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Townley RA, Stacy KS, Cheraghi F, de la Cova CC. The Raf/LIN-45 C-terminal distal tail segment negatively regulates signaling in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603803. [PMID: 39071268 PMCID: PMC11275798 DOI: 10.1101/2024.07.16.603803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Raf protein kinases act as Ras-GTP sensing components of the ERK signal transduction pathway in animal cells, influencing cell proliferation, differentiation, and survival. In humans, somatic and germline mutations in the genes BRAF and RAF1 are associated with malignancies and developmental disorders. Recent studies shed light on the structure of activated Raf, a heterotetramer consisting of Raf and 14-3-3 dimers, and raised the possibility that a Raf C-terminal distal tail segment (DTS) regulates activation. We investigated the role of the DTS using the Caenorhabditis elegans, which has a single Raf ortholog termed lin-45 . We discovered that truncations removing the DTS strongly enhanced lin-45(S312A) , a weak gain-of-function allele equivalent to RAF1 mutations found in patients with Noonan Syndrome. We generated mutations to test three elements of the LIN-45 DTS, which we termed the active site binding sequence (ASBS), the KTP motif, and the aromatic cluster. In the context of lin-45(S312A), mutation of either the ASBS, KTP motif, or aromatic cluster enhanced activity. We used AlphaFold to predict DTS protein interactions for LIN-45, fly Raf, and human BRAF, within the activated heterotetramer complex. We propose distinct functions for the LIN-45 DTS elements: i) the ASBS binds the kinase active site as an inhibitor, ii) phosphorylation of the KTP motif modulates DTS-kinase domain interaction, and iii) the aromatic cluster anchors the DTS in an inhibitory conformation. This work establishes that the Raf/LIN-45 DTS negatively regulates signaling in C. elegans and provides a model for its function in other Raf proteins.
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Guerrero Zuniga A, Aikin TJ, McKenney C, Lendner Y, Phung A, Hook PW, Meltzer A, Timp W, Regot S. Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication. Dev Cell 2024; 59:1724-1736.e4. [PMID: 38640927 PMCID: PMC11233237 DOI: 10.1016/j.devcel.2024.03.032] [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: 10/28/2022] [Revised: 01/30/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
Whole-genome duplication (WGD) is a frequent event in cancer evolution that fuels chromosomal instability. WGD can result from mitotic errors or endoreduplication, yet the molecular mechanisms that drive WGD remain unclear. Here, we use live single-cell analysis to characterize cell-cycle dynamics upon aberrant Ras-ERK signaling. We find that sustained ERK signaling in human cells leads to reactivation of the APC/C in G2, resulting in tetraploid G0-like cells that are primed for WGD. This process is independent of DNA damage or p53 but dependent on p21. Transcriptomics analysis and live-cell imaging showed that constitutive ERK activity promotes p21 expression, which is necessary and sufficient to inhibit CDK activity and which prematurely activates the anaphase-promoting complex (APC/C). Finally, either loss of p53 or reduced ERK signaling allowed for endoreduplication, completing a WGD event. Thus, sustained ERK signaling-induced G2 cell cycle exit represents an alternative path to WGD.
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Affiliation(s)
- Adler Guerrero Zuniga
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Biochemistry, Cellular and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Timothy J Aikin
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Biochemistry, Cellular and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Biochemistry, Cellular and Molecular Biology Graduate Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yovel Lendner
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alain Phung
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Paul W Hook
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21205, USA
| | - Amy Meltzer
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21205, USA
| | - Winston Timp
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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3
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Bennett JJR, Stern AD, Zhang X, Birtwistle MR, Pandey G. Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events. NPJ Syst Biol Appl 2024; 10:65. [PMID: 38834572 PMCID: PMC11150372 DOI: 10.1038/s41540-024-00389-7] [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: 01/29/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024] Open
Abstract
Understanding the dynamics of intracellular signaling pathways, such as ERK1/2 (ERK) and Akt1/2 (Akt), in the context of cell fate decisions is important for advancing our knowledge of cellular processes and diseases, particularly cancer. While previous studies have established associations between ERK and Akt activities and proliferative cell fate, the heterogeneity of single-cell responses adds complexity to this understanding. This study employed a data-driven approach to address this challenge, developing machine learning models trained on a dataset of growth factor-induced ERK and Akt activity time courses in single cells, to predict cell division events. The most predictive models were developed by applying discrete wavelet transforms (DWTs) to extract low-frequency features from the time courses, followed by using Ensemble Integration, a data integration and predictive modeling framework. The results demonstrated that these models effectively predicted cell division events in MCF10A cells (F-measure=0.524, AUC=0.726). ERK dynamics were found to be more predictive than Akt, but the combination of both measurements further enhanced predictive performance. The ERK model`s performance also generalized to predicting division events in RPE cells, indicating the potential applicability of these models and our data-driven methodology for predicting cell division across different biological contexts. Interpretation of these models suggested that ERK dynamics throughout the cell cycle, rather than immediately after growth factor stimulation, were associated with the likelihood of cell division. Overall, this work contributes insights into the predictive power of intra-cellular signaling dynamics for cell fate decisions, and highlights the potential of machine learning approaches in unraveling complex cellular behaviors.
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Affiliation(s)
- Jamie J R Bennett
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan D Stern
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiang Zhang
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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VanSlyke JK, Boswell BA, Musil LS. Tonic ErbB signaling underlies TGFβ-induced activation of ERK and is required for lens cell epithelial to myofibroblast transition. Mol Biol Cell 2024; 35:ar35. [PMID: 38170570 PMCID: PMC10916858 DOI: 10.1091/mbc.e23-07-0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/01/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Fibrosis is a major, but incompletely understood, component of many diseases. The most common vision-disrupting complication of cataract surgery involves differentiation of residual lens cells into myofibroblasts. In serum-free primary cultures of lens epithelial cells (DCDMLs), inhibitors of either ERK or of ErbB signaling prevent TGFβ from upregulating both early (fibronectin) and late (αSMA) markers of myofibroblast differentiation. TGFβ stimulates ERK in DCDMLs within 1.5 h. Kinase inhibitors of ErbBs, but not of several other growth factor receptors in lens cells, reduce phospho ERK to below basal levels in the absence or presence of TGFβ. This effect is attributable to constitutive ErbB activity playing a major role in regulating the basal levels pERK. Additional studies support a model in which TGFβ-generated reactive oxygen species serve to indirectly amplify ERK signaling downstream of tonically active ErbBs to mediate myofibroblast differentiation. ERK activity is in turn essential for expression of ErbB1 and ErbB2, major inducers of ERK signaling. By mechanistically linking TGFβ, ErbB, and ERK signaling to myofibroblast differentiation, our data elucidate a new role for ErbBs in fibrosis and reveal a novel mode by which TGFβ directs lens cell fate.
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Affiliation(s)
- Judy K. VanSlyke
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239
| | - Bruce A. Boswell
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239
| | - Linda S. Musil
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239
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Ram A, Pargett M, Choi Y, Murphy D, Cabel M, Kosaisawe N, Quon G, Albeck J. Deciphering the History of ERK Activity from Fixed-Cell Immunofluorescence Measurements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580760. [PMID: 38405841 PMCID: PMC10889026 DOI: 10.1101/2024.02.16.580760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The Ras/ERK pathway drives cell proliferation and other oncogenic behaviors, and quantifying its activity in situ is of high interest in cancer diagnosis and therapy. Pathway activation is often assayed by measuring phosphorylated ERK. However, this form of measurement overlooks dynamic aspects of signaling that can only be observed over time. In this study, we combine a live, single-cell ERK biosensor approach with multiplexed immunofluorescence staining of downstream target proteins to ask how well immunostaining captures the dynamic history of ERK activity. Combining linear regression, machine learning, and differential equation models, we develop an interpretive framework for immunostains, in which Fra-1 and pRb levels imply long term activation of ERK signaling, while Egr-1 and c-Myc indicate recent activation. We show that this framework can distinguish different classes of ERK dynamics within a heterogeneous population, providing a tool for annotating ERK dynamics within fixed tissues.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Yongin Choi
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Markhus Cabel
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, Davis
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, Davis
| | - John Albeck
- Department of Molecular and Cellular Biology, University of California, Davis
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6
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Hu M, Li H, Zhu K, Guo L, Zhao M, Zhan H, Devreotes PN, Qing Q. Electric field modulation of ERK dynamics shows dependency on waveform and timing. Sci Rep 2024; 14:3167. [PMID: 38326365 PMCID: PMC10850077 DOI: 10.1038/s41598-024-53018-y] [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: 09/24/2023] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
Different exogenous electric fields (EF) can guide cell migration, disrupt proliferation, and program cell development. Studies have shown that many of these processes were initiated at the cell membrane, but the mechanism has been unclear, especially for conventionally non-excitable cells. In this study, we focus on the electrostatic aspects of EF coupling with the cell membrane by eliminating Faradaic processes using dielectric-coated microelectrodes. Our data unveil a distinctive biphasic response of the ERK signaling pathway of epithelial cells (MCF10A) to alternate current (AC) EF. The ERK signal exhibits both inhibition and activation phases, with the former triggered by a lower threshold of AC EF, featuring a swifter peaking time and briefer refractory periods than the later-occurring activation phase, induced at a higher threshold. Interestingly, the biphasic ERK responses are sensitive to the waveform and timing of EF stimulation pulses, depicting the characteristics of electrostatic and dissipative interactions. Blocker tests and correlated changes of active Ras on the cell membrane with ERK signals indicated that both EGFR and Ras were involved in the rich ERK dynamics induced by EF. We propose that the frequency-dependent dielectric relaxation process could be an important mechanism to couple EF energy to the cell membrane region and modulate membrane protein-initiated signaling pathways, which can be further explored to precisely control cell behavior and fate with high temporal and spatial resolution.
