1
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Larey AM, Spoerer TM, Daga KR, Morfin MG, Hynds HM, Carpenter J, Hines KM, Marklein RA. High throughput screening of mesenchymal stromal cell morphological response to inflammatory signals for bioreactor-based manufacturing of extracellular vesicles that modulate microglia. Bioact Mater 2024; 37:153-171. [PMID: 38549769 PMCID: PMC10972802 DOI: 10.1016/j.bioactmat.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024] Open
Abstract
Due to their immunomodulatory function, mesenchymal stromal cells (MSCs) are a promising therapeutic with the potential to treat neuroinflammation associated with neurodegenerative diseases. This function is mediated by secreted extracellular vesicles (MSC-EVs). Despite established safety, MSC clinical translation has been unsuccessful due to inconsistent clinical outcomes resulting from functional heterogeneity. Current approaches to mitigate functional heterogeneity include 'priming' MSCs with inflammatory signals to enhance function. However, comprehensive evaluation of priming and its effects on MSC-EV function has not been performed. Furthermore, clinical translation of MSC-EV therapies requires significant manufacturing scale-up, yet few studies have investigated the effects of priming in bioreactors. As MSC morphology has been shown to predict their immunomodulatory function, we screened MSC morphological response to an array of priming signals and evaluated MSC-EV identity and potency in response to priming in flasks and bioreactors. We identified unique priming conditions corresponding to distinct morphologies. These conditions demonstrated a range of MSC-EV preparation quality and lipidome, allowing us to discover a novel MSC-EV manufacturing condition, as well as gain insight into potential mechanisms of MSC-EV microglia modulation. Our novel screening approach and application of priming to MSC-EV bioreactor manufacturing informs refinement of larger-scale manufacturing and enhancement of MSC-EV function.
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Affiliation(s)
- Andrew M. Larey
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Thomas M. Spoerer
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Kanupriya R. Daga
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Maria G. Morfin
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Hannah M. Hynds
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Jana Carpenter
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Ross A. Marklein
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
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2
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Kalinin AA, Arevalo J, Vulliard L, Serrano E, Tsang H, Bornholdt M, Rajwa B, Carpenter AE, Way GP, Singh S. A versatile information retrieval framework for evaluating profile strength and similarity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587631. [PMID: 38617315 PMCID: PMC11014546 DOI: 10.1101/2024.04.01.587631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
In profiling assays, thousands of biological properties are measured in a single test, yielding biological discoveries by capturing the state of a cell population, often at the single-cell level. However, for profiling datasets, it has been challenging to evaluate the phenotypic activity of a sample and the phenotypic consistency among samples, due to profiles' high dimensionality, heterogeneous nature, and non-linear properties. Existing methods leave researchers uncertain where to draw boundaries between meaningful biological response and technical noise. Here, we developed a statistical framework that uses the well-established mean average precision (mAP) as a single, data-driven metric to bridge this gap. We validated the mAP framework against established metrics through simulations and real-world data applications, revealing its ability to capture subtle and meaningful biological differences in cell state. Specifically, we used mAP to assess both phenotypic activity for a given perturbation (or a sample) as well as consistency within groups of perturbations (or samples) across diverse high-dimensional datasets. We evaluated the framework on different profile types (image, protein, and mRNA profiles), perturbation types (CRISPR gene editing, gene overexpression, and small molecules), and profile resolutions (single-cell and bulk). Our open-source software allows this framework to be applied to identify interesting biological phenomena and promising therapeutics from large-scale profiling data.
