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Ong Q, Lim LTR, Goh C, Liao Y, Chan SE, Lim CJY, Kam V, Yap J, Tseng T, Desrouleaux R, Wang LC, Ler SG, Lim SL, Kim SY, Sobota RM, Bennett AM, Han W, Yang X. Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT. Nat Chem Biol 2025; 21:300-308. [PMID: 39543398 DOI: 10.1038/s41589-024-01770-7] [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: 07/03/2021] [Accepted: 10/03/2024] [Indexed: 11/17/2024]
Abstract
The post-translational modification of intracellular proteins through O-linked β-N-acetylglucosamine (O-GlcNAc) is a conserved regulatory mechanism in multicellular organisms. Catalyzed by O-GlcNAc transferase (OGT), this dynamic modification has an essential role in signal transduction, gene expression, organelle function and systemic physiology. Here, we present Opto-OGT, an optogenetic probe that allows for precise spatiotemporal control of OGT activity through light stimulation. By fusing a photosensitive cryptochrome protein to OGT, Opto-OGT can be robustly and reversibly activated with high temporal resolution by blue light and exhibits minimal background activity without illumination. Transient activation of Opto-OGT results in mTORC activation and AMPK suppression, which recapitulate nutrient-sensing signaling. Furthermore, Opto-OGT can be customized to localize to specific subcellular sites. By targeting OGT to the plasma membrane, we demonstrate the downregulation of site-specific AKT phosphorylation and signaling outputs in response to insulin stimulation. Thus, Opto-OGT is a powerful tool for defining the role of O-GlcNAcylation in cell signaling and physiology.
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Affiliation(s)
- Qunxiang Ong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Ler Ting Rachel Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Cameron Goh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yilie Liao
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Sher En Chan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Crystal Jing Yi Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Valerie Kam
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jerome Yap
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Tiffany Tseng
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Reina Desrouleaux
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Loo Chien Wang
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siok Ghee Ler
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Lan Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sun-Yee Kim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Anton M Bennett
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Weiping Han
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Xiaoyong Yang
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, USA.
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2
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Huang Q, Hu B, Zhang P, Yuan Y, Yue S, Chen X, Liang J, Tang Z, Zhang B. Neuroscience of cancer: unraveling the complex interplay between the nervous system, the tumor and the tumor immune microenvironment. Mol Cancer 2025; 24:24. [PMID: 39825376 PMCID: PMC11740516 DOI: 10.1186/s12943-024-02219-0] [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: 11/21/2024] [Accepted: 12/26/2024] [Indexed: 01/20/2025] Open
Abstract
The study of the multifaceted interactions between neuroscience and cancer is an emerging field with significant implications for understanding tumor biology and the innovation in therapeutic approaches. Increasing evidence suggests that neurological functions are connected with tumorigenesis. In particular, the peripheral and central nervous systems, synapse, neurotransmitters, and neurotrophins affect tumor progression and metastasis through various regulatory approaches and the tumor immune microenvironment. In this review, we summarized the neurological functions that affect tumorigenesis and metastasis, which are controlled by the central and peripheral nervous systems. We also explored the roles of neurotransmitters and neurotrophins in cancer progression. Moreover, we examined the interplay between the nervous system and the tumor immune microenvironment. We have also identified drugs that target the nervous system for cancer treatment. In this review we present the work supporting that therapeutic agent targeting the nervous system could have significant potential to improve cancer therapy.
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Affiliation(s)
- Qibo Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, NHC Key Laboratory of Organ Transplantation, Wuhan, China
| | - Bai Hu
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Zhang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ye Yuan
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Shiwei Yue
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, NHC Key Laboratory of Organ Transplantation, Wuhan, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China.
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China.
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, NHC Key Laboratory of Organ Transplantation, Wuhan, China.
| | - Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China.
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China.
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, NHC Key Laboratory of Organ Transplantation, Wuhan, China.
| | - Zhouping Tang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China.
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China.
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, NHC Key Laboratory of Organ Transplantation, Wuhan, China.
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3
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Muth LT, Van Bogaert INA. Let it stick: Strategies and applications for intracellular plasma membrane targeting of proteins in Saccharomyces cerevisiae. Yeast 2024; 41:315-329. [PMID: 38444057 DOI: 10.1002/yea.3933] [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: 07/06/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Lipid binding domains and protein lipidations are essential features to recruit proteins to intracellular membranes, enabling them to function at specific sites within the cell. Membrane association can also be exploited to answer fundamental and applied research questions, from obtaining insights into the understanding of lipid metabolism to employing them for metabolic engineering to redirect fluxes. This review presents a broad catalog of membrane binding strategies focusing on the plasma membrane of Saccharomyces cerevisiae. Both lipid binding domains (pleckstrin homology, discoidin-type C2, kinase associated-1, basic-rich and bacterial phosphoinositide-binding domains) and co- and post-translational lipidations (prenylation, myristoylation and palmitoylation) are introduced as tools to target the plasma membrane. To provide a toolset of membrane targeting modules, respective candidates that facilitate plasma membrane targeting are showcased including their in vitro and in vivo properties. The relevance and versatility of plasma membrane targeting modules are further highlighted by presenting a selected set of use cases.
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Affiliation(s)
- Liv Teresa Muth
- Department of Biotechnology, Centre for Synthetic Biology, Ghent University, Ghent, Belgium
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4
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Wang Y, Bi Z, Song Y, Duan L, Chen SC. Selective activation of photoactivatable fluorescent protein based on binary holography. BIOMEDICAL OPTICS EXPRESS 2024; 15:3382-3393. [PMID: 38855656 PMCID: PMC11161383 DOI: 10.1364/boe.519531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 06/11/2024]
Abstract
The ability to deliver laser doses to different target locations with high spatial and temporal resolution has been a long-sought goal in photo-stimulation and optogenetics research via, for example, photoactivatable proteins. These light-sensitive proteins undergo conformational changes upon photoactivation, serving functions such as triggering fluorescence, modulating ion channel activities, or initiating biochemical reactions within cells. Conventionally, photo-stimulation on light-sensitive proteins is performed by serially scanning a laser focus or via 2D projection, which is limited by relatively low spatiotemporal resolution. In this work, we present a programmable two-photon stimulation method based on a digital micromirror device (DMD) and binary holography to perform the activation of photoactivatable green fluorescent protein (PAGFP) in live cells. This method achieved grayscale and 3D selective PAGFP activation with subcellular resolution. In the experiments, we demonstrated the 3D activation capability and investigated the diffusion dynamics of activated PAGFP on the cell membrane. A regional difference in cell membrane diffusivity was observed, indicating the great potential of our approach in interrogating the spatiotemporal dynamics of cellular processes inside living cells.
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Affiliation(s)
- Yintao Wang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
- Centre for Perceptual and Interactive Intelligence (CPII), Hong Kong Science Park, N.T., Hong Kong SAR, China
| | - Zhenyu Bi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Yutong Song
- Department of Biomedical Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Liting Duan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
| | - Shih-Chi Chen
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, N.T., Hong Kong SAR, China
- Centre for Perceptual and Interactive Intelligence (CPII), Hong Kong Science Park, N.T., Hong Kong SAR, China
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5
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Takada A, Asano T, Nakahama KI, Ono T, Nakata T, Ishii T. Development of an optogenetics tool, Opto-RANK, for control of osteoclast differentiation using blue light. Sci Rep 2024; 14:1749. [PMID: 38242937 PMCID: PMC10799070 DOI: 10.1038/s41598-024-52056-w] [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: 10/24/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
Optogenetics enables precise regulation of intracellular signaling in target cells. However, the application of optogenetics to induce the differentiation of precursor cells and generate mature cells with specific functions has not yet been fully explored. Here, we focused on osteoclasts, which play an important role in bone remodeling, to develop a novel optogenetics tool, Opto-RANK, which can manipulate intracellular signals involved in osteoclast differentiation and maturation using blue light. We engineered Opto-RANK variants, Opto-RANKc and Opto-RANKm, and generated stable cell lines through retroviral transduction. Differentiation was induced by blue light, and various assays were conducted for functional analysis. Osteoclast precursor cells expressing Opto-RANK differentiated into multinucleated giant cells on light exposure and displayed upregulation of genes normally induced in differentiated osteoclasts. Furthermore, the differentiated cells exhibited bone-resorbing activities, with the possibility of spatial control of the resorption by targeted light illumination. These results suggested that Opto-RANK cells differentiated by light possess the features of osteoclasts, both morphological and functional. Thus, Opto-RANK should be useful for detailed spatiotemporal analysis of intracellular signaling during osteoclast differentiation and the development of new therapies for various bone diseases.