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Affiliation(s)
- Minxi Hu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Houpu Li
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Kan Zhu
- Department of Dermatology, University of California, Davis, CA, 95616, USA
| | - Liang Guo
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Min Zhao
- Department of Dermatology, University of California, Davis, CA, 95616, USA
- Department of Ophthalmology and Vision Science, University of California, Davis, CA, 95616, USA
| | - Huiwang Zhan
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA.
- Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
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Ram A, Murphy D, DeCuzzi N, Patankar M, Hu J, Pargett M, Albeck JG. A guide to ERK dynamics, part 1: mechanisms and models. Biochem J 2023; 480:1887-1907. [PMID: 38038974 PMCID: PMC10754288 DOI: 10.1042/bcj20230276] [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: 07/09/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Extracellular signal-regulated kinase (ERK) has long been studied as a key driver of both essential cellular processes and disease. A persistent question has been how this single pathway is able to direct multiple cell behaviors, including growth, proliferation, and death. Modern biosensor studies have revealed that the temporal pattern of ERK activity is highly variable and heterogeneous, and critically, that these dynamic differences modulate cell fate. This two-part review discusses the current understanding of dynamic activity in the ERK pathway, how it regulates cellular decisions, and how these cell fates lead to tissue regulation and pathology. In part 1, we cover the optogenetic and live-cell imaging technologies that first revealed the dynamic nature of ERK, as well as current challenges in biosensor data analysis. We also discuss advances in mathematical models for the mechanisms of ERK dynamics, including receptor-level regulation, negative feedback, cooperativity, and paracrine signaling. While hurdles still remain, it is clear that higher temporal and spatial resolution provide mechanistic insights into pathway circuitry. Exciting new algorithms and advanced computational tools enable quantitative measurements of single-cell ERK activation, which in turn inform better models of pathway behavior. However, the fact that current models still cannot fully recapitulate the diversity of ERK responses calls for a deeper understanding of network structure and signal transduction in general.
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Affiliation(s)
- Abhineet Ram
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Devan Murphy
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Nicholaus DeCuzzi
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Madhura Patankar
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Jason Hu
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
| | - John G. Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, U.S.A
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8
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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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9
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Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023; 480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
Abstract
As cell signaling research has advanced, it has become clearer that signal transduction has complex spatiotemporal regulation that goes beyond foundational linear transduction models. Several technologies have enabled these discoveries, including fluorescent biosensors designed to report live biochemical signaling events. As genetically encoded and live-cell compatible tools, fluorescent biosensors are well suited to address diverse cell signaling questions across different spatial scales of regulation. In this review, methods of examining spatial signaling regulation and the design of fluorescent biosensors are introduced. Then, recent biosensor developments that illuminate the importance of spatial regulation in cell signaling are highlighted at several scales, including membranes and organelles, molecular assemblies, and cell/tissue heterogeneity. In closing, perspectives on how fluorescent biosensors will continue enhancing cell signaling research are discussed.
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Affiliation(s)
- Anne C. Lyons
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, U.S.A
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10
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Liu Q, Contreras A, Afaq MS, Yang W, Hsu DK, Russell M, Lyeth B, Zanto TP, Zhao M. Intensity-dependent gamma electrical stimulation regulates microglial activation, reduces beta-amyloid load, and facilitates memory in a mouse model of Alzheimer's disease. Cell Biosci 2023; 13:138. [PMID: 37507776 PMCID: PMC10386209 DOI: 10.1186/s13578-023-01085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Gamma sensory stimulation may reduce AD-specific pathology. Yet, the efficacy of alternating electrical current stimulation in animal models of AD is unknown, and prior research has not addressed intensity-dependent effects. METHODS The intensity-dependent effect of gamma electrical stimulation (GES) with a sinusoidal alternating current at 40 Hz on Aβ clearance and microglia modulation were assessed in 5xFAD mouse hippocampus and cortex, as well as the behavioral performance of the animals with the Morris Water Maze. RESULTS One hour of epidural GES delivered over a month significantly (1) reduced Aβ load in the AD brain, (2) increased microglia cell counts, decreased cell body size, increased length of cellular processes of the Iba1 + cells, and (3) improved behavioral performance (learning & memory). All these effects were most pronounced when a higher stimulation current was applied. CONCLUSION The efficacy of GES on the reduction of AD pathology and the intensity-dependent feature provide guidance for the development of this promising therapeutic approach.
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Affiliation(s)
- Qian Liu
- Institute for Regenerative Cures, Department of Ophthalmology & Vision Science, Department of Dermatology, University of California Davis, Sacramento, CA, 95817, USA
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen, China
| | - Adam Contreras
- Institute for Regenerative Cures, Department of Ophthalmology & Vision Science, Department of Dermatology, University of California Davis, Sacramento, CA, 95817, USA
| | - Muhammad Shan Afaq
- Institute for Regenerative Cures, Department of Ophthalmology & Vision Science, Department of Dermatology, University of California Davis, Sacramento, CA, 95817, USA
| | - Weijian Yang
- Department of Electrical and Computer Engineering, University of California, Davis, CA, 95616, USA
| | - Daniel K Hsu
- Institute for Regenerative Cures, Department of Ophthalmology & Vision Science, Department of Dermatology, University of California Davis, Sacramento, CA, 95817, USA
| | - Michael Russell
- Institute for Regenerative Cures, Department of Ophthalmology & Vision Science, Department of Dermatology, University of California Davis, Sacramento, CA, 95817, USA
| | - Bruce Lyeth
- Department of Neurological Surgery, University of California, Davis, CA, 95616, USA
| | - Theodore P Zanto
- Neuroscape, Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA.
| | - Min Zhao
- Institute for Regenerative Cures, Department of Ophthalmology & Vision Science, Department of Dermatology, University of California Davis, Sacramento, CA, 95817, USA.
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11
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Pargett M, Ram AR, Murthy V, Davies AE. Live-Cell Sender-Receiver Co-cultures for Quantitative Measurement of Paracrine Signaling Dynamics, Gene Expression, and Drug Response. Methods Mol Biol 2023; 2634:285-314. [PMID: 37074584 DOI: 10.1007/978-1-0716-3008-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Paracrine signaling is a fundamental process regulating tissue development, repair, and pathogenesis of diseases such as cancer. Herein we describe a method for quantitatively measuring paracrine signaling dynamics, and resultant gene expression changes, in living cells using genetically encoded signaling reporters and fluorescently tagged gene loci. We discuss considerations for selecting paracrine "sender-receiver" cell pairs, appropriate reporters, the use of this system to ask diverse experimental questions and screen drugs blocking intracellular communication, data collection, and the use of computational approaches to model and interpret these experiments.
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Affiliation(s)
- Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Abhineet R Ram
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Vaibhav Murthy
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
- Knight Cancer Institute, Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Alexander E Davies
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
- Knight Cancer Institute, Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA.
