1
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Wu SY, Shen Y, Shkolnikov I, Campbell RE. Fluorescent Indicators For Biological Imaging of Monatomic Ions. Front Cell Dev Biol 2022; 10:885440. [PMID: 35573682 PMCID: PMC9093666 DOI: 10.3389/fcell.2022.885440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Monatomic ions play critical biological roles including maintaining the cellular osmotic pressure, transmitting signals, and catalyzing redox reactions as cofactors in enzymes. The ability to visualize monatomic ion concentration, and dynamic changes in the concentration, is essential to understanding their many biological functions. A growing number of genetically encodable and synthetic indicators enable the visualization and detection of monatomic ions in biological systems. With this review, we aim to provide a survey of the current landscape of reported indicators. We hope this review will be a useful guide to researchers who are interested in using indicators for biological applications and to tool developers seeking opportunities to create new and improved indicators.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Irene Shkolnikov
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
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2
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Watson ER, Taherian Fard A, Mar JC. Computational Methods for Single-Cell Imaging and Omics Data Integration. Front Mol Biosci 2022; 8:768106. [PMID: 35111809 PMCID: PMC8801747 DOI: 10.3389/fmolb.2021.768106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.
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Affiliation(s)
| | - Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Jessica Cara Mar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
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3
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Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol 2021; 4:1261. [PMID: 34737378 PMCID: PMC8569150 DOI: 10.1038/s42003-021-02779-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/05/2021] [Indexed: 01/02/2023] Open
Abstract
Simultaneous longitudinal imaging across multiple conditions and replicates has been crucial for scientific studies aiming to understand biological processes and disease. Yet, imaging systems capable of accomplishing these tasks are economically unattainable for most academic and teaching laboratories around the world. Here, we propose the Picroscope, which is the first low-cost system for simultaneous longitudinal biological imaging made primarily using off-the-shelf and 3D-printed materials. The Picroscope is compatible with standard 24-well cell culture plates and captures 3D z-stack image data. The Picroscope can be controlled remotely, allowing for automatic imaging with minimal intervention from the investigator. Here, we use this system in a range of applications. We gathered longitudinal whole organism image data for frogs, zebrafish, and planaria worms. We also gathered image data inside an incubator to observe 2D monolayers and 3D mammalian tissue culture models. Using this tool, we can measure the behavior of entire organisms or individual cells over long-time periods.
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Affiliation(s)
- Victoria T Ly
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
| | - Pierre V Baudin
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Pattawong Pansodtee
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Erik A Jung
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Kateryna Voitiuk
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Yohei M Rosen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Gary L Mantalas
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Spencer T Seiler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - John A Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sergio A Cordero
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Jayden M Ross
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Tomasz J Nowakowski
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mohammed A Mostajo-Radji
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
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4
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Liu L, He F, Yu Y, Wang Y. Application of FRET Biosensors in Mechanobiology and Mechanopharmacological Screening. Front Bioeng Biotechnol 2020; 8:595497. [PMID: 33240867 PMCID: PMC7680962 DOI: 10.3389/fbioe.2020.595497] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/19/2020] [Indexed: 12/15/2022] Open
Abstract
Extensive studies have shown that cells can sense and modulate the biomechanical properties of the ECM within their resident microenvironment. Thus, targeting the mechanotransduction signaling pathways provides a promising way for disease intervention. However, how cells perceive these mechanical cues of the microenvironment and transduce them into biochemical signals remains to be answered. Förster or fluorescence resonance energy transfer (FRET) based biosensors are a powerful tool that can be used in live-cell mechanotransduction imaging and mechanopharmacological drug screening. In this review, we will first introduce FRET principle and FRET biosensors, and then, recent advances on the integration of FRET biosensors and mechanobiology in normal and pathophysiological conditions will be discussed. Furthermore, we will summarize the current applications and limitations of FRET biosensors in high-throughput drug screening and the future improvement of FRET biosensors. In summary, FRET biosensors have provided a powerful tool for mechanobiology studies to advance our understanding of how cells and matrices interact, and the mechanopharmacological screening for disease intervention.