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Affiliation(s)
- Aiko Takada
- Department of Orthodontic Science, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Toshifumi Asano
- Department of Cell Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Ken-Ichi Nakahama
- Department of Cellular Physiological Chemistry, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Takashi Ono
- Department of Orthodontic Science, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Takao Nakata
- Department of Cell Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
- The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
| | - Tomohiro Ishii
- Department of Cell Biology, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
- Present Address: Center for Integrative Biosciences, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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6
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Xu W, Dahlke SP, Sung M, Samal B, Emery AC, Elkahloun A, Eiden LE. ERK-dependent induction of the immediate-early gene Egr1 and the late gene Gpr50 contribute to two distinct phases of PACAP Gs-GPCR signaling for neuritogenesis. J Neuroendocrinol 2022; 34:e13182. [PMID: 35841324 PMCID: PMC9529758 DOI: 10.1111/jne.13182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Gs-coupled GPCR-stimulated neuritogenesis in PC12 and NS-1 - cells depends on activation of the MAP kinase ERK. Here, we examine changes in ERK activation (phosphorylation), and the time course of ERK-dependent gene induction, to seek transcriptional determinants for this process. Quenching of ERK activation by inhibition of MEK with U0126 at any time point for at least 24 h following addition of PACAP resulted in arrest of neurite formation. Changes in the transcriptome profile throughout this time period revealed at least two phases of gene induction: an early phase dominated by induction of immediate-early genes, and a later phase of gene induction after 4-6 h of exposure to PACAP with persistent elevation of phospho-ERK levels. Genes induced by PACAP in both phases consisted in those whose induction was dependent on ERK (i.e., blocked by U0126), and some whose induction was blocked by the protein kinase A inhibitor H89. ERK-dependent "late gene" transcripts included Gpr50, implicated earlier in facilitation of NGF-induced neurite formation in NS-1 cells. Gpr50 induction by PACAP, but not NGF, was dependent on the guanine nucleotide exchange factor RapGEF2, which has been shown to be required for PACAP-induced neuritogenesis in NS-1 cells. Expression of a Gpr50-directed shRNA lowered basal levels of Gpr50 mRNA and attenuated Gpr50 mRNA and GPR50 protein induction by PACAP, with a corresponding attenuation of PACAP-induced neuritogenesis. Gs-GPCR-stimulated neuritogenesis first requires immediate-early gene induction, including that of Egr1 (Zif268/NGF1A/Krox24) as previously reported. This early phase of gene induction, however, is insufficient to maintain the neuritogenic process without ERK-dependent induction of additional late genes, including Gpr50, upon continuous exposure to neurotrophic neuropeptide. Early (Egr1) and late (Gpr50) gene induction by NGF, like that for PACAP, was inhibited by U0126, but was independent of RapGEF2, confirming distinct modes of ERK activation by Gs-coupled GPCRs and neurotrophic tyrosine receptor kinases, converging on a final common ERK-dependent signaling pathway for neuritogenesis.
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Affiliation(s)
- Wenqin Xu
- Section on Molecular Neuroscience, National Institute of Mental Health-Intramural Research Program
| | - Sam P. Dahlke
- Section on Molecular Neuroscience, National Institute of Mental Health-Intramural Research Program
| | - Michelle Sung
- Section on Molecular Neuroscience, National Institute of Mental Health-Intramural Research Program
| | - Babru Samal
- Section on Molecular Neuroscience, National Institute of Mental Health-Intramural Research Program
| | - Andrew C. Emery
- Section on Molecular Neuroscience, National Institute of Mental Health-Intramural Research Program
| | - Abdel Elkahloun
- Microarray Core, National Human Genome Research Institute, Bethesda, MD, USA
| | - Lee E. Eiden
- Section on Molecular Neuroscience, National Institute of Mental Health-Intramural Research Program
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Alizadeh S, Esmaeili A, Barar J, Omidi Y. Optogenetics: A new tool for cancer investigation and treatment. BIOIMPACTS 2022; 12:295-299. [PMID: 35975208 PMCID: PMC9376163 DOI: 10.34172/bi.2021.22179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/21/2021] [Accepted: 09/30/2021] [Indexed: 11/24/2022]
Abstract
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Despite the progress made in the diagnosis and treatment of cancer, it has remained the second cause of death in industrial countries. Cancer is a complex multifaceted disease with unique genomic and proteomic hallmarks. Optogenetics is a biological approach, in which the light-sensitive protein modules in combination with effector proteins that trigger reversibly fundamental cell functions without producing a long-term effect. The technology was first used to address some key issues in neurology. Later on, it was also used for other diseases such as cancer. In the case of cancer, there exist several signaling pathways with key proteins that are involved in the initiation and/or progression of cancer. Such aberrantly expressed proteins and the related signaling pathways need to be carefully investigated in terms of cancer diagnosis and treatment, which can be managed with optogenetic tools. Notably, optogenetics systems offer some advantages compared to the traditional methods, including spatial-temporal control of protein or gene expression, cost-effective and fewer off-target side effects, and reversibility potential. Such noticeable features make this technology a unique drug-free approach for diagnosis and treatment of cancer. It can be used to control tumor cells, which is a favorable technique to investigate the heterogeneous and complex features of cancerous cells. Remarkably, optogenetics approaches can provide us with outstanding tool to extend our understanding of how cells perceive, respond, and behave in meeting with complex signals, particularly in terms of cancer evasion from the anticancer immune system functions.
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Affiliation(s)
- Siamak Alizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Esmaeili
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida 33328, USA
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8
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Crossman SH, Janovjak H. Light-activated receptor tyrosine kinases: Designs and applications. Curr Opin Pharmacol 2022; 63:102197. [PMID: 35245796 DOI: 10.1016/j.coph.2022.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
Abstract
Receptor tyrosine kinases (RTKs) are a large and essential membrane receptor family. The molecular mechanisms and physiological consequences of RTK activation depend on, for example, ligand identity, subcellular localization, and developmental or disease stage. In the past few years, genetically-encoded light-activated RTKs (Opto-RTKs) have been developed to dissect these complexities by providing reversible and spatio-temporal control over cell signaling. These methods have very recently matured to include highly-sensitive multi-color actuators. The new ability to regulate RTK activity with high precision has been recently harnessed to gain mechanistic insights in subcellular, tissue, and animal models. Because of their sophisticated engineering, Opto-RTKs may only mirror some aspects of natural activation mechanisms but nevertheless offer unique opportunities to study RTK signaling and physiology.
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Affiliation(s)
- Samuel H Crossman
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia.
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9
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Zhao X, Tang W, Wang H, He H. Femtosecond-laser stimulation induces senescence of tumor cells in vitro and in vivo. BIOMEDICAL OPTICS EXPRESS 2022; 13:791-804. [PMID: 35284179 PMCID: PMC8884195 DOI: 10.1364/boe.449456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 05/30/2023]
Abstract
Tumor cells present anti-apoptosis and abnormal proliferation during development. Senescence and stemness of tumor cells play key roles in tumor development and malignancy. In this study, we show the transient stimulation by a single-time scanning of tightly focused femtosecond laser to tumor cells can modulate the stemness and senescence in vitro and in vivo. The laser-induced cellular senescence and stemness present distinct transitions in vitro and in vivo. The cells 1.2 mm deep in tumor tissue are found with significant senescence induced by the transient photostimulations in 100-200 µm shallow layer in vivo, which suppresses the growth of whole tumor in living mice.