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Affiliation(s)
| | - John Arevalo
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Loan Vulliard
- Systems Immunology and Single-Cell Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Erik Serrano
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora CO, USA
| | - Hillary Tsang
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Michael Bornholdt
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette IN, USA
| | - Anne E. Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Gregory P. Way
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora CO, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
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3
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Faghtmann J, Eugui M, Nygaard Lamhauge J, Sofie Pladsbjerg Andresen S, Rask Østergaard A, Bjerregaard Svenningsen E, B Poulsen T, Anker Jørgensen K. An Enantioselective Aminocatalytic Cascade Reaction Affording Bioactive Hexahydroazulene Scaffolds. Chemistry 2024:e202401156. [PMID: 38564298 DOI: 10.1002/chem.202401156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/04/2024]
Abstract
A novel cascade reaction initiated by an enantioselective aminocatalysed 1,3-dipolar [6+4] cycloaddition between catalytically generated trienamines and 3-oxidopyridinium betaines is presented. The [6+4] cycloadduct spontaneously undergoes an intramolecular enamine-mediated aldol, hydrolysis, and E1cb sequence, which ultimately affords a chiral hexahydroazulene framework. In this process, three new C-C bonds and three new stereocenters are formed, enabled by a formal unfolding of the pyridine moiety from the dipolar reagent. The hexahydroazulenes are formed with excellent diastereo-, regio- and periselectivity (>20 : 1), up to 96 % ee, and yields up to 52 %. Synthetic elaborations of this scaffold were performed, providing access to a variety of functionalised hydroazulene compounds, of which some were found to display biological activity in U-2OS osteosarcoma cells in cell painting assays.
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Affiliation(s)
- Jonas Faghtmann
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Macarena Eugui
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | | | | | - Anne Rask Østergaard
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | | | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Karl Anker Jørgensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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4
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Larey AM, Spoerer TM, Daga KR, Morfin MG, Hynds HM, Carpenter J, Hines KM, Marklein RA. High throughput screening of mesenchymal stromal cell morphological response to inflammatory signals for bioreactor-based manufacturing of extracellular vesicles that modulate microglia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567730. [PMID: 38014258 PMCID: PMC10680807 DOI: 10.1101/2023.11.19.567730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Due to their immunomodulatory function, mesenchymal stromal cells (MSCs) are a promising therapeutic with the potential to treat neuroinflammation associated with neurodegenerative diseases. This function can be mediated by secreted extracellular vesicles (MSC-EVs). Despite established safety, MSC clinical translation has been unsuccessful due to inconsistent clinical outcomes resulting from functional heterogeneity. Current approaches to mitigate functional heterogeneity include 'priming' MSCs with inflammatory signals to enhance function. However, comprehensive evaluation of priming and its effects on MSC-EV function has not been performed. Clinical translation of MSC-EV therapies requires significant manufacturing scale-up, yet few studies have investigated the effects of priming in bioreactors. As MSC morphology has been shown to predict their immunomodulatory function, we screened MSC morphological response to an array of priming signals and evaluated MSC-EV identity and potency in response to priming in flasks and bioreactors. We identified unique priming conditions corresponding to distinct morphologies. These conditions demonstrated a range of MSC-EV preparation quality and lipidome, allowing us to discover a novel MSC-EV manufacturing condition, as well as gain insight into potential mechanisms of MSC-EV microglia modulation. Our novel screening approach and application of priming to MSC-EV bioreactor manufacturing informs refinement of larger-scale manufacturing and enhancement of MSC-EV function.
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Affiliation(s)
- Andrew M. Larey
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Thomas M. Spoerer
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Kanupriya R. Daga
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Maria G. Morfin
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Hannah M. Hynds
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Jana Carpenter
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Kelly M. Hines
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Ross A. Marklein
- School of Chemical, Materials, and Biomedical Engineering, University of Georgia, Athens, GA, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
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5
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Dahlin JL, Hua BK, Zucconi BE, Nelson SD, Singh S, Carpenter AE, Shrimp JH, Lima-Fernandes E, Wawer MJ, Chung LPW, Agrawal A, O'Reilly M, Barsyte-Lovejoy D, Szewczyk M, Li F, Lak P, Cuellar M, Cole PA, Meier JL, Thomas T, Baell JB, Brown PJ, Walters MA, Clemons PA, Schreiber SL, Wagner BK. Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nat Commun 2023; 14:1364. [PMID: 36914634 PMCID: PMC10011410 DOI: 10.1038/s41467-023-36829-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Robust, generalizable approaches to identify compounds efficiently with undesirable mechanisms of action in complex cellular assays remain elusive. Such a process would be useful for hit triage during high-throughput screening and, ultimately, predictive toxicology during drug development. Here we generate cell painting and cellular health profiles for 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in a concentration-response format. A diversity of compounds that cause cellular damage produces bioactive cell painting morphologies, including cytoskeletal poisons, genotoxins, nonspecific electrophiles, and redox-active compounds. Further, we show that lower quality lysine acetyltransferase inhibitors and nonspecific electrophiles can be distinguished from more selective counterparts. We propose that the purposeful inclusion of cytotoxic and nuisance reference compounds such as those profiled in this resource will help with assay optimization and compound prioritization in complex cellular assays like cell painting.