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Affiliation(s)
| | | | | | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
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5
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Dhyani V, Gare S, Gupta RK, Swain S, Venkatesh K, Giri L. GPCR mediated control of calcium dynamics: A systems perspective. Cell Signal 2020; 74:109717. [PMID: 32711109 PMCID: PMC7375278 DOI: 10.1016/j.cellsig.2020.109717] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 02/09/2023]
Abstract
G-protein coupled receptor (GPCR) mediated calcium (Ca2+)-signaling transduction remains crucial in designing drugs for various complex diseases including neurodegeneration, chronic heart failure as well as respiratory diseases. Although there are several reviews detailing various aspects of Ca2+-signaling such as the role of IP3 receptors and Ca2+-induced-Ca2+-release, none of them provide an integrated view of the mathematical descriptions of GPCR signal transduction and investigations on dose-response curves. This article is the first study in reviewing the network structures underlying GPCR signal transduction that control downstream [Cac2+]-oscillations. The central theme of this paper is to present the biochemical pathways, as well as molecular mechanisms underlying the GPCR-mediated Ca2+-dynamics in order to facilitate a better understanding of how agonist concentration is encoded in Ca2+-signals for Gαq, Gαs, and Gαi/o signaling pathways. Moreover, we present the GPCR targeting drugs that are relevant for treating cardiac, respiratory, and neuro-diseases. The current paper presents the ODE formulation for various models along with the detailed schematics of signaling networks. To provide a systems perspective, we present the network motifs that can provide readers an insight into the complex and intriguing science of agonist-mediated Ca2+-dynamics. One of the features of this review is to pinpoint the interplay between positive and negative feedback loops that are involved in controlling intracellular [Cac2+]-oscillations. Furthermore, we review several examples of dose-response curves obtained from [Cac2+]-spiking for various GPCR pathways. This paper is expected to be useful for pharmacologists and computational biologists for designing clinical applications of GPCR targeting drugs through modulation of Ca2+-dynamics.
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Affiliation(s)
- Vaibhav Dhyani
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Suman Gare
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Rishikesh Kumar Gupta
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Sarpras Swain
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - K.V. Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India.
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6
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Wu N, Nishioka WK, Derecki NC, Maher MP. High-throughput-compatible assays using a genetically-encoded calcium indicator. Sci Rep 2019; 9:12692. [PMID: 31481721 PMCID: PMC6722131 DOI: 10.1038/s41598-019-49070-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Measurement of intracellular calcium in live cells is a key component of a wide range of basic life science research, and crucial for many high-throughput assays used in modern drug discovery. Synthetic calcium indicators have become the industry standard, due their ease of use, high reliability, wide dynamic range, and availability of a large variety of spectral and chemical properties. Genetically-encoded calcium indicators (GECIs) have been optimized to the point where their performance rivals that of synthetic calcium indicators in many applications. Stable expression of a GECI has distinct advantages over synthetic calcium indicators in terms of reagent cost and simplification of the assay process. We generated a clonal cell line constitutively expressing GCaMP6s; high expression of the GECI was driven by coupling to a blasticidin resistance gene with a self-cleaving cis-acting hydrolase element (CHYSEL) 2A peptide. Here, we compared the performance of the GECI GCaMP6s to the synthetic calcium indicator fluo-4 in a variety of assay formats. We demonstrate that the pharmacology of ion channel and GPCR ligands as determined using the two indicators is highly similar, and that GCaMP6s is viable as a direct replacement for a synthetic calcium indicator.
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Affiliation(s)
- Nyantsz Wu
- Janssen Research & Development, LLC, San Diego, CA, 92121, USA
| | | | - Noël C Derecki
- Janssen Research & Development, LLC, San Diego, CA, 92121, USA
| | - Michael P Maher
- Janssen Research & Development, LLC, San Diego, CA, 92121, USA.