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12
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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: 0] [Impact Index Per Article: 0] [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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13
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Zhu K, Guo L, Patel P, Albeck J, Qing Q, Losert W, Zhao M. Protocol for electrical modulation of ERK signaling dynamics in cell lines. STAR Protoc 2022; 3:101752. [PMID: 36208452 PMCID: PMC9562398 DOI: 10.1016/j.xpro.2022.101752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/22/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
Here, we describe a protocol for modulating the dynamics of the extracellular signal-regulated kinases (ERK) pathway in a customized alternating current (AC) electric field stimulation chamber. We use an ERK translocation reporter that can accurately represent the intracellular ERK activity in real time without chemical agents or gene disruption. ERK activation is assessed by comparing the relative intensity of nuclear fluorescence to cytosolic fluorescence in live-cell conditions. The approach can be applied to other signaling pathways as well. For complete details on the use and execution of this protocol, please refer to Guo et al. (2021).
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Affiliation(s)
- Kan Zhu
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA
| | - Liang Guo
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA,College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China
| | - Preena Patel
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA
| | - John Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Quan Qing
- Department of Physics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Min Zhao
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA,Corresponding author
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14
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Ender P, Gagliardi PA, Dobrzyński M, Frismantiene A, Dessauges C, Höhener T, Jacques MA, Cohen AR, Pertz O. Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis. Dev Cell 2022; 57:2153-2167.e6. [PMID: 36113484 DOI: 10.1016/j.devcel.2022.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/06/2022] [Accepted: 08/20/2022] [Indexed: 12/30/2022]
Abstract
The signaling events controlling proliferation, survival, and apoptosis during mammary epithelial acinar morphogenesis remain poorly characterized. By imaging single-cell ERK activity dynamics in MCF10A acini, we find that these fates depend on the average frequency of non-periodic ERK pulses. High pulse frequency is observed during initial acinus growth, correlating with rapid cell motility and proliferation. Subsequent decrease in motility correlates with lower ERK pulse frequency and quiescence. Later, during lumen formation, coordinated multicellular ERK waves emerge, correlating with high and low ERK pulse frequencies in outer surviving and inner dying cells, respectively. Optogenetic entrainment of ERK pulses causally connects high ERK pulse frequency with inner cell survival. Acini harboring the PIK3CA H1047R mutation display increased ERK pulse frequency and inner cell survival. Thus, fate decisions during acinar morphogenesis are coordinated by different spatiotemporal modalities of ERK pulse frequency.
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Affiliation(s)
- Pascal Ender
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | | | - Maciej Dobrzyński
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Agne Frismantiene
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Coralie Dessauges
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Thomas Höhener
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Marc-Antoine Jacques
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Andrew R Cohen
- Department of Electrical and Computer Engineering, Drexel University, 3120-40 Market Street, Suite 313, Philadelphia, PA 19104, USA
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
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15
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Krause HB, Karls AL, McClean MN, Kreeger PK. Cellular context alters EGF-induced ERK dynamics and reveals potential crosstalk with GDF-15. BIOMICROFLUIDICS 2022; 16:054104. [PMID: 36217350 PMCID: PMC9547670 DOI: 10.1063/5.0114334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Cellular signaling dynamics are sensitive to differences in ligand identity, levels, and temporal patterns. These signaling patterns are also impacted by the larger context that the cell experiences (i.e., stimuli such as media formulation or substrate stiffness that are constant in an experiment exploring a particular variable but may differ between independent experiments which explore that variable) although the reason for different dynamics is not always obvious. Here, we compared extracellular-regulated kinase (ERK) signaling in response to epidermal growth factor treatment of human mammary epithelial cells cultures in either well culture or a microfluidic device. Using a single-cell ERK kinase translocation reporter, we observed extended ERK activation in well culture and only transient activity in microfluidic culture. The activity in microfluidic culture resembled that of the control condition, suggesting that shear stress led to the early activity and a loss of autocrine factors dampened extended signaling. Through experimental analysis we identified growth differentiation factor-15 as a candidate factor that led to extended ERK activation through a protein kinase C-α/β dependent pathway. Our results demonstrate that context impacts ERK dynamics and that comparison of distinct contexts can be used to elucidate new aspects of the cell signaling network.
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Affiliation(s)
- Harris B. Krause
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Alexis L. Karls
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Pamela K. Kreeger
- Author to whom correspondence should be addressed:. Telephone: 608-890-2915
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16
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Rogers MA, Campaña MB, Long R, Fantauzzo KA. PDGFR dimer-specific activation, trafficking and downstream signaling dynamics. J Cell Sci 2022; 135:jcs259686. [PMID: 35946433 PMCID: PMC9482349 DOI: 10.1242/jcs.259686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Signaling through the platelet-derived growth factor receptors (PDGFRs) plays a critical role in multiple cellular processes during development. The two PDGFRs, PDGFRα and PDGFRβ, dimerize to form homodimers and/or heterodimers. Here, we overcome previous limitations in studying PDGFR dimer-specific dynamics by generating cell lines stably expressing C-terminal fusions of each PDGFR with bimolecular fluorescence complementation (BiFC) fragments corresponding to the N-terminal or C-terminal regions of the Venus fluorescent protein. We find that PDGFRβ receptors homodimerize more quickly than PDGFRα receptors in response to PDGF ligand, with increased levels of autophosphorylation. Furthermore, we demonstrate that PDGFRα homodimers are trafficked and degraded more quickly, whereas PDGFRβ homodimers are more likely to be recycled back to the cell membrane. We show that PDGFRβ homodimer activation results in a greater amplitude of phospho-ERK1/2 and phospho-AKT signaling, as well as increased proliferation and migration. Finally, we demonstrate that inhibition of clathrin-mediated endocytosis leads to changes in cellular trafficking and downstream signaling, particularly for PDGFRα homodimers. Collectively, our findings provide significant insight into how biological specificity is introduced to generate unique responses downstream of PDGFR engagement. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | | | | | - Katherine A. Fantauzzo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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17
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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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18
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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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19
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Phillips SMB, Bergstrom C, Walker B, Wang G, Alfaro T, Stromberg ZR, Hess BM. Engineered Cell Line Imaging Assay Differentiates Pathogenic from Non-Pathogenic Bacteria. Pathogens 2022; 11:pathogens11020209. [PMID: 35215152 PMCID: PMC8874627 DOI: 10.3390/pathogens11020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 01/27/2023] Open
Abstract
Cell culture systems have greatly expanded our understanding of how bacterial pathogens target signaling pathways to manipulate the host and cause infection. Advances in genetic engineering have allowed for the creation of fluorescent protein readouts within signaling pathways, but these techniques have been underutilized in pathogen biology. Here, we genetically engineered a lung cell line with fluorescent reporters for extracellular signal-related kinase (ERK) and the downstream transcription factor FOS-related antigen 1 (Fra1) and evaluated signaling after inoculation with pathogenic and non-pathogenic bacteria. Cells were inoculated with 100 colony-forming units of Acinetobacter baylyi, Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus agalactiae, or Staphylococcus epidermidis and imaged in a multi-mode reader. The alamarBlue cell viability assay was used as a reference test and showed that pathogenic P. aeruginosa induced significant (p < 0.05) cell death after 8 h in both wild-type and engineered cell lines compared to non-pathogenic S. epidermidis. In engineered cells, we found that Fra1 signaling was disrupted in as little as 4 h after inoculation with bacterial pathogens compared to delayed disruption in signaling by non-pathogenic S. epidermidis. Overall, we demonstrate that low levels of pathogenic versus non-pathogenic bacteria can be rapidly and sensitively screened based on ERK-Fra1 signaling.