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Grants
- R35 GM127045 NIGMS NIH HHS
- U01 CA272612 NCI NIH HHS
- T32 HL007627 NHLBI NIH HHS
- R37 GM062437 NIGMS NIH HHS
- S10 OD026839 NIH HHS
- R35 GM122481 NIGMS NIH HHS
- U01 DK123717 NIDDK NIH HHS
- Wellcome Trust
- R35 GM122547 NIGMS NIH HHS
- U01 CA217848 NCI NIH HHS
- K99 GM124357 NIGMS NIH HHS
- R35 GM149229 NIGMS NIH HHS
- This study was supported by the Ono Pharma Breakthrough Science Initiative Award (to BKW). Authors acknowledge the following financial support: JLD (NIH NHLBI, T32-HL007627); BKH (National Science Foundation, DGE1144152 and DGE1745303); BEZ (NIH NIGMS, K99-GM124357); SDN (Harvard University’s Graduate Prize Fellowship, Eli Lilly Graduate Fellowship in Chemistry); PA Cole (NIH NIGMS, R37-GM62437); SLS (NIGMS, R35-GM127045); BKW (Ono Pharma Foundation; NIH NIDDK, U01-DK123717); SS (NIH NIGMS, R35-GM122547). The authors gratefully acknowledge the use of the Opera Phenix High-Content/High-Throughput imaging system at the Broad Institute, funded by the NIH S10 grant OD026839. This research was supported in part by the Intramural/Extramural research program of the NCATS, NIH.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Beth E Zucconi
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Lawrence P W Chung
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Ayushi Agrawal
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | | | | | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Parnian Lak
- Department of Pharmaceutical Chemistry and Quantitative Biology Institute, University of California San Francisco, San Francisco, CA, USA
| | - Matthew Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Tim Thomas
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
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6
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Vulliard L, Hancock J, Kamnev A, Fell CW, Ferreira da Silva J, Loizou JI, Nagy V, Dupré L, Menche J. BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. Bioinformatics 2022; 38:1692-1699. [PMID: 34935929 PMCID: PMC8896612 DOI: 10.1093/bioinformatics/btab853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION High-content imaging screens provide a cost-effective and scalable way to assess cell states across diverse experimental conditions. The analysis of the acquired microscopy images involves assembling and curating raw cellular measurements into morphological profiles suitable for testing biological hypotheses. Despite being a critical step, general-purpose and adaptable tools for morphological profiling are lacking and no solution is available for the high-performance Julia programming language. RESULTS Here, we introduce BioProfiling.jl, an efficient end-to-end solution for compiling and filtering informative morphological profiles in Julia. The package contains all the necessary data structures to curate morphological measurements and helper functions to transform, normalize and visualize profiles. Robust statistical distances and permutation tests enable quantification of the significance of the observed changes despite the high fraction of outliers inherent to high-content screens. This package also simplifies visual artifact diagnostics, thus streamlining a bottleneck of morphological analyses. We showcase the features of the package by analyzing a chemical imaging screen, in which the morphological profiles prove to be informative about the compounds' mechanisms of action and can be conveniently integrated with the network localization of molecular targets. AVAILABILITY AND IMPLEMENTATION The Julia package is available on GitHub: https://github.com/menchelab/BioProfiling.jl. We also provide Jupyter notebooks reproducing our analyses: https://github.com/menchelab/BioProfilingNotebooks. The data underlying this article are available from FigShare, at https://doi.org/10.6084/m9.figshare.14784678.v2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Loan Vulliard
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna 1030, Austria
| | - Joel Hancock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna 1030, Austria
| | - Anton Kamnev
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
| | - Christopher W Fell
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Neurology, Medical University of Vienna, Vienna 1090, Austria
| | - Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna 1090, Austria
| | - Vanja Nagy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Neurology, Medical University of Vienna, Vienna 1090, Austria
| | - Loïc Dupré
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna 1090, Austria
- Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR1291, CNRS UMR5051, Toulouse III Paul Sabatier University, Toulouse 31024, France
