumor cells. Among vertebrate model organisms, zebrafish is uniquely suited for in vivo imaging studies. In recent years zebrafish has also become a valuable model in cancer research. In this chapter, we will summarize, how zebrafish has been used to characterize cells of the tumor microenvironment. We will cover both genetically engineered cancer models and xenograft models in zebrafish. The majority of work has been done on the role of innate immune cells and their role during tumor initiation and metastasis, but we will also cover studies focusing on adipocytes, fibroblasts, and endothelial cells. Taken together, we will highlight the versatile use of the zebrafish model for in vivo tumor microenvironment studies.
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19
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Garcia-Gonzalez I, Mühleder S, Fernández-Chacón M, Benedito R. Genetic Tools to Study Cardiovascular Biology. Front Physiol 2020; 11:1084. [PMID: 33071802 PMCID: PMC7541935 DOI: 10.3389/fphys.2020.01084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Progress in biomedical science is tightly associated with the improvement of methods and genetic tools to manipulate and analyze gene function in mice, the most widely used model organism in biomedical research. The joint effort of numerous individual laboratories and consortiums has contributed to the creation of a large genetic resource that enables scientists to image cells, probe signaling pathways activities, or modify a gene function in any desired cell type or time point, à la carte. However, as these tools significantly increase in number and become more sophisticated, it is more difficult to keep track of each tool's possibilities and understand their advantages and disadvantages. Knowing the best currently available genetic technology to answer a particular biological question is key to reach a higher standard in biomedical research. In this review, we list and discuss the main advantages and disadvantages of available mammalian genetic technology to analyze cardiovascular cell biology at higher cellular and molecular resolution. We start with the most simple and classical genetic approaches and end with the most advanced technology available to fluorescently label cells, conditionally target their genes, image their clonal expansion, and decode their lineages.
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Affiliation(s)
| | | | | | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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20
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Expanding the Toolkit of Fluorescent Biosensors for Studying Mitogen Activated Protein Kinases in Plants. Int J Mol Sci 2020; 21:ijms21155350. [PMID: 32731410 PMCID: PMC7432370 DOI: 10.3390/ijms21155350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/25/2020] [Accepted: 07/26/2020] [Indexed: 12/11/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) are key regulators of numerous biological processes in plants. To better understand the mechanisms by which these kinases function, high resolution measurement of MAPK activation kinetics in different biological contexts would be beneficial. One method to measure MAPK activation in plants is via fluorescence-based genetically-encoded biosensors, which can provide real-time readouts of the temporal and spatial dynamics of kinase activation in living tissue. Although fluorescent biosensors have been widely used to study MAPK dynamics in animal cells, there is currently only one MAPK biosensor that has been described for use in plants. To facilitate creation of additional plant-specific MAPK fluorescent biosensors, we report the development of two new tools: an in vitro assay for efficiently characterizing MAPK docking domains and a translocation-based kinase biosensor for use in plants. The implementation of these two methods has allowed us to expand the available pool of plant MAPK biosensors, while also providing a means to generate more specific and selective MAPK biosensors in the future. Biosensors developed using these methods have the potential to enhance our understanding of the roles MAPKs play in diverse plant signaling networks affecting growth, development, and stress response.
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21
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Ghilardi SJ, O'Reilly BM, Sgro AE. Intracellular signaling dynamics and their role in coordinating tissue repair. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1479. [PMID: 32035001 PMCID: PMC7187325 DOI: 10.1002/wsbm.1479] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/20/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
Tissue repair is a complex process that requires effective communication and coordination between cells across multiple tissues and organ systems. Two of the initial intracellular signals that encode injury signals and initiate tissue repair responses are calcium and extracellular signal-regulated kinase (ERK). However, calcium and ERK signaling control a variety of cellular behaviors important for injury repair including cellular motility, contractility, and proliferation, as well as the activity of several different transcription factors, making it challenging to relate specific injury signals to their respective repair programs. This knowledge gap ultimately hinders the development of new wound healing therapies that could take advantage of native cellular signaling programs to more effectively repair tissue damage. The objective of this review is to highlight the roles of calcium and ERK signaling dynamics as mechanisms that link specific injury signals to specific cellular repair programs during epithelial and stromal injury repair. We detail how the signaling networks controlling calcium and ERK can now also be dissected using classical signal processing techniques with the advent of new biosensors and optogenetic signal controllers. Finally, we advocate the importance of recognizing calcium and ERK dynamics as key links between injury detection and injury repair programs that both organize and execute a coordinated tissue repair response between cells across different tissues and organs. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Biological Mechanisms > Cell Signaling Laboratory Methods and Technologies > Imaging Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models.