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20
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Guo L, Zhu K, Pargett M, Contreras A, Tsai P, Qing Q, Losert W, Albeck J, Zhao M. Electrically synchronizing and modulating the dynamics of ERK activation to regulate cell fate. iScience 2021; 24:103240. [PMID: 34746704 PMCID: PMC8554532 DOI: 10.1016/j.isci.2021.103240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/18/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
Intracellular signaling dynamics play fundamental roles in cell biology. Precise modulation of the amplitude, duration, and frequency of signaling activation will be a powerful approach to investigate molecular mechanisms as well as to engineer signaling to control cell behaviors. Here, we showed a practical approach to achieve precise amplitude modulation (AM), frequency modulation (FM), and duration modulation (DM) of MAP kinase activation. Alternating current (AC) electrical stimulation induced synchronized ERK activation. Amplitude and duration of ERK activation were controlled by varying stimulation strength and duration. ERK activation frequencies were arbitrarily modulated with trains of short AC applications with accurately defined intervals. Significantly, ERK dynamics coded by well-designed AC can rewire PC12 cell fate independent of growth factors. This technique can be used to synchronize and modulate ERK activation dynamics, thus would offer a practical way to control cell behaviors in vivo without the use of biochemical agents or genetic manipulation. Alternating-current (AC) electric field activates ERK independently of growth factors AC stimulation length modulates the amplitude and duration of ERK activation On-off time interval of AC modulates the frequency of ERK activation peaks Electrical modulation of ERK dynamics promotes neuronal differentiation of PC12 cells
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Affiliation(s)
- Liang Guo
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA.,College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China
| | - Kan Zhu
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
| | - Adam Contreras
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA
| | - Patrick Tsai
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA
| | - Quan Qing
- Department of Physics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wolfgang Losert
- Department of Physics, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - John Albeck
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA
| | - Min Zhao
- Department of Ophthalmology & Vision Science, Department of Dermatology, Institute for Regenerative Cures, University of California, Davis, Sacramento, CA 95817, USA
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21
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González Wusener AE, González Á, Perez Collado ME, Maza MR, General IJ, Arregui CO. Protein tyrosine phosphatase 1B targets focal adhesion kinase and paxillin in cell-matrix adhesions. J Cell Sci 2021; 134:272564. [PMID: 34553765 DOI: 10.1242/jcs.258769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B, also known as PTPN1) is an established regulator of cell-matrix adhesion and motility. However, the nature of substrate targets at adhesion sites remains to be validated. Here, we used bimolecular fluorescence complementation assays, in combination with a substrate trapping mutant of PTP1B, to directly examine whether relevant phosphotyrosines on paxillin and focal adhesion kinase (FAK, also known as PTK2) are substrates of the phosphatase in the context of cell-matrix adhesion sites. We found that the formation of catalytic complexes at cell-matrix adhesions requires intact tyrosine residues Y31 and Y118 on paxillin, and the localization of FAK at adhesion sites. Additionally, we found that PTP1B specifically targets Y925 on the focal adhesion targeting (FAT) domain of FAK at adhesion sites. Electrostatic analysis indicated that dephosphorylation of this residue promotes the closed conformation of the FAT 4-helix bundle and its interaction with paxillin at adhesion sites.
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Affiliation(s)
- Ana E González Wusener
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - Ángela González
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - María E Perez Collado
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
| | - Melina R Maza
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martin, Instituto de Ciencias Físicas and CONICET, San Martin, Buenos Aires 1650, Argentina
| | - Ignacio J General
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martin, Instituto de Ciencias Físicas and CONICET, San Martin, Buenos Aires 1650, Argentina
| | - Carlos O Arregui
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires 1650, Argentina
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22
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Sipieter F, Cappe B, Leray A, De Schutter E, Bridelance J, Hulpiau P, Van Camp G, Declercq W, Héliot L, Vincent P, Vandenabeele P, Riquet FB. Characteristic ERK1/2 signaling dynamics distinguishes necroptosis from apoptosis. iScience 2021; 24:103074. [PMID: 34568795 PMCID: PMC8449238 DOI: 10.1016/j.isci.2021.103074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/21/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022] Open
Abstract
ERK1/2 involvement in cell death remains unclear, although many studies have demonstrated the importance of ERK1/2 dynamics in determining cellular responses. To untangle how ERK1/2 contributes to two cell death programs, we investigated ERK1/2 signaling dynamics during hFasL-induced apoptosis and TNF-induced necroptosis in L929 cells. We observed that ERK1/2 inhibition sensitizes cells to apoptosis while delaying necroptosis. By monitoring ERK1/2 activity by live-cell imaging using an improved ERK1/2 biosensor (EKAR4.0), we reported differential ERK1/2 signaling dynamics between cell survival, apoptosis, and necroptosis. We also decrypted a temporally shifted amplitude- and frequency-modulated (AM/FM) ERK1/2 activity profile in necroptosis versus apoptosis. ERK1/2 inhibition, which disrupted ERK1/2 signaling dynamics, prevented TNF and IL-6 gene expression increase during TNF-induced necroptosis. Using an inducible cell line for activated MLKL, the final executioner of necroptosis, we showed ERK1/2 and its distinctive necroptotic ERK1/2 activity dynamics to be positioned downstream of MLKL.
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Affiliation(s)
- François Sipieter
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, Lille, France
| | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Aymeric Leray
- Laboratoire Interdisciplinaire Carnot De Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, 21078 Dijon, France
| | - Elke De Schutter
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, Edegem, 2650 Antwerp, Belgium
| | - Jolien Bridelance
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Paco Hulpiau
- Data Mining and Modeling for Biomedicine (DaMBi), VIB Center for Inflammation Research, Ghent, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, Edegem, 2650 Antwerp, Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, Wilrijk, 2610 Antwerp, Belgium
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Laurent Héliot
- Team Biophotonique Cellulaire Fonctionnelle, Laboratoire de Physique des Lasers, Atomes et Molécules (PhLAM), CNRS UMR 8523, 59655 Villeneuve d'Ascq, France
| | - Pierre Vincent
- Sorbonne Université, CNRS, Neurobiology of Adaptative Processes, UMR8256, 75005 Paris, France
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research, Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, Lille, France
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23
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Ueki R, Hayashi S, Tsunoda M, Akiyama M, Liu H, Ueno T, Urano Y, Sando S. Nongenetic control of receptor signaling dynamics using a DNA-based optochemical tool. Chem Commun (Camb) 2021; 57:5969-5972. [PMID: 34027523 DOI: 10.1039/d1cc01968f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Optochemical tools that can modulate the activity of the target protein provide an opportunity for studying and regulating the related biological processes. Here we present a DNA-based nongenetic optochemical tool that can control the dynamics of growth factor signaling. This photo-caged mimicry of growth factor can be a promising tool for elucidating a linkage between the dynamics of signaling and the resulting biological outcomes, as well as for manipulating cellular functions and the fate of living cells.
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Affiliation(s)
- Ryosuke Ueki
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shota Hayashi
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masaya Tsunoda
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Momoko Akiyama
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hanrui Liu
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan and Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan and Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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24
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Gillies TE, Pargett M, Silva JM, Teragawa CK, McCormick F, Albeck JG. Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway. Mol Syst Biol 2021; 16:e9518. [PMID: 33073539 PMCID: PMC7569415 DOI: 10.15252/msb.20209518] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 09/02/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
Activating mutations in RAS are present in ~ 30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activation in vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live‐cell imaging in cells expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway‐level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the signaling changes induced by RAS mutations early in oncogenesis are subtle.
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Affiliation(s)
- Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Jillian M Silva
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Carolyn K Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.,Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
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25
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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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26
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Gagliardi PA, Dobrzyński M, Jacques MA, Dessauges C, Ender P, Blum Y, Hughes RM, Cohen AR, Pertz O. Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival. Dev Cell 2021; 56:1712-1726.e6. [PMID: 34081908 DOI: 10.1016/j.devcel.2021.05.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/16/2021] [Accepted: 05/09/2021] [Indexed: 12/20/2022]
Abstract
Cell death events continuously challenge epithelial barrier function yet are crucial to eliminate old or critically damaged cells. How such apoptotic events are spatio-temporally organized to maintain epithelial homeostasis remains unclear. We observe waves of extracellular-signal-regulated kinase (ERK) and AKT serine/threonine kinase (Akt) activity pulses that originate from apoptotic cells and propagate radially to healthy surrounding cells. This requires epidermal growth factor receptor (EGFR) and matrix metalloproteinase (MMP) signaling. At the single-cell level, ERK/Akt waves act as spatial survival signals that locally protect cells in the vicinity of the epithelial injury from apoptosis for a period of 3-4 h. At the cell population level, ERK/Akt waves maintain epithelial homeostasis (EH) in response to mild or intense environmental insults. Disruption of this spatial signaling system results in the inability of a model epithelial tissue to ensure barrier function in response to environmental insults.