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10
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Bansal A, Shikha S, Zhang Y. Towards translational optogenetics. Nat Biomed Eng 2022; 7:349-369. [PMID: 35027688 DOI: 10.1038/s41551-021-00829-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/21/2021] [Indexed: 02/07/2023]
Abstract
Optogenetics is widely used to interrogate the neural circuits underlying disease and has most recently been harnessed for therapeutic applications. The optogenetic toolkit consists of light-responsive proteins that modulate specific cellular functions, vectors for the delivery of the transgenes that encode the light-responsive proteins to targeted cellular populations, and devices for the delivery of light of suitable wavelengths at effective fluence rates. A refined toolkit with a focus towards translational uses would include efficient and safer viral and non-viral gene-delivery vectors, increasingly red-shifted photoresponsive proteins, nanomaterials that efficiently transduce near-infrared light deep into tissue, and wireless implantable light-delivery devices that allow for spatiotemporally precise interventions at clinically relevant tissue depths. In this Review, we examine the current optogenetics toolkit and the most notable preclinical and translational uses of optogenetics, and discuss future methodological and translational developments and bottlenecks.
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Affiliation(s)
- Akshaya Bansal
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Swati Shikha
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore
| | - Yong Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore. .,NUS Suzhou Research Institute, Suzhou, Jiangsu, P. R. China.
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11
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Shen Y, Luchetti A, Fernandes G, Do Heo W, Silva AJ. The emergence of molecular systems neuroscience. Mol Brain 2022; 15:7. [PMID: 34983613 PMCID: PMC8728933 DOI: 10.1186/s13041-021-00885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Systems neuroscience is focused on how ensemble properties in the brain, such as the activity of neuronal circuits, gives rise to internal brain states and behavior. Many of the studies in this field have traditionally involved electrophysiological recordings and computational approaches that attempt to decode how the brain transforms inputs into functional outputs. More recently, systems neuroscience has received an infusion of approaches and techniques that allow the manipulation (e.g., optogenetics, chemogenetics) and imaging (e.g., two-photon imaging, head mounted fluorescent microscopes) of neurons, neurocircuits, their inputs and outputs. Here, we will review novel approaches that allow the manipulation and imaging of specific molecular mechanisms in specific cells (not just neurons), cell ensembles and brain regions. These molecular approaches, with the specificity and temporal resolution appropriate for systems studies, promise to infuse the field with novel ideas, emphases and directions, and are motivating the emergence of a molecularly oriented systems neuroscience, a new discipline that studies how the spatial and temporal patterns of molecular systems modulate circuits and brain networks, and consequently shape the properties of brain states and behavior.
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Affiliation(s)
- Yang Shen
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Alessandro Luchetti
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Giselle Fernandes
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Alcino J Silva
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA.
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12
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Abstract
Research on type 1 rhodopsins spans now a history of 50 years. Originally, just archaeal ion pumps and sensors have been discovered. However, with modern genetic techniques and gene sequencing tools, more and more proteins were identified in all kingdoms of life. Spectroscopic and other biophysical studies revealed quite diverse functions. Ion pumps, sensors, and channels are imprinted in the same seven-helix transmembrane protein scaffold carrying a retinal prosthetic group. In this review, molecular biology methods are described, which enabled the elucidation of their function and structure leading to optogenetic applications.
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Affiliation(s)
- Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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13
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Bourke AM, Kennedy MJ. Spatial and Temporal Control of Protein Secretion with Light. Methods Mol Biol 2022; 2473:29-45. [PMID: 35819757 PMCID: PMC10907983 DOI: 10.1007/978-1-0716-2209-4_4] [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] [Indexed: 10/17/2022]
Abstract
How newly synthesized integral membrane proteins and secreted factors are sorted and trafficked to the appropriate location in different cell types remains an important problem in cell biology. One powerful approach for elucidating the trafficking route of a specific protein is to sequester it following synthesis in the endoplasmic reticulum and trigger its release with an externally applied cue. Combined with fluorescent probes, this approach can be used to directly visualize each trafficking step as cargo molecules progress through the different organelles of the secretory network. Here, we discuss design strategies and practical implementation of an inducible protein secretion system we recently developed (zapalog mediated ER trap: zapERtrap) that allows one to use light to initiate secretory trafficking from targeted cells or subcellular domains. We provide detailed protocols for experiments using this approach to visualize protein trafficking from the endoplasmic reticulum to the plasma membrane in fibroblast cell lines and primary cultured neurons.
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Affiliation(s)
- Ashley M Bourke
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Matthew J Kennedy
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA.
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14
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The Influence of Burst-Firing EMF on Forskolin-Induced Pheochromocytoma (PC12) Plasma Membrane Extensions. NEUROSCI 2021. [DOI: 10.3390/neurosci2040028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Previous research has demonstrated that pheochromocytoma (PC12) cells treated with forskolin provides a model for the in vitro examination of neuritogenesis. Exposure to electromagnetic fields (EMFs), especially those which have been designed to mimic biological function, can influence the functions of various biological systems. We aimed to assess whether exposure of PC12 cells treated with forskolin to patterned EMF would produce more plasma membrane extensions (PME) as compared to PC12 cells treated with forskolin alone (i.e., no EMF exposure). In addition, we aimed to determine whether the differences observed between the proportion of PME of PC12 cells treated with forskolin and exposed to EMF were specific to the intensity, pattern, or timing of the applied EMF. Our results showed an overall increase in PME for PC12 cells treated with forskolin and exposed to Burst-firing EMF as compared to PC12 cells receiving forskolin alone. No other patterned EMF investigated were deemed to be effective. Furthermore, intensity and timing of the Burst-firing pattern did not significantly alter the proportion of PME of PC12 cells treated with forskolin and exposed to patterned EMF.
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15
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Abstract
Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.
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Affiliation(s)
- Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea;
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA;
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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16
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Song Y, Huang P, Liu X, Zhao Z, Wang Y, Cui B, Duan L. Light-inducible deformation of mitochondria in live cells. Cell Chem Biol 2021; 29:109-119.e3. [PMID: 34157274 DOI: 10.1016/j.chembiol.2021.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/30/2021] [Accepted: 05/26/2021] [Indexed: 12/22/2022]
Abstract
Mitochondria, the powerhouse of the cell, are dynamic organelles that undergo constant morphological changes. Increasing evidence indicates that mitochondria morphologies and functions can be modulated by mechanical cues. However, the mechano-sensing and -responding properties of mitochondria and the relation between mitochondrial morphologies and functions are unclear due to the lack of methods to precisely exert mechano-stimulation on and deform mitochondria inside live cells. Here, we present an optogenetic approach that uses light to induce deformation of mitochondria by recruiting molecular motors to the outer mitochondrial membrane via light-activated protein-protein hetero-dimerization. Mechanical forces generated by motor proteins distort the outer membrane, during which the inner mitochondrial membrane can also be deformed. Moreover, this optical method can achieve subcellular spatial precision and be combined with different optical dimerizers and molecular motors. This method presents a mitochondria-specific mechano-stimulator for studying mitochondria mechanobiology and the interplay between mitochondria shapes and functions.
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Affiliation(s)
- Yutong Song
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Peiyuan Huang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Xiaoying Liu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Zhihao Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Yijin Wang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Liting Duan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China; Shun Hing Institute of Advanced Engineering (SHIAE), The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.
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17
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Kramer MM, Lataster L, Weber W, Radziwill G. Optogenetic Approaches for the Spatiotemporal Control of Signal Transduction Pathways. Int J Mol Sci 2021; 22:5300. [PMID: 34069904 PMCID: PMC8157557 DOI: 10.3390/ijms22105300] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Biological signals are sensed by their respective receptors and are transduced and processed by a sophisticated intracellular signaling network leading to a signal-specific cellular response. Thereby, the response to the signal depends on the strength, the frequency, and the duration of the stimulus as well as on the subcellular signal progression. Optogenetic tools are based on genetically encoded light-sensing proteins facilitating the precise spatiotemporal control of signal transduction pathways and cell fate decisions in the absence of natural ligands. In this review, we provide an overview of optogenetic approaches connecting light-regulated protein-protein interaction or caging/uncaging events with steering the function of signaling proteins. We briefly discuss the most common optogenetic switches and their mode of action. The main part deals with the engineering and application of optogenetic tools for the control of transmembrane receptors including receptor tyrosine kinases, the T cell receptor and integrins, and their effector proteins. We also address the hallmarks of optogenetics, the spatial and temporal control of signaling events.