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7
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Yang XA, Zweifach A. Temperature-Dependent Expression of a CFP-YFP FRET Diacylglycerol Sensor Enables Multiple-Read Screening for Compounds That Affect C1 Domains. SLAS DISCOVERY 2019; 24:682-692. [PMID: 30802416 DOI: 10.1177/2472555219830086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intramolecular CFP-YFP fluorescence resonance energy transfer (FRET) sensors expressed in cells are powerful research tools but have seen relatively little use in screening. We exploited the discovery that the expression of a CFP-YFP FRET diacylglycerol sensor (DAGR) increases over time when cells are incubated at room temperature to assess requirements for robust measurements using a Molecular Devices Spectramax i3x fluorescence plate reader. Expression levels resulting in YFP fluorescence >10-fold higher than untransfected cells and phorbol ester-stimulated FRET ratio changes of 60% or more were required to consistently give robust Z' > 0.5. As a means of confirming that these conditions are suitable for screening, we developed a novel multiple-read protocol to assay the NCI's Mechanistic Set III for agonists and antagonists of C1 domain activation. Sixteen compounds prevented C1 domain translocation. However, none blocked phorbol ester-stimulated protein kinase C (PKC) activity assessed using a phospho-specific antibody-six actually stimulated PKC activity. Cytometry, which produces higher Z' for a given FRET ratio change, might have been a better approach for discovering antagonists, as it would have allowed lower phorbol ester concentrations to be used. We conclude that CFP-YFP FRET measured in a Spectramax i3x plate reader can be used for screening under the conditions we defined. Our strategy of varying expression level and FRET ratio could be useful to others for determining conditions needed for robust cell-based intramolecular CFP-YFP FRET measurements on their instrumentation.
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Affiliation(s)
- Xiuyi Alexander Yang
- 1 Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT, USA
| | - Adam Zweifach
- 1 Department of Molecular and Cell Biology, University of Connecticut at Storrs, Storrs, CT, USA
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8
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Pomerantz AK, Sari-Sarraf F, Grove KJ, Pedro L, Rudewicz PJ, Fathman JW, Krucker T. Enabling drug discovery and development through single-cell imaging. Expert Opin Drug Discov 2018; 14:115-125. [DOI: 10.1080/17460441.2019.1559147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Andrea K. Pomerantz
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research Inc., Cambridge, MA, USA
| | - Farid Sari-Sarraf
- Analytical Sciences & Imaging, Novartis Institutes for BioMedical Research Inc., Cambridge, MA, USA
| | - Kerri J. Grove
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research Inc., Emeryville, CA, USA
| | - Liliana Pedro
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research Inc., Emeryville, CA, USA
| | - Patrick J. Rudewicz
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research Inc., Emeryville, CA, USA
| | - John W. Fathman
- Cancer Therapeutics, Genomics Institute of the Novartis Research Foundation, La Jolla, CA, USA
| | - Thomas Krucker
- Alliance Management and Partnering, Novartis Institutes for BioMedical Research Inc., Emeryville, CA, USA
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9
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Swain S, Gupta RK, Ratnayake K, Priyanka PD, Singh R, Jana S, Mitra K, Karunarathne A, Giri L. Confocal Imaging and k-Means Clustering of GABA B and mGluR Mediated Modulation of Ca 2+ Spiking in Hippocampal Neurons. ACS Chem Neurosci 2018; 9:3094-3107. [PMID: 30044088 DOI: 10.1021/acschemneuro.8b00297] [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: 12/26/2022] Open
Abstract
Imaging cytosolic calcium in neurons is emerging as a new tool in neurological disease diagnosis, drug screening, and toxicity testing. Ca2+ oscillation signatures show a significant variation depending on GPCR targeting agonists. Quantification of Ca2+ spike trains in ligand induced Ca2+ oscillations remains challenging due to their inherent heterogeneity in primary culture. Moreover, there is no framework available for identification of optimal number of clusters and distance metric to cluster Ca2+ spike trains. Using quantitative confocal imaging and clustering analysis, we show the characterization of Ca2+ spiking in GPCR targeting drug-treated primary culture of hippocampal neurons. A systematic framework for selection of the clustering method instead of an intuition-based method was used to optimize the cluster number and distance metric. The results discern neurons with diverse Ca2+ response patterns, including higher amplitude fast spiking and lower spiking responses, and their relative percentage in a neuron population in absence and presence of GPCR-targeted drugs. The proposed framework was employed to show that the clustering pattern of Ca2+ spiking can be controlled using GABAB and mGluR targeting drugs. This approach can be used for unbiased measurement of neural activity and identification of spiking population with varying amplitude and frequencies, providing a platform for high-content drug screening.