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Affiliation(s)
| | - Maciej Dobrzyński
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Marc-Antoine Jacques
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Coralie Dessauges
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Pascal Ender
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Yannick Blum
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
| | - Robert M Hughes
- Department of Chemistry, East Carolina University, 300 Science and Technology Building, Greenville, NC 27858-4353, USA
| | - Andrew R Cohen
- Department of Electrical and Computer Engineering, Drexel University, 3120-40 Market Street, Suite 313, Philadelphia, PA 19104, USA
| | - Olivier Pertz
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
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27
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Mehta S, Zhang J. Biochemical Activity Architectures Visualized-Using Genetically Encoded Fluorescent Biosensors to Map the Spatial Boundaries of Signaling Compartments. Acc Chem Res 2021; 54:2409-2420. [PMID: 33949851 DOI: 10.1021/acs.accounts.1c00056] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All biological processes arise through the coordinated actions of biochemical pathways. How such functional diversity is achieved by a finite cast of molecular players remains a central mystery in biology. Spatial compartmentation-the idea that biochemical activities are organized around discrete spatial domains within cells-was first proposed nearly 40 years ago and has become firmly rooted in our understanding of how biochemical pathways are regulated to ensure specificity. However, directly interrogating spatial compartmentation and its mechanistic origins has only really become possible in the last 20 or so years, following technological advances such as the development of genetically encoded fluorescent biosensors. These powerful molecular tools permit a direct, real-time visualization of dynamic biochemical processes in native biological contexts, and they are essential for probing the spatial regulation of biochemical activities. In this Account, we review our lab's efforts in developing and using biosensors to map the spatial compartmentation of intracellular signaling pathways and illuminate key mechanisms that establish the boundaries of an intricate biochemical activity architecture. We first discuss the role of regulatory fences, wherein the dynamic activation and deactivation of diffusible messengers produce diverse signaling compartments. For example, we used biosensors for the Ca2+ effector calmodulin and its downstream target calcineurin to reveal a spatial gradient of calmodulin that controls the temporal dynamics of calcineurin signaling. Our studies using cyclic adenosine monophosphate (cAMP) biosensors have similarly elucidated fenced cAMP domains generated by competing production and degradation pathways, ranging in size from cell-spanning gradients to nanoscale hotspots. Second, we describe the role played by intracellular membranes in creating unique signaling platforms with distinctive pathway regulation, as revealed through studies using subcellularly targeted fluorescent biosensors. Using biosensors to visualize subcellular extracellular response kinase (ERK) pathway activity, for example, led us to discover a local signaling circuit that mediates distinct plasma membrane ERK dynamics versus global ERK signaling. Similarly, our work developing biosensors to monitor the subcellular mechanistic target of rapamycin complex 1 (mTORC1) signaling allowed us to not only clarify the presence of mTORC1 activity in the nucleus but also identify a novel mechanism governing the activation of mTORC1 in this location. Finally, we detail how molecular assemblies enable the precise spatial tuning of biochemical activity, through investigations enabled by cutting-edge advances in biosensor design. We recently identified liquid-liquid phase separation as a major factor in cAMP compartmentation aided by a new strategy for targeting biosensors to endogenously expressed proteins via genome editing, for instance, and have also been able to directly visualize nanometer-scale protein kinase signalosomes using an entirely new class of biosensors specifically developed for the dynamic super-resolution imaging of live-cell biochemical activities. Our work provides key insights into the molecular logic of spatially regulated signaling and lays the foundation for a broader exploration of biochemical activity architectures across multiple spatial scales.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Jin Zhang
- Departments of Pharmacology, Bioengineering, and Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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28
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Quantifying single-cell ERK dynamics in colorectal cancer organoids reveals EGFR as an amplifier of oncogenic MAPK pathway signalling. Nat Cell Biol 2021; 23:377-390. [PMID: 33795873 PMCID: PMC7610573 DOI: 10.1038/s41556-021-00654-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/24/2021] [Indexed: 02/07/2023]
Abstract
Direct targeting of the downstream mitogen-activated protein kinase (MAPK) pathway to suppress extracellular-regulated kinase (ERK) activation in KRAS and BRAF mutant colorectal cancer (CRC) has proven clinically unsuccessful, but promising results have been obtained with combination therapies including epidermal growth factor receptor (EGFR) inhibition. To elucidate the interplay between EGF signalling and ERK activation in tumours, we used patient-derived organoids (PDOs) from KRAS and BRAF mutant CRCs. PDOs resemble in vivo tumours, model treatment response and are compatible with live-cell microscopy. We established real-time, quantitative drug response assessment in PDOs with single-cell resolution, using our improved fluorescence resonance energy transfer (FRET)-based ERK biosensor EKAREN5. We show that oncogene-driven signalling is strikingly limited without EGFR activity and insufficient to sustain full proliferative potential. In PDOs and in vivo, upstream EGFR activity rigorously amplifies signal transduction efficiency in KRAS or BRAF mutant MAPK pathways. Our data provide a mechanistic understanding of the effectivity of EGFR inhibitors within combination therapies against KRAS and BRAF mutant CRC.
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29
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Kosaisawe N, Sparta B, Pargett M, Teragawa CK, Albeck JG. Transient phases of OXPHOS inhibitor resistance reveal underlying metabolic heterogeneity in single cells. Cell Metab 2021; 33:649-665.e8. [PMID: 33561427 PMCID: PMC8005262 DOI: 10.1016/j.cmet.2021.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/13/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022]
Abstract
Cell-to-cell heterogeneity in metabolism plays an unknown role in physiology and pharmacology. To functionally characterize cellular variability in metabolism, we treated cells with inhibitors of oxidative phosphorylation (OXPHOS) and monitored their responses with live-cell reporters for ATP, ADP/ATP, or activity of the energy-sensing kinase AMPK. Across multiple OXPHOS inhibitors and cell types, we identified a subpopulation of cells resistant to activation of AMPK and reduction of ADP/ATP ratio. This resistant state persists transiently for at least several hours and can be inherited during cell divisions. OXPHOS inhibition suppresses the mTORC1 and ERK growth signaling pathways in sensitive cells, but not in resistant cells. Resistance is linked to a multi-factorial combination of increased glucose uptake, reduced protein biosynthesis, and G0/G1 cell-cycle status. Our results reveal dynamic fluctuations in cellular energetic balance and provide a basis for measuring and predicting the distribution of cellular responses to OXPHOS inhibition.
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Affiliation(s)
- Nont Kosaisawe
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Breanne Sparta
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Carolyn K Teragawa
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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30
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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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31
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Bunker EN, Wheeler GE, Chapnick DA, Liu X. Suppression of α-catenin and adherens junctions enhances epithelial cell proliferation and motility via TACE-mediated TGF-α autocrine/paracrine signaling. Mol Biol Cell 2020; 32:348-361. [PMID: 33378218 PMCID: PMC8098817 DOI: 10.1091/mbc.e19-08-0474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sustained cell migration is essential for wound healing and cancer metastasis. The epidermal growth factor receptor (EGFR) signaling cascade is known to drive cell migration and proliferation. While the signal transduction downstream of EGFR has been extensively investigated, our knowledge of the initiation and maintenance of EGFR signaling during cell migration remains limited. The metalloprotease TACE (tumor necrosis factor alpha converting enzyme) is responsible for producing active EGFR family ligands in the via ligand shedding. Sustained TACE activity may perpetuate EGFR signaling and reduce a cell’s reliance on exogenous growth factors. Using a cultured keratinocyte model system, we show that depletion of α-catenin perturbs adherens junctions, enhances cell proliferation and motility, and decreases dependence on exogenous growth factors. We show that the underlying mechanism for these observed phenotypical changes depends on enhanced autocrine/paracrine release of the EGFR ligand transforming growth factor alpha in a TACE-dependent manner. We demonstrate that proliferating keratinocyte epithelial cell clusters display waves of oscillatory extracellular signal–regulated kinase (ERK) activity, which can be eliminated by TACE knockout, suggesting that these waves of oscillatory ERK activity depend on autocrine/paracrine signals produced by TACE. These results provide new insights into the regulatory role of adherens junctions in initiating and maintaining autocrine/paracrine signaling with relevance to wound healing and cellular transformation.
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Affiliation(s)
- Eric N Bunker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Graycen E Wheeler
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | | | - Xuedong Liu
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
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32
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Artim SC, Kiyatkin A, Lemmon MA. Comparison of tyrosine kinase domain properties for the neurotrophin receptors TrkA and TrkB. Biochem J 2020; 477:4053-4070. [PMID: 33043964 PMCID: PMC7606831 DOI: 10.1042/bcj20200695] [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: 08/27/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022]
Abstract
The tropomyosin-related kinase (Trk) family consists of three receptor tyrosine kinases (RTKs) called TrkA, TrkB, and TrkC. These RTKs are regulated by the neurotrophins, a class of secreted growth factors responsible for the development and function of neurons. The Trks share a high degree of homology and utilize overlapping signaling pathways, yet their signaling is associated with starkly different outcomes in certain cancers. For example, in neuroblastoma, TrkA expression and signaling correlates with a favorable prognosis, whereas TrkB is associated with poor prognoses. To begin to understand how activation of the different Trks can lead to such distinct cellular outcomes, we investigated differences in kinase activity and duration of autophosphorylation for the TrkA and TrkB tyrosine kinase domains (TKDs). We find that the TrkA TKD has a catalytic efficiency that is ∼2-fold higher than that of TrkB, and becomes autophosphorylated in vitro more rapidly than the TrkB TKD. Studies with mutated TKD variants suggest that a crystallographic dimer seen in many TrkA (but not TrkB) TKD crystal structures, which involves the kinase-insert domain, may contribute to this enhanced TrkA autophosphorylation. Consistent with previous studies showing that cellular context determines whether TrkB signaling is sustained (promoting differentiation) or transient (promoting proliferation), we also find that TrkB signaling can be made more transient in PC12 cells by suppressing levels of p75NTR. Our findings shed new light on potential differences between TrkA and TrkB signaling, and suggest that subtle differences in signaling dynamics can lead to substantial shifts in the cellular outcome.