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Affiliation(s)
- Markus M. Kramer
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Levin Lataster
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
- SGBM—Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany; (M.M.K.); (L.L.); (W.W.)
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18
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Abreu N, Levitz J. Optogenetic Techniques for Manipulating and Sensing G Protein-Coupled Receptor Signaling. Methods Mol Biol 2021; 2173:21-51. [PMID: 32651908 DOI: 10.1007/978-1-0716-0755-8_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors (GPCRs) form the largest class of membrane receptors in the mammalian genome with nearly 800 human genes encoding for unique subtypes. Accordingly, GPCR signaling is implicated in nearly all physiological processes. However, GPCRs have been difficult to study due in part to the complexity of their function which can lead to a plethora of converging or diverging downstream effects over different time and length scales. Classic techniques such as pharmacological control, genetic knockout and biochemical assays often lack the precision required to probe the functions of specific GPCR subtypes. Here we describe the rapidly growing set of optogenetic tools, ranging from methods for optical control of the receptor itself to optical sensing and manipulation of downstream effectors. These tools permit the quantitative measurements of GPCRs and their downstream signaling with high specificity and spatiotemporal precision.
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Affiliation(s)
- Nohely Abreu
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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19
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Inaba H, Miao Q, Nakata T. Optogenetic control of small GTPases reveals RhoA mediates intracellular calcium signaling. J Biol Chem 2021; 296:100290. [PMID: 33453281 PMCID: PMC7949103 DOI: 10.1016/j.jbc.2021.100290] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
Rho/Ras family small GTPases are known to regulate numerous cellular processes, including cytoskeletal reorganization, cell proliferation, and cell differentiation. These processes are also controlled by Ca2+, and consequently, cross talk between these signals is considered likely. However, systematic quantitative evaluation has not yet been reported. To fill this gap, we constructed optogenetic tools to control the activity of small GTPases (RhoA, Rac1, Cdc42, Ras, Rap, and Ral) using an improved light-inducible dimer system (iLID). We characterized these optogenetic tools with genetically encoded red fluorescence intensity-based small GTPase biosensors and confirmed these optogenetic tools’ specificities. Using these optogenetic tools, we investigated calcium mobilization immediately after small GTPase activation. Unexpectedly, we found that a transient intracellular calcium elevation was specifically induced by RhoA activation in RPE1 and HeLa cells. RhoA activation also induced transient intracellular calcium elevation in MDCK and HEK293T cells, suggesting that generally RhoA induces calcium signaling. Interestingly, the molecular mechanisms linking RhoA activation to calcium increases were shown to be different among the different cell types: In RPE1 and HeLa cells, RhoA activated phospholipase C epsilon (PLCε) at the plasma membrane, which in turn induced Ca2+ release from the endoplasmic reticulum (ER). The RhoA–PLCε axis induced calcium-dependent nuclear factor of activated T cells nuclear translocation, suggesting that it does activate intracellular calcium signaling. Conversely, in MDCK and HEK293T cells, RhoA–ROCK–myosin II axis induced the calcium transients. These data suggest universal coordination of RhoA and calcium signaling in cellular processes, such as cellular contraction and gene expression.
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Affiliation(s)
- Hironori Inaba
- Department of Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Qianqian Miao
- Department of Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takao Nakata
- Department of Cell Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; The Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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20
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Mumford TR, Roth L, Bugaj LJ. Reverse and Forward Engineering Multicellular Structures with Optogenetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 16:61-71. [PMID: 33718689 PMCID: PMC7945718 DOI: 10.1016/j.cobme.2020.100250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how cells self-organize into functional higher-order structures is of great interest, both towards deciphering animal development, as well as for our ability to predictably build custom tissues to meet research and therapeutic needs. The proper organization of cells across length-scales results from interconnected and dynamic networks of molecules and cells. Optogenetic probes provide dynamic and tunable control over molecular events within cells, and thus represent a powerful approach to both dissect and control collective cell behaviors. Here we emphasize the breadth of the optogenetic toolkit and discuss how these methods have already been used to reverse-engineer the design rules of developing organisms. We also offer our perspective on the rich potential for optogenetics to power forward-engineering of tissue assembly towards the generation of bespoke tissues with user-defined properties.
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Affiliation(s)
- Thomas R. Mumford
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lee Roth
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lukasz J. Bugaj
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
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21
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Wang Q, Fan H, Li F, Skeeters SS, Krishnamurthy VV, Song Y, Zhang K. Optical control of ERK and AKT signaling promotes axon regeneration and functional recovery of PNS and CNS in Drosophila. eLife 2020; 9:57395. [PMID: 33021199 PMCID: PMC7567606 DOI: 10.7554/elife.57395] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Neuroregeneration is a dynamic process synergizing the functional outcomes of multiple signaling circuits. Channelrhodopsin-based optogenetics shows the feasibility of stimulating neural repair but does not pin down specific signaling cascades. Here, we utilized optogenetic systems, optoRaf and optoAKT, to delineate the contribution of the ERK and AKT signaling pathways to neuroregeneration in live Drosophila larvae. We showed that optoRaf or optoAKT activation not only enhanced axon regeneration in both regeneration-competent and -incompetent sensory neurons in the peripheral nervous system but also allowed temporal tuning and proper guidance of axon regrowth. Furthermore, optoRaf and optoAKT differ in their signaling kinetics during regeneration, showing a gated versus graded response, respectively. Importantly in the central nervous system, their activation promotes axon regrowth and functional recovery of the thermonociceptive behavior. We conclude that non-neuronal optogenetics targets damaged neurons and signaling subcircuits, providing a novel strategy in the intervention of neural damage with improved precision. Most cells have a built-in regeneration signaling program that allows them to divide and repair. But, in the cells of the central nervous system, which are called neurons, this program is ineffective. This is why accidents and illnesses affecting the brain and spinal cord can cause permanent damage. Reactivating regeneration in neurons could help them repair, but it is not easy. Certain small molecules can switch repair signaling programs back on. Unfortunately, these molecules diffuse easily through tissues, spreading around the body and making it hard to target individual damaged cells. This both hampers research into neuronal repair and makes treatments directed at healing damage to the nervous system more likely to have side-effects. It is unclear whether reactivating regeneration signaling in individual neurons is possible. One way to address this question is to use optogenetics. This technique uses genetic engineering to fuse proteins that are light-sensitive to proteins responsible for relaying signals in the cell. When specific wavelengths of light hit the light-sensitive proteins, the fused signaling proteins switch on, leading to the activation of any proteins they control, for example, those involved in regeneration. Wang et al. used optogenetic tools to determine if light can help repair neurons in fruit fly larvae. First, a strong laser light was used to damage an individual neuron in a fruit fly larva that had been genetically modified so that blue light would activate the regeneration program in its neurons. Then, Wang et al. illuminated the cell with dim blue light, switching on the regeneration program. Not only did this allow the neuron to repair itself, it also allowed the light to guide its regeneration. By focusing the blue light on the damaged end of the neuron, it was possible to guide the direction of the cell's growth as it regenerated. Regeneration programs in flies and mammals involve similar signaling proteins, but blue light does not penetrate well into mammalian tissues. This means that further research into LEDs that can be implanted may be necessary before neuronal repair experiments can be performed in mammals. In any case, the ability to focus treatment on individual neurons paves the way for future work into the regeneration of the nervous system, and the combination of light and genetics could reveal more about how repair signals work.