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7
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German Y, Vulliard L, Kamnev A, Pfajfer L, Huemer J, Mautner AK, Rubio A, Kalinichenko A, Boztug K, Ferrand A, Menche J, Dupré L. Morphological profiling of human T and NK lymphocytes by high-content cell imaging. Cell Rep 2021; 36:109318. [PMID: 34233185 DOI: 10.1016/j.celrep.2021.109318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 02/25/2021] [Accepted: 06/07/2021] [Indexed: 01/21/2023] Open
Abstract
The immunological synapse is a complex structure that decodes stimulatory signals into adapted lymphocyte responses. It is a unique window to monitor lymphocyte activity because of development of systematic quantitative approaches. Here we demonstrate the applicability of high-content imaging to human T and natural killer (NK) cells and develop a pipeline for unbiased analysis of high-definition morphological profiles. Our approach reveals how distinct facets of actin cytoskeleton remodeling shape immunological synapse architecture and affect lytic granule positioning. Morphological profiling of CD8+ T cells from immunodeficient individuals allows discrimination of the roles of the ARP2/3 subunit ARPC1B and the ARP2/3 activator Wiskott-Aldrich syndrome protein (WASP) in immunological synapse assembly. Single-cell analysis further identifies uncoupling of lytic granules and F-actin radial distribution in ARPC1B-deficient lymphocytes. Our study provides a foundation for development of morphological profiling as a scalable approach to monitor primary lymphocyte responsiveness and to identify complex aspects of lymphocyte micro-architecture.
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Affiliation(s)
- Yolla German
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR1291, CNRS UMR5051, Toulouse III Paul Sabatier University, Toulouse, France; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria
| | - Loan Vulliard
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Anton Kamnev
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria; Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Laurène Pfajfer
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR1291, CNRS UMR5051, Toulouse III Paul Sabatier University, Toulouse, France; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria
| | - Jakob Huemer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria; St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Anna-Katharina Mautner
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria; Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Aude Rubio
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
| | - Artem Kalinichenko
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria; St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Audrey Ferrand
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, 31024 Toulouse, France
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria; Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Loïc Dupré
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR1291, CNRS UMR5051, Toulouse III Paul Sabatier University, Toulouse, France; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria; Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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8
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Liu Y, Izzo JA, McLeod D, Ričko S, Svenningsen EB, Poulsen TB, Jørgensen KA. Organocatalytic Asymmetric Multicomponent Cascade Reaction for the Synthesis of Contiguously Substituted Tetrahydronaphthols. J Am Chem Soc 2021; 143:8208-8220. [PMID: 34028261 DOI: 10.1021/jacs.1c03923] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Isobenzopyrylium ions are unique, highly reactive, aromatic intermediates which are largely unexplored in asymmetric catalysis despite their high potential synthetic utility. In this study, an organocatalytic asymmetric multicomponent cascade via dienamine catalysis, involving a cycloaddition, a nucleophilic addition, and a ring-opening reaction, is disclosed. The reaction furnishes chiral tetrahydronaphthols containing four contiguous stereocenters in good to high yield, high diastereoselectivity (up to >20:1), and excellent enantioselectivity (93-98% ee). The obtained products are important synthetic intermediates, and it is demonstrated that they can be used for the generation of frameworks such as octahydrobenzo[h]isoquinoline and [2.2.2]octane scaffolds. Furthermore, mechanistic experiments involving oxygen-18-labeling studies and density functional theory calculations provide a vivid picture of the reaction mechanism. Finally, the bioactivity of 16 representative tetrahydronaphthol compounds has been evaluated in U-2OS cancer cells with some compounds showing a unique profile and a clear morphological change.