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Affiliation(s)
- Stephen C. Artim
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Present address: Merck Research Laboratories, Merck, South San Francisco, CA 94080, USA
| | - Anatoly Kiyatkin
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Pharmacology and Cancer Biology Institute, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mark A. Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Pharmacology and Cancer Biology Institute, Yale University School of Medicine, New Haven, CT, 06520, USA
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33
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Zhou X, Mehta S, Zhang J. Genetically Encodable Fluorescent and Bioluminescent Biosensors Light Up Signaling Networks. Trends Biochem Sci 2020; 45:889-905. [PMID: 32660810 PMCID: PMC7502535 DOI: 10.1016/j.tibs.2020.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
Cell signaling networks are intricately regulated in time and space to determine the responses and fates of cells to different cues. Genetically encodable fluorescent and bioluminescent biosensors enable the direct visualization of these spatiotemporal signaling dynamics within the native biological context, and have therefore become powerful molecular tools whose unique benefits are being used to address challenging biological questions. We first review the basis of biosensor design and remark on recent technologies that are accelerating biosensor development. We then discuss a few of the latest advances in the development and application of genetically encodable fluorescent and bioluminescent biosensors that have led to scientific or technological breakthroughs.
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Affiliation(s)
- Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
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34
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Davies AE, Pargett M, Siebert S, Gillies TE, Choi Y, Tobin SJ, Ram AR, Murthy V, Juliano C, Quon G, Bissell MJ, Albeck JG. Systems-Level Properties of EGFR-RAS-ERK Signaling Amplify Local Signals to Generate Dynamic Gene Expression Heterogeneity. Cell Syst 2020; 11:161-175.e5. [PMID: 32726596 PMCID: PMC7856305 DOI: 10.1016/j.cels.2020.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/06/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023]
Abstract
Intratumoral heterogeneity is associated with aggressive tumor behavior, therapy resistance, and poor patient outcomes. Such heterogeneity is thought to be dynamic, shifting over periods of minutes to hours in response to signaling inputs from the tumor microenvironment. However, models of this process have been inferred from indirect or post-hoc measurements of cell state, leaving the temporal details of signaling-driven heterogeneity undefined. Here, we developed a live-cell model system in which microenvironment-driven signaling dynamics can be directly observed and linked to variation in gene expression. Our analysis reveals that paracrine signaling between two cell types is sufficient to drive continual diversification of gene expression programs. This diversification emerges from systems-level properties of the EGFR-RAS-ERK signaling cascade, including intracellular amplification of amphiregulin-mediated paracrine signals and differential kinetic filtering by target genes including Fra-1, c-Myc, and Egr1. Our data enable more precise modeling of paracrine-driven transcriptional variation as a generator of gene expression heterogeneity. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Alexander E Davies
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Michael Pargett
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Taryn E Gillies
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Yongin Choi
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Savannah J Tobin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA; Department of Veterinary Biosciences, College of Veterinary Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Abhineet R Ram
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Vaibhav Murthy
- Department of Veterinary Biosciences, College of Veterinary Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Celina Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Mina J Bissell
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
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35
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Kiyatkin A, van Alderwerelt van Rosenburgh IK, Klein DE, Lemmon MA. Kinetics of receptor tyrosine kinase activation define ERK signaling dynamics. Sci Signal 2020; 13:13/645/eaaz5267. [PMID: 32817373 DOI: 10.1126/scisignal.aaz5267] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In responses to activation of receptor tyrosine kinases (RTKs), crucial cell fate decisions depend on the duration and dynamics of ERK signaling. In PC12 cells, epidermal growth factor (EGF) induces transient ERK activation that leads to cell proliferation, whereas nerve growth factor (NGF) promotes sustained ERK activation and cell differentiation. These differences have typically been assumed to reflect distinct feedback mechanisms in the Raf-MEK-ERK signaling network, with the receptors themselves acting as simple upstream inputs. We failed to confirm the expected differences in feedback type when investigating transient versus sustained signaling downstream of the EGF receptor (EGFR) and NGF receptor (TrkA). Instead, we found that ERK signaling faithfully followed RTK dynamics when receptor signaling was modulated in different ways. EGFR activation kinetics, and consequently ERK signaling dynamics, were switched from transient to sustained when receptor internalization was inhibited with drugs or mutations, or when cells expressed a chimeric receptor likely to have impaired dimerization. In addition, EGFR and ERK signaling both became more sustained when substoichiometric levels of erlotinib were added to reduce duration of EGFR kinase activation. Our results argue that RTK activation kinetics play a crucial role in determining MAP kinase cascade signaling dynamics and cell fate decisions, and that signaling outcome can be modified by activating a given RTK in different ways.
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Affiliation(s)
- Anatoly Kiyatkin
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Iris K van Alderwerelt van Rosenburgh
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daryl E Klein
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA. .,Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
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36
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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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37
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Min M, Rong Y, Tian C, Spencer SL. Temporal integration of mitogen history in mother cells controls proliferation of daughter cells. Science 2020; 368:1261-1265. [PMID: 32241885 PMCID: PMC8363187 DOI: 10.1126/science.aay8241] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/19/2019] [Accepted: 03/17/2020] [Indexed: 01/17/2023]
Abstract
Multicellular organisms use mitogens to regulate cell proliferation, but how fluctuating mitogenic signals are converted into proliferation-quiescence decisions is poorly understood. In this work, we combined live-cell imaging with temporally controlled perturbations to determine the time scale and mechanisms underlying this system in human cells. Contrary to the textbook model that cells sense mitogen availability only in the G1 cell cycle phase, we find that mitogenic signaling is temporally integrated throughout the entire mother cell cycle and that even a 1-hour lapse in mitogen signaling can influence cell proliferation more than 12 hours later. Protein translation rates serve as the integrator that proportionally converts mitogen history into corresponding levels of cyclin D in the G2 phase of the mother cell, which controls the proliferation-quiescence decision in daughter cells and thereby couples protein production with cell proliferation.
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Affiliation(s)
- Mingwei Min
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
| | - Yao Rong
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Chengzhe Tian
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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38
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Keyes J, Ganesan A, Molinar-Inglis O, Hamidzadeh A, Zhang J, Ling M, Trejo J, Levchenko A, Zhang J. Signaling diversity enabled by Rap1-regulated plasma membrane ERK with distinct temporal dynamics. eLife 2020; 9:57410. [PMID: 32452765 PMCID: PMC7289600 DOI: 10.7554/elife.57410] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022] Open
Abstract
A variety of different signals induce specific responses through a common, extracellular-signal regulated kinase (ERK)-dependent cascade. It has been suggested that signaling specificity can be achieved through precise temporal regulation of ERK activity. Given the wide distrubtion of ERK susbtrates across different subcellular compartments, it is important to understand how ERK activity is temporally regulated at specific subcellular locations. To address this question, we have expanded the toolbox of Förster Resonance Energy Transfer (FRET)-based ERK biosensors by creating a series of improved biosensors targeted to various subcellular regions via sequence specific motifs to measure spatiotemporal changes in ERK activity. Using these sensors, we showed that EGF induces sustained ERK activity near the plasma membrane in sharp contrast to the transient activity observed in the cytoplasm and nucleus. Furthermore, EGF-induced plasma membrane ERK activity involves Rap1, a noncanonical activator, and controls cell morphology and EGF-induced membrane protrusion dynamics. Our work strongly supports that spatial and temporal regulation of ERK activity is integrated to control signaling specificity from a single extracellular signal to multiple cellular processes.