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Affiliation(s)
- Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
| | - Huaxun Fan
- Department of Biochemistry, Urbana, United States
| | - Feng Li
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
| | | | | | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
| | - Kai Zhang
- Department of Biochemistry, Urbana, United States.,Neuroscience Program, Urbana, United States.,Center for Biophysics and Quantitative Biology, Urbana, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
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22
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Shaaya M, Fauser J, Zhurikhina A, Conage-Pough JE, Huyot V, Brennan M, Flower CT, Matsche J, Khan S, Natarajan V, Rehman J, Kota P, White FM, Tsygankov D, Karginov AV. Light-regulated allosteric switch enables temporal and subcellular control of enzyme activity. eLife 2020; 9:e60647. [PMID: 32965214 PMCID: PMC7577742 DOI: 10.7554/elife.60647] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 12/24/2022] Open
Abstract
Engineered allosteric regulation of protein activity provides significant advantages for the development of robust and broadly applicable tools. However, the application of allosteric switches in optogenetics has been scarce and suffers from critical limitations. Here, we report an optogenetic approach that utilizes an engineered Light-Regulated (LightR) allosteric switch module to achieve tight spatiotemporal control of enzymatic activity. Using the tyrosine kinase Src as a model, we demonstrate efficient regulation of the kinase and identify temporally distinct signaling responses ranging from seconds to minutes. LightR-Src off-kinetics can be tuned by modulating the LightR photoconversion cycle. A fast cycling variant enables the stimulation of transient pulses and local regulation of activity in a selected region of a cell. The design of the LightR module ensures broad applicability of the tool, as we demonstrate by achieving light-mediated regulation of Abl and bRaf kinases as well as Cre recombinase.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Anastasia Zhurikhina
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of MedicineAtlantaUnited States
| | - Jason E Conage-Pough
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Vincent Huyot
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Martin Brennan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Cameron T Flower
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Program in Computational and Systems Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Jacob Matsche
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Shahzeb Khan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Viswanathan Natarajan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
- University of Illinois Cancer Center, The University of Illinois at ChicagoChicagoUnited States
- Division of Cardiology, Department of Medicine, The University of Illinois, College of MedicineChicagoUnited States
| | - Pradeep Kota
- Marsico Lung Institute, Cystic Fibrosis Center and Department of Medicine, University of North CarolinaChapel HillUnited States
| | - Forest M White
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Program in Computational and Systems Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of MedicineAtlantaUnited States
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
- University of Illinois Cancer Center, The University of Illinois at ChicagoChicagoUnited States
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23
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Lu X, Shen Y, Campbell RE. Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators. Int J Mol Sci 2020; 21:E6522. [PMID: 32906617 PMCID: PMC7555876 DOI: 10.3390/ijms21186522] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/17/2022] Open
Abstract
Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).
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Affiliation(s)
- Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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24
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Matsuoka H, Pokorski M, Harada K, Yoshimura R, Inoue M. Expression of p11 and Heteromeric TASK Channels in Rat Carotid Body Glomus Cells and Nerve Growth Factor-differentiated PC12 Cells. J Histochem Cytochem 2020; 68:679-690. [PMID: 32886017 DOI: 10.1369/0022155420955246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
TWIK-related acid-sensitive K+ (TASK) homomeric channels, TASK1 and TASK3, are present in PC12 cells. The channels do not heteromerize due plausibly to a lack of p11 protein. Single-channel recording reveals that most of the rat carotid body (CB) glomus cells express heteromeric TASK1-TASK3 channels, but the presence of p11 in glomus cells has not yet been verified. TASK1, but not TASK3, binds to p11, which has a retention signal for the endoplasmic reticulum. We hypothesized that p11 could facilitate heteromeric TASK1-TASK3 formation in glomus cells. We investigated this hypothesis in isolated immunocytochemically identified rat CB glomus cells. The findings were that glomus cells expressed p11-like immunoreactive (IR) material, and TASK1- and TASK3-like IR material mainly coincided in the cytoplasm. The proximity ligation assay showed that TASK1 and TASK3 heteromerized. In separate experiments, supporting evidence for the major role of p11 for channel heteromerization was provided in PC12 cells stimulated by nerve growth factor. p11 production took place there via multiple signaling pathways comprising mitogen-activated protein kinase and phospholipase C, and heteromeric TASK1-TASK3 channels were formed. We conclude that p11 is expressed and TASK1 and TASK3 heteromerize in rat CB glomus cells.
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Affiliation(s)
- Hidetada Matsuoka
- Department of Cell and Systems Physiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Mieczyslaw Pokorski
- Department of Cell and Systems Physiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan.,Institute of Sciences, University of Opole, Opole, Poland
| | - Keita Harada
- Department of Cell and Systems Physiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Reiji Yoshimura
- Department of Psychiatry, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Masumi Inoue
- Department of Cell and Systems Physiology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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25
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Krishnaswamy B, McClean MN. Shining light on molecular communication. PROCEEDINGS OF THE 7TH ACM INTERNATIONAL CONFERENCE ON NANOSCALE COMPUTING AND COMMUNICATION : VIRTUAL CONFERENCE, SEPTEMBER 23-25, 2020 : NANOCOM 2020. ACM INTERNATIONAL CONFERENCE ON NANOSCALE COMPUTING AND COMMUNICATION (7TH : 2020 :... 2020; 2020:11. [PMID: 35425948 PMCID: PMC9006593 DOI: 10.1145/3411295.3411307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecules and combinations of molecules are the natural communication currency of microbes; microbes have evolved and been engineered to sense a variety of compounds, often with exquisite sensitivity. The availability of microbial biosensors, combined with the ability to genetically engineer biological circuits to process information, make microbes attractive bionanomachines for propagating information through molecular communication (MC) networks. However, MC networks built entirely of biological components suffer a number of limitations. They are extremely slow due to processing and propagation delays and must employ simple algorithms due to the still limited computational capabilities of biological circuits. In this work, we propose a hybrid bio-electronic framework which utilizes biological components for sensing but offloads processing and computation to traditional electronic systems and communication infrastructure. This is achieved by using tools from the burgeoning field of optogenetics to trigger biosensing through an optoelectronic interface, alleviating the need for computation and communication in the biological domain.
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Nakamura A, Oki C, Sawada S, Yoshii T, Kuwata K, Rudd AK, Devaraj NK, Noma K, Tsukiji S. Designer Palmitoylation Motif-Based Self-Localizing Ligand for Sustained Control of Protein Localization in Living Cells and Caenorhabditis elegans. ACS Chem Biol 2020; 15:837-843. [PMID: 32182034 DOI: 10.1021/acschembio.0c00014] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inducing protein translocation to the plasma membrane (PM) is an important approach for manipulating diverse signaling molecules/pathways in living cells. We previously devised a new chemogenetic system, in which a protein fused to Escherichia coli dihydrofolate reductase (eDHFR) can be rapidly translocated from the cytoplasm to the PM using a trimethoprim (TMP)-based self-localizing ligand (SL), mgcTMP. However, mgcTMP-induced protein translocation turned out to be transient and spontaneously reversed within 1 h, limiting its application. Here, we first demonstrated that the spontaneous reverse translocation was caused by cellular degradation of mgcTMP, presumably by proteases. To address this problem, we newly developed a proteolysis-resistant SL, mDcTMP. This mDcTMP now allows sustained PM localization of eDHFR-fusion proteins (over several hours to a day), and it was applicable to inducing prolonged signal activation and cell differentiation. mDcTMP also worked in live nematodes, making it an attractive new tool for probing and controlling living systems.
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Affiliation(s)
- Akinobu Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shunsuke Sawada
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Andrew K. Rudd
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Kentaro Noma
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Group of Nutritional Neuroscience, Neuroscience Institute, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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Blue light-triggered optogenetic system for treating uveal melanoma. Oncogene 2019; 39:2118-2124. [PMID: 31811271 DOI: 10.1038/s41388-019-1119-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 11/09/2022]
Abstract
Uveal melanoma is the most common intraocular primary malignancy in adults and has been considered a fatal disease for decades. Optogenetics is an emerging technique that can control the activation of signaling components via irradiation with visible light. The clinical translation of optogenetics has been limited because of the need for surgical implantation of electrodes and relatively shallow tissue penetration. As visible light easily penetrates the eyes, we hypothesized that an optogenetics approach can be an effective treatment of uveal melanoma without surgery. In this study, we evaluated the feasibility of this strategy by using a genetically encoded optogenetic system based on reversible blue light-induced binding pairs between Fas-CIB1-EGFP and CRY2-mCherry-FADD. Subretinal injection of B16 cells was performed to create a uveal melanoma model. Plasmids pairs were co-transfected into B16 cells. We found that blue light irradiation dynamically controlled the translocation of FADD to Fas on the plasma membrane and induced the apoptosis of B16 cells transfected with the optogenetic nanosystem in vitro. Moreover, the blue light-controlled optogenetic nanosystem suppressed the growth of uveal melanoma in vivo by inducing apoptosis. These results suggest that light-controlled optogenetic therapy can be used as a potential novel therapeutic strategy for uveal melanoma.