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Affiliation(s)
- Yidong Liu
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Joseph A Izzo
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - David McLeod
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Sebastijan Ričko
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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9
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Ziegler S, Sievers S, Waldmann H. Morphological profiling of small molecules. Cell Chem Biol 2021; 28:300-319. [PMID: 33740434 DOI: 10.1016/j.chembiol.2021.02.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/22/2021] [Accepted: 02/17/2021] [Indexed: 12/30/2022]
Abstract
Profiling approaches such as gene expression or proteome profiling generate small-molecule bioactivity profiles that describe a perturbed cellular state in a rather unbiased manner and have become indispensable tools in the evaluation of bioactive small molecules. Automated imaging and image analysis can record morphological alterations that are induced by small molecules through the detection of hundreds of morphological features in high-throughput experiments. Thus, morphological profiling has gained growing attention in academia and the pharmaceutical industry as it enables detection of bioactivity in compound collections in a broader biological context in the early stages of compound development and the drug-discovery process. Profiling may be used successfully to predict mode of action or targets of unexplored compounds and to uncover unanticipated activity for already characterized small molecules. Here, we review the reported approaches to morphological profiling and the kind of bioactivity that can be detected so far and, thus, predicted.
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Affiliation(s)
- Slava Ziegler
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Sonja Sievers
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany.
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10
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Lin S, Liu H, Svenningsen EB, Wollesen M, Jacobsen KM, Andersen FD, Moyano-Villameriel J, Pedersen CN, Nørby P, Tørring T, Poulsen TB. Expanding the antibacterial selectivity of polyether ionophore antibiotics through diversity-focused semisynthesis. Nat Chem 2020; 13:47-55. [PMID: 33353970 PMCID: PMC7610524 DOI: 10.1038/s41557-020-00601-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
Polyether ionophores are complex natural products capable of transporting cations across biological membranes. Many polyether ionophores possess potent antimicrobial activity and a few selected compounds have ability to target aggressive cancer cells. Nevertheless, ionophore function is believed to be associated with idiosyncratic cellu-lar toxicity and, consequently, human clinical development has not been pursued. Here, we demonstrate that structurally novel polyether ionophores can be efficiently constructed by recycling components of highly abundant polyethers to afford analogues with enhanced anti-bacterial selectivity compared to a panel of natural polyether ionophores. We used classic degradation reactions of the natural polyethers lasalocid and monensin and combined the resulting fragments with building blocks provided by total synthesis, including halogen-functionalized tetronic acids as cation-binding groups. Our results suggest that structural optimization of polyether ionophores is possible and that this area represents a potential opportunity for future methodological innovation.