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Affiliation(s)
- Jeremiah Keyes
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Ambhighainath Ganesan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Olivia Molinar-Inglis
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Archer Hamidzadeh
- Department of Biomedical Engineering and Yale Systems Biology Institute, Yale University, New Haven, United States
| | - Jinfan Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Megan Ling
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, United States
| | - JoAnn Trejo
- Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Andre Levchenko
- Department of Biomedical Engineering and Yale Systems Biology Institute, Yale University, New Haven, United States
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, United States.,Department of Bioengineering, University of California San Diego, La Jolla, United States
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39
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Tetrastigma hemsleyanum Vine Flavone Ameliorates Glutamic Acid-Induced Neurotoxicity via MAPK Pathways. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7509612. [PMID: 32273948 PMCID: PMC7118691 DOI: 10.1155/2020/7509612] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/21/2020] [Indexed: 12/15/2022]
Abstract
Glutamic acid (Glu) is a worldwide flavor enhancer with various positive effects. However, Glu-induced neurotoxicity has been reported less. Tetrastigma hemsleyanum (TH), a rare herbal plant in China, possesses high medicinal value. More studies paid attention to tuber of TH whereas vine part (THV) attracts fewer focus. In this study, we extracted and purified flavones from THV (THVF), and UPLC-TOF/MS showed THVF was consisted of 3-caffeoylquinic acid, 5-caffeoylquinic acid, quercetin-3-O-rutinoside, and kaempferol-3-O-rutinoside. In vitro, Glu caused severe cytotoxicity, genotoxicity, mitochondrial dysfunction, and oxidative damage to rat phaeochromocytoma (PC12) cells. Conversely, THVF attenuated Glu-induced toxicity via MAPK pathways. In vivo, the neurotoxicity triggered by Glu restrained the athletic ability in Caenorhabditis elegans (C. elegans). The treatment of THVF reversed the situation induced by Glu. In a word, Glu could cause neurotoxicity and THVF owns potential neuroprotective effects both in vitro and in vivo via MAPK pathways.
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40
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Mukherjee A, Singh R, Udayan S, Biswas S, Reddy PP, Manmadhan S, George G, Kumar S, Das R, Rao BM, Gulyani A. A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells. eLife 2020; 9:50571. [PMID: 32017701 PMCID: PMC7000222 DOI: 10.7554/elife.50571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cell behavior is controlled through spatio-temporally localized protein activity. Despite unique and often contradictory roles played by Src-family-kinases (SFKs) in regulating cell physiology, activity patterns of individual SFKs have remained elusive. Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells. We deployed combinatorial library screening to isolate a binding-protein (F29) targeting activated Fyn. Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs. Using F29, we engineered a sensitive, minimally-perturbing fluorescence-resonance-energy-transfer (FRET) biosensor (FynSensor) that reveals cellular Fyn activity to be spatially localized, pulsatile and sensitive to adhesion/integrin signaling. Strikingly, growth factor stimulation further enhanced Fyn activity in pre-activated intracellular zones. However, inhibition of focal-adhesion-kinase activity not only attenuates Fyn activity, but abolishes growth-factor modulation. FynSensor imaging uncovers spatially organized, sensitized signaling clusters, direct crosstalk between integrin and growth-factor-signaling, and clarifies how compartmentalized Src-kinase activity may drive cell fate.
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Affiliation(s)
- Ananya Mukherjee
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,SASTRA University, Thanjavur, India
| | - Randhir Singh
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sreeram Udayan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Sayan Biswas
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | | | - Saumya Manmadhan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Geen George
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Shilpa Kumar
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Ranabir Das
- National Centre for Biological Sciences, Bangalore, India
| | - Balaji M Rao
- North Carolina State University, Raleigh, United States
| | - Akash Gulyani
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
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41
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Guo L, Li H, Wang Y, Li Z, Albeck J, Zhao M, Qing Q. Controlling ERK Activation Dynamics in Mammary Epithelial Cells with Alternating Electric Fields through Microelectrodes. NANO LETTERS 2019; 19:7526-7533. [PMID: 31487192 PMCID: PMC6786939 DOI: 10.1021/acs.nanolett.9b03411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Amplitude, duration, and frequency of activation of the extracellular-signal-regulated kinase (ERK) pathway code distinct information to instruct cells to migrate, proliferate, or differentiate. Synchronized frequency control of ERK activation would provide a powerful approach to regulate cell behaviors. Here we demonstrated modulation of ERK activities using alternative current (AC) electric fields (EFs) applied through high-k dielectric passivated microelectrodes. Both the amplitude and frequency of ERK activation can be precisely synchronized and modulated. ERK activation in our system is independent of Faradaic currents and electroporation, thus excluding mechanisms of changes in pH, reactive oxygen species, and other electrochemical reaction. Further experiments pinpointed a mechanism of phosphorylation site of epidermal growth factor (EGF) receptor to activate the EGFR-ERK pathway, and independent of EGF. AC EFs thus provide a powerful platform for practical and precise control of EGFR-ERK pathway.
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Affiliation(s)
| | | | | | - Zhuo Li
- Key Laboratory of Radar Imaging and Microwave Photonics, Ministry of Education, College of Electronic and Information Engineering , Nanjing University of Aeronautics and Astronautics , Nanjing 211106 , People's Republic of China
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42
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Chen Z, Zhang W, Zhang N, Zhou Y, Hu G, Xue M, Liu J, Li Y. Down-regulation of insulin-like growth factor binding protein 5 is involved in intervertebral disc degeneration via the ERK signalling pathway. J Cell Mol Med 2019; 23:6368-6377. [PMID: 31290273 PMCID: PMC6714225 DOI: 10.1111/jcmm.14525] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
It is obvious that epigenetic processes influence the evolution of intervertebral disc degeneration (IDD). However, its molecular mechanisms are poorly understood. Therefore, we tested the hypothesis that IGFBP5, a potential regulator of IDD, modulates IDD via the ERK signalling pathway. We showed that IGFBP5 mRNA was significantly down-regulated in degenerative nucleus pulposus (NP) tissues. IGFBP5 was shown to significantly promote NP cell proliferation and inhibit apoptosis in vitro, which was confirmed by MTT, flow cytometry and colony formation assays. Furthermore, IGFBP5 was shown to exert its effects by inhibiting the ERK signalling pathway. The effects induced by IGFBP5 overexpression on NP cells were similar to those induced by treatment with an ERK pathway inhibitor (PD98059). Moreover, qRT-PCR and Western blot analyses were performed to examine the levels of apoptosis-related factors, including Bax, caspase-3 and Bcl2. The silencing of IGFBP5 up-regulated the levels of Bax and caspase-3 and down-regulated the level of Bcl2, thereby contributing to the development of human IDD. Furthermore, these results were confirmed in vivo using an IDD rat model, which showed that the induction of Igfbp5 mRNA expression abrogated the effects of IGFBP5 silencing on intervertebral discs. Overall, our findings elucidate the role of IGFBP5 in the pathogenesis of IDD and provide a potential novel therapeutic target for IDD.
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Affiliation(s)
- Zhonghui Chen
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Weibing Zhang
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Nu Zhang
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Yan Zhou
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Geliang Hu
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Mingdi Xue
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
| | - Junhua Liu
- Orthopedic SurgeryChibi Third Renmin HospitalChibiChina
| | - Yaming Li
- Orthopedic SurgeryRenmin Hospital of Wuhan University, Hubei General HospitalWuchang District, WuhanChina
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43
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Sammons RM, Ghose R, Tsai KY, Dalby KN. Targeting ERK beyond the boundaries of the kinase active site in melanoma. Mol Carcinog 2019; 58:1551-1570. [PMID: 31190430 DOI: 10.1002/mc.23047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022]
Abstract
Extracellular signal-regulated kinase 1/2 (ERK1/2) constitute a point of convergence for complex signaling events that regulate essential cellular processes, including proliferation and survival. As such, dysregulation of the ERK signaling pathway is prevalent in many cancers. In the case of BRAF-V600E mutant melanoma, ERK inhibition has emerged as a viable clinical approach to abrogate signaling through the ERK pathway, even in cases where MEK and Raf inhibitor treatments fail to induce tumor regression due to resistance mechanisms. Several ERK inhibitors that target the active site of ERK have reached clinical trials, however, many critical ERK interactions occur at other potentially druggable sites on the protein. Here we discuss the role of ERK signaling in cell fate, in driving melanoma, and in resistance mechanisms to current BRAF-V600E melanoma treatments. We explore targeting ERK via a distinct site of protein-protein interaction, known as the D-recruitment site (DRS), as an alternative or supplementary mode of ERK pathway inhibition in BRAF-V600E melanoma. Targeting the DRS with inhibitors in melanoma has the potential to not only disrupt the catalytic apparatus of ERK but also its noncatalytic functions, which have significant impacts on spatiotemporal signaling dynamics and cell fate.