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Affiliation(s)
- Sarpras Swain
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad 502285, India
| | - Rishikesh Kumar Gupta
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad 502285, India
| | - Kasun Ratnayake
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Pantula Devi Priyanka
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad 502285, India
| | - Ranjana Singh
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad 502285, India
| | - Soumya Jana
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad 502285, India
| | - Kishalay Mitra
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad 502285, India
| | - Ajith Karunarathne
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad 502285, India
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Gupta RK, Swain S, Kankanamge D, Priyanka PD, Singh R, Mitra K, Karunarathne A, Giri L. Comparison of Calcium Dynamics and Specific Features for G Protein-Coupled Receptor-Targeting Drugs Using Live Cell Imaging and Automated Analysis. SLAS DISCOVERY 2017; 22:848-858. [PMID: 28267930 DOI: 10.1177/2472555217693378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
G protein-coupled receptors (GPCRs) are targets for designing a large fraction of the drugs in the pharmaceutical industry. For GPCR-targeting drug screening using cell-based assays, measurement of cytosolic calcium has been widely used to obtain dose-response profiles. However, it remains challenging to obtain drug-specific features due to cell-to-cell heterogeneity in drug-cell responses obtained from live cell imaging. Here, we present a framework combining live cell imaging of a cell population and a feature extraction method for classification of responses of drugs targeting GPCRs CXCR4 and α2AR. We measured the calcium dynamics using confocal microscopy and compared the responses for SDF-1α and norepinephrine. The results clearly show that the clustering patterns of responses for the two GPCRs are significantly different. Additionally, we show that different drugs targeting the same GPCR induce different calcium response signatures. We also implemented principal component analysis and k means for feature extraction and used nondominated (ND) sorting for ranking a group of drugs at various doses. The presented approach can be used to model a cell population as a mixture of subpopulations. It also offers specific advantages, such as higher spatial resolution, classification of responses, and ranking of drugs, potentially providing a platform for high-content drug screening.
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Affiliation(s)
- Rishikesh Kumar Gupta
- 1 Department of Chemical Engineering, Indian Institute of Technology-Hyderabad, Hyderabad, Telangana, India
| | - Sarpras Swain
- 1 Department of Chemical Engineering, Indian Institute of Technology-Hyderabad, Hyderabad, Telangana, India
| | - Dinesh Kankanamge
- 2 Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH, USA
| | - Pantula Devi Priyanka
- 1 Department of Chemical Engineering, Indian Institute of Technology-Hyderabad, Hyderabad, Telangana, India
| | - Ranjana Singh
- 1 Department of Chemical Engineering, Indian Institute of Technology-Hyderabad, Hyderabad, Telangana, India
| | - Kishalay Mitra
- 1 Department of Chemical Engineering, Indian Institute of Technology-Hyderabad, Hyderabad, Telangana, India
| | - Ajith Karunarathne
- 2 Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH, USA
| | - Lopamudra Giri
- 1 Department of Chemical Engineering, Indian Institute of Technology-Hyderabad, Hyderabad, Telangana, India
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11
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Schaaf TM, Peterson KC, Grant BD, Thomas DD, Gillispie GD. Spectral Unmixing Plate Reader: High-Throughput, High-Precision FRET Assays in Living Cells. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2017; 22:250-261. [PMID: 27879398 PMCID: PMC5506495 DOI: 10.1177/1087057116679637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have developed a microplate reader that records a complete high-quality fluorescence emission spectrum on a well-by-well basis under true high-throughput screening (HTS) conditions. The read time for an entire 384-well plate is less than 3 min. This instrument is particularly well suited for assays based on fluorescence resonance energy transfer (FRET). Intramolecular protein biosensors with genetically encoded green fluorescent protein (GFP) donor and red fluorescent protein (RFP) acceptor tags at positions sensitive to structural changes were stably expressed and studied in living HEK cells. Accurate quantitation of FRET was achieved by decomposing each observed spectrum into a linear combination of four component (basis) spectra (GFP emission, RFP emission, water Raman, and cell autofluorescence). Excitation and detection are both conducted from the top, allowing for thermoelectric control of the sample temperature from below. This spectral unmixing plate reader (SUPR) delivers an unprecedented combination of speed, precision, and accuracy for studying ensemble-averaged FRET in living cells. It complements our previously reported fluorescence lifetime plate reader, which offers the feature of resolving multiple FRET populations within the ensemble. The combination of these two direct waveform-recording technologies greatly enhances the precision and information content for HTS in drug discovery.