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Affiliation(s)
- Shaoquan Lin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Han Liu
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | | | | | - Frederikke D Andersen
- Department of Engineering-Microbial Biosynthesis, Aarhus University, Aarhus, Denmark
| | | | | | - Peter Nørby
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Thomas Tørring
- Department of Engineering-Microbial Biosynthesis, Aarhus University, Aarhus, Denmark
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11
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Olagnier D, Farahani E, Thyrsted J, Blay-Cadanet J, Herengt A, Idorn M, Hait A, Hernaez B, Knudsen A, Iversen MB, Schilling M, Jørgensen SE, Thomsen M, Reinert LS, Lappe M, Hoang HD, Gilchrist VH, Hansen AL, Ottosen R, Nielsen CG, Møller C, van der Horst D, Peri S, Balachandran S, Huang J, Jakobsen M, Svenningsen EB, Poulsen TB, Bartsch L, Thielke AL, Luo Y, Alain T, Rehwinkel J, Alcamí A, Hiscott J, Mogensen TH, Paludan SR, Holm CK. SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate. Nat Commun 2020; 11:4938. [PMID: 33009401 PMCID: PMC7532469 DOI: 10.1038/s41467-020-18764-3] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023] Open
Abstract
Antiviral strategies to inhibit Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the pathogenic consequences of COVID-19 are urgently required. Here, we demonstrate that the NRF2 antioxidant gene expression pathway is suppressed in biopsies obtained from COVID-19 patients. Further, we uncover that NRF2 agonists 4-octyl-itaconate (4-OI) and the clinically approved dimethyl fumarate (DMF) induce a cellular antiviral program that potently inhibits replication of SARS-CoV2 across cell lines. The inhibitory effect of 4-OI and DMF extends to the replication of several other pathogenic viruses including Herpes Simplex Virus-1 and-2, Vaccinia virus, and Zika virus through a type I interferon (IFN)-independent mechanism. In addition, 4-OI and DMF limit host inflammatory responses to SARS-CoV2 infection associated with airway COVID-19 pathology. In conclusion, NRF2 agonists 4-OI and DMF induce a distinct IFN-independent antiviral program that is broadly effective in limiting virus replication and in suppressing the pro-inflammatory responses of human pathogenic viruses, including SARS-CoV2.
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Affiliation(s)
- David Olagnier
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark.
| | - Ensieh Farahani
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Jacob Thyrsted
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Julia Blay-Cadanet
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Angela Herengt
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Manja Idorn
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Alon Hait
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Bruno Hernaez
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Alice Knudsen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Marie Beck Iversen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Mirjam Schilling
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Sofie E Jørgensen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Michelle Thomsen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | | | - Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8L1, Canada
| | - Victoria H Gilchrist
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8L1, Canada
| | - Anne Louise Hansen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Rasmus Ottosen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Camilla G Nielsen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Charlotte Møller
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Demi van der Horst
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Suraj Peri
- Fox Chase Cancer Center, 333 Cottman Avenue, Philidelphia, PA, 19111-2497, USA
| | | | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Martin Jakobsen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | | | | | - Lydia Bartsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Anne L Thielke
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, BGI-Shenzhen, Shenzhen, 518083, China
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8L1, Canada
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Nicolás Cabrera 1, 28049, Madrid, Spain
| | - John Hiscott
- Istituto Pasteur Italia-Cenci Bolognetti Foundation, Viale Regina Elena 291, 00161, Rome, Italy
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark
| | - Christian K Holm
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, Aarhus University, Aarhus, Denmark.
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12
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Hippman RS, Pavlinov I, Gao Q, Mavlyanova MK, Gerlach EM, Aldrich LN. Multiple Chemical Features Impact Biological Performance Diversity of a Highly Active Natural Product-Inspired Library. Chembiochem 2020; 21:3137-3145. [PMID: 32558167 DOI: 10.1002/cbic.202000356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 12/12/2022]
Abstract
A systematic, diversity-oriented synthesis approach was employed to access a natural product-inspired flavonoid library with diverse chemical features, including chemical properties, scaffold, stereochemistry, and appendages. Using Cell Painting, the effects of these diversity elements were evaluated, and multiple chemical features that predict biological performance diversity were identified. Scaffold identity appears to be the dominant predictor of performance diversity, but stereochemistry and appendages also contribute to a lesser degree. In addition, the diversity of chemical properties contributed to performance diversity, and the driving chemical property was dependent on the scaffold. These results highlight the importance of key chemical features that may inform the creation of small-molecule, performance-diverse libraries to improve the efficiency and success of high-throughput screening campaigns.