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Affiliation(s)
- Samuel J. Ghilardi
- Department of Biomedical Engineering and the Biological Design CenterBoston UniversityBostonMassachusetts
| | - Breanna M. O'Reilly
- Department of Biomedical Engineering and the Biological Design CenterBoston UniversityBostonMassachusetts
| | - Allyson E. Sgro
- Department of Biomedical Engineering and the Biological Design CenterBoston UniversityBostonMassachusetts
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22
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Bertolin G, Tramier M. Insights into the non-mitotic functions of Aurora kinase A: more than just cell division. Cell Mol Life Sci 2020; 77:1031-1047. [PMID: 31562563 PMCID: PMC11104877 DOI: 10.1007/s00018-019-03310-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 02/02/2023]
Abstract
AURKA is a serine/threonine kinase overexpressed in several cancers. Originally identified as a protein with multifaceted roles during mitosis, improvements in quantitative microscopy uncovered several non-mitotic roles as well. In physiological conditions, AURKA regulates cilia disassembly, neurite extension, cell motility, DNA replication and senescence programs. In cancer-like contexts, AURKA actively promotes DNA repair, it acts as a transcription factor, promotes cell migration and invasion, and it localises at mitochondria to regulate mitochondrial dynamics and ATP production. Here we review the non-mitotic roles of AURKA, and its partners outside of cell division. In addition, we give an insight into how structural data and quantitative fluorescence microscopy allowed to understand AURKA activation and its interaction with new substrates, highlighting future developments in fluorescence microscopy needed to better understand AURKA functions in vivo. Last, we will recapitulate the most significant AURKA inhibitors currently in clinical trials, and we will explore how the non-mitotic roles of the kinase may provide new insights to ameliorate current pharmacological strategies against AURKA overexpression.
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Affiliation(s)
- Giulia Bertolin
- Univ Rennes, CNRS, IGDR (Genetics and Development Institute of Rennes), UMR 6290, F-35000, Rennes, France.
| | - Marc Tramier
- Univ Rennes, CNRS, IGDR (Genetics and Development Institute of Rennes), UMR 6290, F-35000, Rennes, France.
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23
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Schmitt DL, Mehta S, Zhang J. Illuminating the kinome: Visualizing real-time kinase activity in biological systems using genetically encoded fluorescent protein-based biosensors. Curr Opin Chem Biol 2020; 54:63-69. [PMID: 31911398 PMCID: PMC7131877 DOI: 10.1016/j.cbpa.2019.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/07/2019] [Accepted: 11/16/2019] [Indexed: 02/06/2023]
Abstract
Genetically encoded fluorescent protein-based kinase biosensors are a central tool for illumination of the kinome. The adaptability and versatility of biosensors have allowed for spatiotemporal observation of real-time kinase activity in living cells and organisms. In this review, we highlight various types of kinase biosensors, along with their burgeoning applications in complex biological systems. Specifically, we focus on kinase activity reporters used in neuronal systems and whole animal settings. Genetically encoded kinase biosensors are key for elucidation of the spatiotemporal regulation of protein kinases, with broader applications beyond the Petri dish.
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Affiliation(s)
- Danielle L Schmitt
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA; Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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24
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Kanai AJ, Konieczko EM, Bennett RG, Samuel CS, Royce SG. Relaxin and fibrosis: Emerging targets, challenges, and future directions. Mol Cell Endocrinol 2019; 487:66-74. [PMID: 30772373 PMCID: PMC6475456 DOI: 10.1016/j.mce.2019.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/15/2023]
Abstract
The peptide hormone relaxin is well-known for its anti-fibrotic actions in several organs, particularly from numerous studies conducted in animals. Acting through its cognate G protein-coupled receptor, relaxin family peptide receptor 1 (RXFP1), serelaxin (recombinant human relaxin) has been shown to consistently inhibit the excessive extracellular matrix production (fibrosis) that results from the aberrant wound-healing response to tissue injury and/or chronic inflammation, and at multiple levels. Furthermore, it can reduce established scarring by promoting the degradation of aberrant extracellular matrix components. Following on from the review that describes the mechanisms and signaling pathways associated with the extracellular matrix remodeling effects of serelaxin (Ng et al., 2019), this review focuses on newly identified tissue targets of serelaxin therapy in fibrosis, and the limitations associated with (se)relaxin research.
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Affiliation(s)
- Anthony J Kanai
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Elisa M Konieczko
- Biology Department, Morosky College of Health Professions and Sciences, Gannon University, Erie, PA, USA.
| | - Robert G Bennett
- Research Service, VA Nebraska-Western Iowa Health Care System, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA; Research Service, VA Nebraska-Western Iowa Health Care System, Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Chrishan S Samuel
- Cardiovascular Disease Theme, Monash Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Clayton, VIC, Australia.
| | - Simon G Royce
- Cardiovascular Disease Theme, Monash Biomedicine Discovery Institute and Department of Pharmacology, Monash University, Clayton, VIC, Australia; Central Clinical School, Monash University, Prahran, VIC, Australia.
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25
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Divergent Dynamics and Functions of ERK MAP Kinase Signaling in Development, Homeostasis and Cancer: Lessons from Fluorescent Bioimaging. Cancers (Basel) 2019; 11:cancers11040513. [PMID: 30974867 PMCID: PMC6520755 DOI: 10.3390/cancers11040513] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
The extracellular signal-regulated kinase (ERK) signaling pathway regulates a variety of biological processes including cell proliferation, survival, and differentiation. Since ERK activation promotes proliferation of many types of cells, its deregulated/constitutive activation is among general mechanisms for cancer. Recent advances in bioimaging techniques have enabled to visualize ERK activity in real-time at the single-cell level. Emerging evidence from such approaches suggests unexpectedly complex spatiotemporal dynamics of ERK activity in living cells and animals and their crucial roles in determining cellular responses. In this review, we discuss how ERK activity dynamics are regulated and how they affect biological processes including cell fate decisions, cell migration, embryonic development, tissue homeostasis, and tumorigenesis.
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