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Affiliation(s)
- Rachel M Sammons
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
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44
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DeFelice MM, Clark HR, Hughey JJ, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S. NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop. Sci Signal 2019; 12:12/579/eaau3568. [PMID: 31040261 DOI: 10.1126/scisignal.aau3568] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the last decade, multiple studies have shown that signaling proteins activated in different temporal patterns, such as oscillatory, transient, and sustained, can result in distinct gene expression patterns or cell fates. However, the molecular events that ensure appropriate stimulus- and dose-dependent dynamics are not often understood and are difficult to investigate. Here, we used single-cell analysis to dissect the mechanisms underlying the stimulus- and dose-encoding patterns in the innate immune signaling network. We found that Toll-like receptor (TLR) and interleukin-1 receptor (IL-1R) signaling dynamics relied on a dose-dependent, autoinhibitory loop that rendered cells refractory to further stimulation. Using inducible gene expression and optogenetics to perturb the network at different levels, we identified IL-1R-associated kinase 1 (IRAK1) as the dose-sensing node responsible for limiting signal flow during the innate immune response. Although the kinase activity of IRAK1 was not required for signal propagation, it played a critical role in inhibiting the nucleocytoplasmic oscillations of the transcription factor NF-κB. Thus, protein activities that may be "dispensable" from a topological perspective can nevertheless be essential in shaping the dynamic response to the external environment.
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Affiliation(s)
- Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Helen R Clark
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jacob J Hughey
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Inbal Maayan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Miriam V Gutschow
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. .,Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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45
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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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46
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Optical approaches for single-cell and subcellular analysis of GPCR-G protein signaling. Anal Bioanal Chem 2019; 411:4481-4508. [PMID: 30927013 DOI: 10.1007/s00216-019-01774-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 01/05/2023]
Abstract
G protein-coupled receptors (GPCRs), G proteins, and their signaling associates are major signal transducers that control the majority of cellular signaling and regulate key biological functions including immune, neurological, cardiovascular, and metabolic processes. These pathways are targeted by over one-third of drugs on the market; however, the current understanding of their function is limited and primarily derived from cell-destructive approaches providing an ensemble of static, multi-cell information about the status and composition of molecules. Spatiotemporal behavior of molecules involved is crucial to understanding in vivo cell behaviors both in health and disease, and the advent of genetically encoded fluorescence proteins and small fluorophore-based biosensors has facilitated the mapping of dynamic signaling in cells with subcellular acuity. Since we and others have developed optogenetic methods to regulate GPCR-G protein signaling in single cells and subcellular regions using dedicated wavelengths, the desire to develop and adopt optogenetically amenable assays to measure signaling has motivated us to take a broader look at the available optical tools and approaches compatible with measuring single-cell and subcellular GPCR-G protein signaling. Here we review such key optical approaches enabling the examination of GPCR, G protein, secondary messenger, and downstream molecules such as kinase and lipid signaling in living cells. The methods reviewed employ both fluorescence and bioluminescence detection. We not only further elaborate the underlying principles of these sensors but also discuss the experimental criteria and limitations to be considered during their use in single-cell and subcellular signal mapping.
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47
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ERK Activity Imaging During Migration of Living Cells In Vitro and In Vivo. Int J Mol Sci 2019; 20:ijms20030679. [PMID: 30764494 PMCID: PMC6387119 DOI: 10.3390/ijms20030679] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Extracellular signal-regulated kinase (ERK) is a major downstream factor of the EGFR-RAS-RAF signalling pathway, and thus the role of ERK in cell growth has been widely examined. The development of biosensors based on fluorescent proteins has enabled us to measure ERK activities in living cells, both after growth factor stimulation and in its absence. Long-term imaging unexpectedly revealed the oscillative activation of ERK in an epithelial sheet or a cyst in vitro. Studies using transgenic mice expressing the ERK biosensor have revealed inhomogeneous ERK activities among various cell species. In vivo Förster (or fluorescence) resonance energy transfer (FRET) imaging shed light on a novel role of ERK in cell migration. Neutrophils and epithelial cells in various organs such as intestine, skin, lung and bladder showed spatio-temporally different cell dynamics and ERK activities. Experiments using inhibitors confirmed that ERK activities are required for various pathological responses, including epithelial repair after injuries, inflammation, and niche formation of cancer metastasis. In conclusion, biosensors for ERK will be powerful and valuable tools to investigate the roles of ERK in situ.
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48
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Goswami M, Wang X, Zhang P, Xiao W, Karlen SJ, Li Y, Zawadzki RJ, Burns ME, Lam KS, Pugh EN. Novel window for cancer nanotheranostics: non-invasive ocular assessments of tumor growth and nanotherapeutic treatment efficacy in vivo. BIOMEDICAL OPTICS EXPRESS 2019; 10:151-166. [PMID: 30775090 PMCID: PMC6363190 DOI: 10.1364/boe.10.000151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 05/03/2023]
Abstract
In cancer research there is a fundamental need for animal models that allow the in vivo longitudinal visualization and quantification of tumor development, nanotherapeutic delivery, the tumor microenvironment including blood vessels, macrophages, fibroblasts, immune cells, and extracellular matrix, and the tissue response to treatment. To address this need, we developed a novel mouse ocular xenograft model. Green fluorescent protein (GFP) expressing human glioblastoma cells (between 500 and 10,000) were implanted into the subretinal space of immunodeficient mice (56 eyes). The resultant xenografts were imaged in vivo non-invasively with combined fluorescence scanning laser ophthalmoscopy (SLO) and volumetric optical coherence tomography (OCT) for a period up to several months. Most xenografts exhibited a latent phase followed by a stable or rapidly increasing volume, but about 1/3 underwent spontaneous remission. After prescribed growth, a population of tumors was treated with intravenously delivered doxorubicin-containing porphyrin and cholic acid-based nanoparticles ("nanodox"). Fluorescence resonance energy transfer (FRET) emission (doxorubicin → porphyrin) was used to localize nanodox in the xenografts, and 690 nm light exposure to activate it. Such photo-nanotherapy was highly effective in reducing tumor volume. Histopathology and flow cytometry revealed CD4 + and CD8 + immune cell infiltration of xenografts. Overall, the ocular model shows potential for examining the relationships between neoplastic growth, neovascularization and other features of the immune microenvironment, and for evaluating treatment response longitudinally in vivo.
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Affiliation(s)
- Mayank Goswami
- EyePod Small Animal Ocular Imaging Laboratory, University of California, Davis, CA 95616, USA
- Currently with Department of Physics, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Xinlei Wang
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, USA
| | - Pengfei Zhang
- EyePod Small Animal Ocular Imaging Laboratory, University of California, Davis, CA 95616, USA
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine and Comprehensive Cancer Center, University of California, Davis, Sacramento, CA 95817, USA
| | - Sarah J Karlen
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, USA
| | - Yuanpei Li
- Department of Biochemistry and Molecular Medicine and Comprehensive Cancer Center, University of California, Davis, Sacramento, CA 95817, USA
| | - Robert J Zawadzki
- EyePod Small Animal Ocular Imaging Laboratory, University of California, Davis, CA 95616, USA
- Vision Science and Advanced Retinal Imaging Laboratory (VSRI) Department of Ophthalmology and Vision Science, University of California, Davis, CA 95616, USA
| | - Marie E Burns
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine and Comprehensive Cancer Center, University of California, Davis, Sacramento, CA 95817, USA
| | - Edward N Pugh
- EyePod Small Animal Ocular Imaging Laboratory, University of California, Davis, CA 95616, USA
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95616, USA
- Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA
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49
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE, Bivona TG, Lim WA. Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway. Science 2018; 361:361/6405/eaao3048. [PMID: 30166458 DOI: 10.1126/science.aao3048] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/16/2018] [Indexed: 12/16/2022]
Abstract
The Ras-Erk (extracellular signal-regulated kinase) pathway encodes information in its dynamics; the duration and frequency of Erk activity can specify distinct cell fates. To enable dynamic encoding, temporal information must be accurately transmitted from the plasma membrane to the nucleus. We used optogenetic profiling to show that both oncogenic B-Raf mutations and B-Raf inhibitors can cause corruption of this transmission, so that short pulses of input Ras activity are distorted into abnormally long Erk outputs. These changes can reshape downstream transcription and cell fates, resulting in improper decisions to proliferate. These findings illustrate how altered dynamic signal transmission properties, and not just constitutively increased signaling, can contribute to cell proliferation and perhaps cancer, and how optogenetic profiling can dissect mechanisms of signaling dysfunction in disease.
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Affiliation(s)
- L J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A J Sabnis
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A Mitchell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Garbarino
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Toettcher
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - T G Bivona
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - W A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
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