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Mondal P, Krishnamurthy VV, Sharum SR, Haack N, Zhou H, Cheng J, Yang J, Zhang K. Repurposing Protein Degradation for Optogenetic Modulation of Protein Activities. ACS Synth Biol 2019; 8:2585-2592. [PMID: 31600062 DOI: 10.1021/acssynbio.9b00285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Non-neuronal optogenetic approaches empower precise regulation of protein dynamics in live cells but often require target-specific protein engineering. To address this challenge, we developed a generalizable light-modulated protein stabilization system (GLIMPSe) to control the intracellular protein level independent of its functionality. We applied GLIMPSe to control two distinct classes of proteins: mitogen-activated protein kinase phosphatase 3 (MKP3), a negative regulator of the extracellular signal-regulated kinase (ERK) pathway, and a constitutively active form of MEK (CA MEK), a positive regulator of the same pathway. Kinetics study showed that light-induced protein stabilization could be achieved within 30 min of blue light stimulation. GLIMPSe enables target-independent optogenetic control of protein activities and therefore minimizes the systematic variation embedded within different photoactivatable proteins. Overall, GLIMPSe promises to achieve light-mediated post-translational stabilization of a wide array of target proteins in live cells.
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Affiliation(s)
| | | | | | | | | | | | - Jing Yang
- Department of Comparative Biosciences, University of Illinois at Urbana−Champaign, 2001 S Lincoln Avenue, Urbana, Illinois 61802, United States
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Cloninger CR, Cloninger KM, Zwir I, Keltikangas-Järvinen L. The complex genetics and biology of human temperament: a review of traditional concepts in relation to new molecular findings. Transl Psychiatry 2019; 9:290. [PMID: 31712636 PMCID: PMC6848211 DOI: 10.1038/s41398-019-0621-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/25/2019] [Accepted: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
Recent genome-wide association studies (GWAS) have shown that temperament is strongly influenced by more than 700 genes that modulate associative conditioning by molecular processes for synaptic plasticity and long-term learning and memory. The results were replicated in three independent samples despite variable cultures and environments. The identified genes were enriched in pathways activated by behavioral conditioning in animals, including the two major molecular pathways for response to extracellular stimuli, the Ras-MEK-ERK and the PI3K-AKT-mTOR cascades. These pathways are activated by a wide variety of physiological and psychosocial stimuli that vary in positive and negative valence and in consequences for health and survival. Changes in these pathways are orchestrated to maintain cellular homeostasis despite changing conditions by modulating temperament and its circadian and seasonal rhythms. In this review we first consider traditional concepts of temperament in relation to the new genetic findings by examining the partial overlap of alternative measures of temperament. Then we propose a definition of temperament as the disposition of a person to learn how to behave, react emotionally, and form attachments automatically by associative conditioning. This definition provides necessary and sufficient criteria to distinguish temperament from other aspects of personality that become integrated with it across the life span. We describe the effects of specific stimuli on the molecular processes underlying temperament from functional, developmental, and evolutionary perspectives. Our new knowledge can improve communication among investigators, increase the power and efficacy of clinical trials, and improve the effectiveness of treatment of personality and its disorders.
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Affiliation(s)
- C Robert Cloninger
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA.
- School of Arts and Sciences, Department of Psychological and Brain Sciences, and School of Medicine, Department of Genetics, Washington University, St. Louis, MO, USA.
- Anthropedia Foundation, St. Louis, MO, USA.
| | | | - Igor Zwir
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Department of Computer Science, University of Granada, Granada, Spain
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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Muldoon JJ, Yu JS, Fassia MK, Bagheri N. Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants. Bioinformatics 2019; 35:3421-3432. [PMID: 30932143 PMCID: PMC6748731 DOI: 10.1093/bioinformatics/btz105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/24/2019] [Accepted: 02/11/2019] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Network inference algorithms aim to uncover key regulatory interactions governing cellular decision-making, disease progression and therapeutic interventions. Having an accurate blueprint of this regulation is essential for understanding and controlling cell behavior. However, the utility and impact of these approaches are limited because the ways in which various factors shape inference outcomes remain largely unknown. RESULTS We identify and systematically evaluate determinants of performance-including network properties, experimental design choices and data processing-by developing new metrics that quantify confidence across algorithms in comparable terms. We conducted a multifactorial analysis that demonstrates how stimulus target, regulatory kinetics, induction and resolution dynamics, and noise differentially impact widely used algorithms in significant and previously unrecognized ways. The results show how even if high-quality data are paired with high-performing algorithms, inferred models are sometimes susceptible to giving misleading conclusions. Lastly, we validate these findings and the utility of the confidence metrics using realistic in silico gene regulatory networks. This new characterization approach provides a way to more rigorously interpret how algorithms infer regulation from biological datasets. AVAILABILITY AND IMPLEMENTATION Code is available at http://github.com/bagherilab/networkinference/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joseph J Muldoon
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Jessica S Yu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Mohammad-Kasim Fassia
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA
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Kinjo T, Terai K, Horita S, Nomura N, Sumiyama K, Togashi K, Iwata S, Matsuda M. FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics. Nat Methods 2019; 16:1029-1036. [DOI: 10.1038/s41592-019-0541-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022]
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Novel Tools towards Magnetic Guidance of Neurite Growth: (I) Guidance of Magnetic Nanoparticles into Neurite Extensions of Induced Human Neurons and In Vitro Functionalization with RAS Regulating Proteins. J Funct Biomater 2019; 10:jfb10030032. [PMID: 31315182 PMCID: PMC6787644 DOI: 10.3390/jfb10030032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 12/18/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disease associated with loss or dysfunction of dopaminergic neurons located in the substantia nigra (SN), and there is no cure available. An emerging new approach for treatment is to transplant human induced dopaminergic neurons directly into the denervated striatal brain target region. Unfortunately, neurons grafted into the substantia nigra are unable to grow axons into the striatum and thus do not allow recovery of the original connectivity. Towards overcoming this general limitation in guided neuronal regeneration, we develop here magnetic nanoparticles functionalized with proteins involved in the regulation of axonal growth. We show covalent binding of constitutive active human rat sarcoma (RAS) proteins or RAS guanine nucleotide exchange factor catalytic domain of son of sevenless (SOS) by fluorescence correlation spectroscopy and multiangle light scattering as well as the characterization of exchange factor activity. Human dopaminergic neurons were differentiated from neural precursor cells and characterized by electrophysiological and immune histochemical methods. Furthermore, we demonstrate magnetic translocation of cytoplasmic γ-Fe2O3@SiO2 core-shell nanoparticles into the neurite extensions of induced human neurons. Altogether, we developed tools towards remote control of directed neurite growth in human dopaminergic neurons. These results may have relevance for future therapeutic approaches of cell replacement therapy in Parkinson’s disease.
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Guo Z, Lou Y, Kong M, Luo Q, Liu Z, Wu J. A Systematic Review of Phytochemistry, Pharmacology and Pharmacokinetics on Astragali Radix: Implications for Astragali Radix as a Personalized Medicine. Int J Mol Sci 2019; 20:E1463. [PMID: 30909474 PMCID: PMC6470777 DOI: 10.3390/ijms20061463] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/20/2019] [Indexed: 12/17/2022] Open
Abstract
Astragali radix (AR) is one of the most widely used traditional Chinese herbal medicines. Modern pharmacological studies and clinical practices indicate that AR possesses various biological functions, including potent immunomodulation, antioxidant, anti-inflammation and antitumor activities. To date, more than 200 chemical constituents have been isolated and identified from AR. Among them, isoflavonoids, saponins and polysaccharides are the three main types of beneficial compounds responsible for its pharmacological activities and therapeutic efficacy. After ingestion of AR, the metabolism and biotransformation of the bioactive compounds were extensive in vivo. The isoflavonoids and saponins and their metabolites are the major type of constituents absorbed in plasma. The bioavailability barrier (BB), which is mainly composed of efflux transporters and conjugating enzymes, is expected to have a significant impact on the bioavailability of AR. This review summarizes studies on the phytochemistry, pharmacology and pharmacokinetics on AR. Additionally, the use of AR as a personalized medicine based on the BB is also discussed, which may provide beneficial information to achieve a better and more accurate therapeutic response of AR in clinical practice.