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Affiliation(s)
- Tory M. Schaaf
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | | | | | - David D. Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Photonic Pharma LLC, Minneapolis, MN 55410
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12
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Ahfeldt T, Litterman NK, Rubin LL. Studying human disease using human neurons. Brain Res 2017; 1656:40-48. [PMID: 27060768 PMCID: PMC5053850 DOI: 10.1016/j.brainres.2016.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 03/08/2016] [Accepted: 03/31/2016] [Indexed: 01/25/2023]
Abstract
Utilizing patient derived cells has enormous promise for discovering new drugs for diseases of the nervous system, a goal that has been historically quite challenging. In this review, we will outline the potential of human stem cell derived neuron models for assessing therapeutics and high-throughput screening and compare to more traditional drug discovery strategies. We summarize recent successes of the approach and discuss special considerations for developing human stem cell based assays. New technologies, such as genome editing, offer improvements to help overcome the challenges that remain. Finally, human neurons derived from patient cells have advantages for translational research beyond drug screening as they can also be used to identify individual efficacy and safety prior to clinical testing and for dissecting disease mechanisms. This article is part of a Special Issue entitled SI: Exploiting human neurons.
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Affiliation(s)
- Tim Ahfeldt
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
| | - Nadia K. Litterman
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
| | - Lee L. Rubin
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
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Majewski L, Kuznicki J. SOCE in neurons: Signaling or just refilling? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1940-52. [DOI: 10.1016/j.bbamcr.2015.01.019] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/22/2015] [Accepted: 01/26/2015] [Indexed: 01/14/2023]
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14
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Edwards BS, Sklar LA. Flow Cytometry: Impact on Early Drug Discovery. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:689-707. [PMID: 25805180 PMCID: PMC4606936 DOI: 10.1177/1087057115578273] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/27/2015] [Indexed: 12/15/2022]
Abstract
Modern flow cytometers can make optical measurements of 10 or more parameters per cell at tens of thousands of cells per second and more than five orders of magnitude dynamic range. Although flow cytometry is used in most drug discovery stages, "sip-and-spit" sampling technology has restricted it to low-sample-throughput applications. The advent of HyperCyt sampling technology has recently made possible primary screening applications in which tens of thousands of compounds are analyzed per day. Target-multiplexing methodologies in combination with extended multiparameter analyses enable profiling of lead candidates early in the discovery process, when the greatest numbers of candidates are available for evaluation. The ability to sample small volumes with negligible waste reduces reagent costs, compound usage, and consumption of cells. Improved compound library formatting strategies can further extend primary screening opportunities when samples are scarce. Dozens of targets have been screened in 384- and 1536-well assay formats, predominantly in academic screening lab settings. In concert with commercial platform evolution and trending drug discovery strategies, HyperCyt-based systems are now finding their way into mainstream screening labs. Recent advances in flow-based imaging, mass spectrometry, and parallel sample processing promise dramatically expanded single-cell profiling capabilities to bolster systems-level approaches to drug discovery.
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Affiliation(s)
- Bruce S Edwards
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Larry A Sklar
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
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Kim TW. Drug repositioning approaches for the discovery of new therapeutics for Alzheimer's disease. Neurotherapeutics 2015; 12:132-42. [PMID: 25549849 PMCID: PMC4322062 DOI: 10.1007/s13311-014-0325-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia and represents one of the highest unmet needs in medicine today. Drug development efforts for AD have been encumbered by largely unsuccessful clinical trials in the last decade. Drug repositioning, a process of discovering a new therapeutic use for existing drugs or drug candidates, is an attractive and timely drug development strategy especially for AD. Compared with traditional de novo drug development, time and cost are reduced as the safety and pharmacokinetic properties of most repositioning candidates have already been determined. A majority of drug repositioning efforts for AD have been based on positive clinical or epidemiological observations or in vivo efficacy found in mouse models of AD. More systematic, multidisciplinary approaches will further facilitate drug repositioning for AD. Some experimental approaches include unbiased phenotypic screening using the library of available drug collections in physiologically relevant model systems (e.g. stem cell-derived neurons or glial cells), computational prediction and selection approaches that leverage the accumulating data resulting from RNA expression profiles, and genome-wide association studies. This review will summarize several notable strategies and representative examples of drug repositioning for AD.
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Affiliation(s)
- Tae-Wan Kim
- Department of Pathology and Cell Biology, and Taub Institute of Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, 10032, USA,
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