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Affiliation(s)
- Zhenzhen Guo
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
| | - Yanmei Lou
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
| | - Muyan Kong
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
| | - Qing Luo
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
| | - Zhongqiu Liu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau (SAR) 999078, China.
| | - Jinjun Wu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
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Membrane-Associated, Not Cytoplasmic or Nuclear, FGFR1 Induces Neuronal Differentiation. Cells 2019; 8:cells8030243. [PMID: 30875802 PMCID: PMC6468866 DOI: 10.3390/cells8030243] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 01/22/2023] Open
Abstract
The intracellular transport of receptor tyrosine kinases results in the differential activation of various signaling pathways. In this study, optogenetic stimulation of fibroblast growth factor receptor type 1 (FGFR1) was performed to study the effects of subcellular targeting of receptor kinases on signaling and neurite outgrowth. The catalytic domain of FGFR1 fused to the algal light-oxygen-voltage-sensing (LOV) domain was directed to different cellular compartments (plasma membrane, cytoplasm and nucleus) in human embryonic kidney (HEK293) and pheochromocytoma (PC12) cells. Blue light stimulation elevated the pERK and pPLCγ1 levels in membrane-opto-FGFR1-transfected cells similarly to ligand-induced receptor activation; however, no changes in pAKT levels were observed. PC12 cells transfected with membrane-opto-FGFR1 exhibited significantly longer neurites after light stimulation than after growth factor treatment, and significantly more neurites extended from their cell bodies. The activation of cytoplasmic FGFR1 kinase enhanced ERK signaling in HEK293 cells but not in PC12 cells and did not induce neuronal differentiation. The stimulation of FGFR1 kinase in the nucleus also did not result in signaling changes or neurite outgrowth. We conclude that FGFR1 kinase needs to be associated with membranes to induce the differentiation of PC12 cells mainly via ERK activation.
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Pan H, Wang H, Yu J, Huang X, Hao Y, Zhang C, Ji W, Yang M, Gong X, Wu X, Chang J. Near-infrared light remotely up-regulate autophagy with spatiotemporal precision via upconversion optogenetic nanosystem. Biomaterials 2019; 199:22-31. [PMID: 30735893 DOI: 10.1016/j.biomaterials.2019.01.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/15/2019] [Accepted: 01/30/2019] [Indexed: 12/31/2022]
Abstract
In vivo noninvasively manipulating biological functions by the mediation of biosafe near infrared (NIR) light is becoming increasingly popular. For these applications, upconversion rare-earth nanomaterial holds great promise as a novel photonic element, and has been widely adopted in optogenetics. In this article, an upconversion optogenetic nanosystem that was promised to achieve autophagy up-regulation with spatiotemporal precision was designed. The implantable, wireless, recyclable, less-invasive and biocompatible system worked via two separated parts: blue light-receptor optogenetics-autophagy upregulation plasmids, for protein import; upconversion rods-encapsulated flexible capsule (UCRs-capsule), for converting tissue-penetrative NIR light into local visible blue light. Results validated that this system could achieve up-regulation of autophagy in vitro (in both HeLa and 293T cell lines) and remotely penetrate tissue (∼3.5 mm) in vivo. Since autophagy serves at a central position in intracellular signalling pathways, which is correlative with diverse pathologies, we expect that this method could establish an upconversion material-based autophagy up-regulation strategy for fundamental and clinical applications.
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Affiliation(s)
- Huizhuo Pan
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Hanjie Wang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.
| | - Jingxian Yu
- School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Xian Huang
- School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Yafeng Hao
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Chaonan Zhang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Wanying Ji
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Minye Yang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Xiaoqun Gong
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Xiaoli Wu
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jin Chang
- School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.
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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: 353] [Impact Index Per Article: 50.4] [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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Perspectives of RAS and RHEB GTPase Signaling Pathways in Regenerating Brain Neurons. Int J Mol Sci 2018; 19:ijms19124052. [PMID: 30558189 PMCID: PMC6321366 DOI: 10.3390/ijms19124052] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
Cellular activation of RAS GTPases into the GTP-binding “ON” state is a key switch for regulating brain functions. Molecular protein structural elements of rat sarcoma (RAS) and RAS homolog protein enriched in brain (RHEB) GTPases involved in this switch are discussed including their subcellular membrane localization for triggering specific signaling pathways resulting in regulation of synaptic connectivity, axonal growth, differentiation, migration, cytoskeletal dynamics, neural protection, and apoptosis. A beneficial role of neuronal H-RAS activity is suggested from cellular and animal models of neurodegenerative diseases. Recent experiments on optogenetic regulation offer insights into the spatiotemporal aspects controlling RAS/mitogen activated protein kinase (MAPK) or phosphoinositide-3 kinase (PI3K) pathways. As optogenetic manipulation of cellular signaling in deep brain regions critically requires penetration of light through large distances of absorbing tissue, we discuss magnetic guidance of re-growing axons as a complementary approach. In Parkinson’s disease, dopaminergic neuronal cell bodies degenerate in the substantia nigra. Current human trials of stem cell-derived dopaminergic neurons must take into account the inability of neuronal axons navigating over a large distance from the grafted site into striatal target regions. Grafting dopaminergic precursor neurons directly into the degenerating substantia nigra is discussed as a novel concept aiming to guide axonal growth by activating GTPase signaling through protein-functionalized intracellular magnetic nanoparticles responding to external magnets.
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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: 110] [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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41
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Kim J, Heo WD. Synergistic Ensemble of Optogenetic Actuators and Dynamic Indicators in Cell Biology. Mol Cells 2018; 41:809-817. [PMID: 30157546 PMCID: PMC6182222 DOI: 10.14348/molcells.2018.0295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bioimaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.
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Affiliation(s)
- Jihoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141,
Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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42
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Luke GA, Ryan MD. "Therapeutic applications of the 'NPGP' family of viral 2As". Rev Med Virol 2018; 28:e2001. [PMID: 30094875 DOI: 10.1002/rmv.2001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 12/15/2022]
Abstract
Oligopeptide "2A" and "2A-like" sequences ("2As"; 18-25aa) are found in a range of RNA virus genomes controlling protein biogenesis through "recoding" of the host-cell translational apparatus. Insertion of multiple 2As within a single open reading frame (ORF) produces multiple proteins; hence, 2As have been used in a very wide range of biotechnological and biomedical applications. During translation, these 2A peptide sequences mediate a eukaryote-specific, self-"cleaving" event, termed "ribosome skipping" with very high efficiency. A particular advantage of using 2As is the ability to simultaneously translate a number of proteins at an equal level in all eukaryotic systems although, naturally, final steady-state levels depend upon other factors-notably protein stability. By contrast, the use of internal ribosome entry site elements for co-expression results in an unbalanced expression due to the relative inefficiency of internal initiation. For example, a 1:1 ratio is of particular importance for the biosynthesis of the heavy-chain and light-chain components of antibodies: highly valuable as therapeutic proteins. Furthermore, each component of these "artificial polyprotein" systems can be independently targeted to different sub-cellular sites. The potential of this system was vividly demonstrated by concatenating multiple gene sequences, linked via 2A sequences, into a single, long, ORF-a polycistronic construct. Here, ORFs comprising the biosynthetic pathways for violacein (five gene sequences) and β-carotene (four gene sequences) were concatenated into a single cistron such that all components were co-expressed in the yeast Pichia pastoris. In this review, we provide useful information on 2As to serve as a guide for future utilities of this co-expression technology in basic research, biotechnology, and clinical applications.
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Affiliation(s)
- Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, St Andrews, UK
| | - Martin D Ryan
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, St Andrews, UK
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43
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Duan L, Hope JM, Guo S, Ong Q, François A, Kaplan L, Scherrer G, Cui B. Optical Activation of TrkA Signaling. ACS Synth Biol 2018; 7:1685-1693. [PMID: 29975841 DOI: 10.1021/acssynbio.8b00126] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nerve growth factor/tropomyosin receptor kinase A (NGF/TrkA) signaling plays a key role in neuronal development, function, survival, and growth. The pathway is implicated in neurodegenerative disorders including Alzheimer's disease, chronic pain, inflammation, and cancer. NGF binds the extracellular domain of TrkA, leading to the activation of the receptor's intracellular kinase domain. As TrkA signaling is highly dynamic, mechanistic studies would benefit from a tool with high spatial and temporal resolution. Here we present the design and evaluation of four strategies for light-inducible activation of TrkA in the absence of NGF. Our strategies involve the light-sensitive protein Arabidopsis cryptochrome 2 and its binding partner CIB1. We demonstrate successful recapitulation of native NGF/TrkA functions by optical induction of plasma membrane recruitment and homo-interaction of the intracellular domain of TrkA. This approach activates PI3K/AKT and Raf/ERK signaling pathways, promotes neurite growth in PC12 cells, and supports survival of dorsal root ganglion neurons in the absence of NGF. This ability to activate TrkA using light bestows high spatial and temporal resolution for investigating NGF/TrkA signaling.
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Affiliation(s)
- Liting Duan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jen M. Hope
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Shunling Guo
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Qunxiang Ong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Amaury François
- Department of Anesthesiology, Perioperative and Pain Medicine, Department of Molecular and Cellular Physiology, Department of Neurosurgery, Stanford Neurosciences Institute, Stanford University, Palo Alto, California 94304, United States
| | - Luke Kaplan
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Grégory Scherrer
- Department of Anesthesiology, Perioperative and Pain Medicine, Department of Molecular and Cellular Physiology, Department of Neurosurgery, Stanford Neurosciences Institute, Stanford University, Palo Alto, California 94304, United States
- Robertson Investigator, New York Stem Cell Foundation, New York, New York 10019, United States
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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44
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Ishizuka S, Lai CY, Otsu M, Nakauchi H, Nagamune T, Kawahara M. Designing Motif-Engineered Receptors To Elucidate Signaling Molecules Important for Proliferation of Hematopoietic Stem Cells. ACS Synth Biol 2018; 7:1709-1714. [PMID: 29920201 DOI: 10.1021/acssynbio.8b00163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The understanding of signaling events is critical for attaining long-term expansion of hematopoietic stem cells ex vivo. In this study, we aim to analyze the contribution of multiple signaling molecules in proliferation of hematopoietic stem cells. To this end, we design a bottom-up engineered receptor with multiple tyrosine motifs, which can recruit multiple signaling molecules of interest. This is followed by a top-down approach, where one of the multiple tyrosine motifs in the bottom-up engineered receptor is functionally knocked out by tyrosine-to-phenylalanine mutation. The combination of these two approaches demonstrates the importance of Shc in cooperation with STAT3 or STAT5 in the proliferation of hematopoietic stem cells. The platform developed herein may be applied for analyzing other cells and/or other cell fate regulation systems.
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Affiliation(s)
- Shuta Ishizuka
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Chen-Yi Lai
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Otsu
- Division of Stem Cell Processing/Stem Cell Bank, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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45
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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46
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A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging. Sci Rep 2018; 8:8984. [PMID: 29895862 PMCID: PMC5997707 DOI: 10.1038/s41598-018-27174-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/25/2018] [Indexed: 02/04/2023] Open
Abstract
Genetically encoded biosensors based on the principle of Förster resonance energy transfer comprise two major classes: biosensors based on fluorescence resonance energy transfer (FRET) and those based on bioluminescence energy transfer (BRET). The FRET biosensors visualize signaling-molecule activity in cells or tissues with high resolution. Meanwhile, due to the low background signal, the BRET biosensors are primarily used in drug screening. Here, we report a protocol to transform intramolecular FRET biosensors to BRET-FRET hybrid biosensors called hyBRET biosensors. The hyBRET biosensors retain all properties of the prototype FRET biosensors and also work as BRET biosensors with dynamic ranges comparable to the prototype FRET biosensors. The hyBRET biosensors are compatible with optogenetics, luminescence microplate reader assays, and non-invasive whole-body imaging of xenograft and transgenic mice. This simple protocol will expand the use of FRET biosensors and enable visualization of the multiscale dynamics of cell signaling in live animals.
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47
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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48
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Tsuchiya T, Fujii M, Matsuda N, Kunida K, Uda S, Kubota H, Konishi K, Kuroda S. System identification of signaling dependent gene expression with different time-scale data. PLoS Comput Biol 2017; 13:e1005913. [PMID: 29281625 PMCID: PMC5760096 DOI: 10.1371/journal.pcbi.1005913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/09/2018] [Accepted: 12/01/2017] [Indexed: 01/11/2023] Open
Abstract
Cells decode information of signaling activation at a scale of tens of minutes by downstream gene expression with a scale of hours to days, leading to cell fate decisions such as cell differentiation. However, no system identification method with such different time scales exists. Here we used compressed sensing technology and developed a system identification method using data of different time scales by recovering signals of missing time points. We measured phosphorylation of ERK and CREB, immediate early gene expression products, and mRNAs of decoder genes for neurite elongation in PC12 cell differentiation and performed system identification, revealing the input-output relationships between signaling and gene expression with sensitivity such as graded or switch-like response and with time delay and gain, representing signal transfer efficiency. We predicted and validated the identified system using pharmacological perturbation. Thus, we provide a versatile method for system identification using data with different time scales.
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Affiliation(s)
- Takaho Tsuchiya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Masashi Fujii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Molecular Genetics Research Laboratory, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Naoki Matsuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Laboratory of Computational Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsumi Konishi
- Department of Computer Science, Faculty of Informatics, Kogakuin University, Tokyo, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Corporation, Tokyo, Japan
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49
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Optogenetic Tools for Subcellular Applications in Neuroscience. Neuron 2017; 96:572-603. [PMID: 29096074 DOI: 10.1016/j.neuron.2017.09.047] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/30/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Abstract
The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications.
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50
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Turning Death to Growth: Hematopoietic Growth Factors Promote Neurite Outgrowth through MEK/ERK/p53 Pathway. Mol Neurobiol 2017; 55:5913-5925. [PMID: 29119536 DOI: 10.1007/s12035-017-0814-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/27/2017] [Indexed: 12/23/2022]
Abstract
Stem cell factor (SCF) and granulocyte colony-stimulating factor (G-CSF) are the essential hematopoietic growth factors to control hematopoiesis. However, the role of SCF and G-CSF in the central nervous system remains poorly understood. Here, we have demonstrated the involvement of MEK/ERK/p53 signaling in SCF + G-CSF-enhanced neurite extension. Cortical neurons dissected from embryonic rat brains were seeded onto the membranes of transwell inserts, and neurite outgrowth was determined by using both the neurite outgrowth quantification assay kit and immunostaining of β III tubulin. Quantitative RT-PCR and western blotting were used for determining gene and protein expression of ERK and p53, respectively. p53 small interfering RNA (siRNAs) were introduced into neurons for examining the involvement of p53 in SCF + G-CSF-mediated neurite outgrowth. We observed that both SCF and G-CSF alone increased activation of MEK/ERK and gene expression of p53, while SCF + G-CSF synergistically activated the MEK/ERK signaling and upregulated p53 expression. MEK specific inhibitors (PD98059 and U0126) blocked the SCF + G-CSF-increased ERK phosphorylation and p53 gene and protein expression, and the MEK specific inhibitors also eliminated the SCF + G-CSF-promoted neurite outgrowth. p53 siRNAs knocked down the SCF + G-CSF-elevated p53 protein and prevented the SCF + G-CSF-enhanced neurite outgrowth. These findings suggest that activation of MEK/ERK/p53 signaling is required for SCF + G-CSF-promoted neurite outgrowth. Through the pro-apoptotic pathway of the MEK/ERK/p53, SCF + G-CSF turns neuronal fate from apoptotic commitment toward neural network generation. This observation provides novel insights into the putative role of SCF + G-CSF in supporting generation of neural connectivity during CNS development and in brain repair under pathological or neurodegenerative conditions.
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