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Affiliation(s)
- Ryan S Hippman
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Ivan Pavlinov
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Qiwen Gao
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Michelle K Mavlyanova
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Erica M Gerlach
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Leslie N Aldrich
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
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13
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Mapping the perturbome network of cellular perturbations. Nat Commun 2019; 10:5140. [PMID: 31723137 PMCID: PMC6853941 DOI: 10.1038/s41467-019-13058-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/15/2019] [Indexed: 12/15/2022] Open
Abstract
Drug combinations provide effective treatments for diverse diseases, but also represent a major cause of adverse reactions. Currently there is no systematic understanding of how the complex cellular perturbations induced by different drugs influence each other. Here, we introduce a mathematical framework for classifying any interaction between perturbations with high-dimensional effects into 12 interaction types. We apply our framework to a large-scale imaging screen of cell morphology changes induced by diverse drugs and their combination, resulting in a perturbome network of 242 drugs and 1832 interactions. Our analysis of the chemical and biological features of the drugs reveals distinct molecular fingerprints for each interaction type. We find a direct link between drug similarities on the cell morphology level and the distance of their respective protein targets within the cellular interactome of molecular interactions. The interactome distance is also predictive for different types of drug interactions. Our understanding of the mechanisms of drug interactions remains limited. Here the authors introduce a framework to study how complex cellular perturbations induced by different drugs affect each other in morphological feature space.
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14
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Gerlach EM, Korkmaz MA, Pavlinov I, Gao Q, Aldrich LN. Systematic Diversity-Oriented Synthesis of Reduced Flavones from γ-Pyrones to Probe Biological Performance Diversity. ACS Chem Biol 2019; 14:1536-1545. [PMID: 31184855 DOI: 10.1021/acschembio.9b00294] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Diversity-oriented synthesis (DOS) has historically focused on the development of small-molecule collections with considerable chemical diversity with the hypothesis that chemical diversity will lead to diverse biological activities. We took a systematic approach to DOS to develop a focused library of reduced flavones from γ-pyrones with diversity of appendage, stereochemistry, and chemical properties to determine which features of small molecules are most predictive of biological performance diversity. The effects of these systematic modifications on biodiversity were determined using Cell Painting and cytotoxicity assays to compare the results of multiple methods of assessment. We observed that a greater fraction of sp3 hybridized atoms (fsp3) does not always lead to enhanced biodiversity, that stereochemistry and appendage diversity both contribute to biodiversity, and that lipophilicity of the pyrone class of compounds correlates with biodiversity. These results will contribute to the development of a general algorithm to predict which chemical features should be considered during the synthesis of DOS libraries to create biological performance-diverse collections of small molecules for probe and drug discovery.
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Affiliation(s)
- Erica M. Gerlach
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Melissa A. Korkmaz
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Ivan Pavlinov
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Qiwen Gao
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Leslie N. Aldrich
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
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15
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Pavlinov I, Gerlach EM, Aldrich LN. Next generation diversity-oriented synthesis: a paradigm shift from chemical diversity to biological diversity. Org Biomol Chem 2019; 17:1608-1623. [PMID: 30328455 DOI: 10.1039/c8ob02327a] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Diversity-oriented synthesis adds biological performance as a new diversity element.
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Affiliation(s)
- Ivan Pavlinov
- University of Illinois at Chicago
- Department of Chemistry
- 845 West Taylor Street
- USA
| | - Erica M. Gerlach
- University of Illinois at Chicago
- Department of Chemistry
- 845 West Taylor Street
- USA
| | - Leslie N. Aldrich
- University of Illinois at Chicago
- Department of Chemistry
- 845 West Taylor Street
- USA
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16
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Pahl A, Sievers S. The Cell Painting Assay as a Screening Tool for the Discovery of Bioactivities in New Chemical Matter. Methods Mol Biol 2019; 1888:115-126. [PMID: 30519943 DOI: 10.1007/978-1-4939-8891-4_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiparametric phenotypic screening based on cellular morphology interrogates many biological pathways simultaneously and is therefore a valuable screening tool for the discovery of new biological activities. The cell painting assay stains various cellular features using six different dyes in one well. By automated image analysis, hundreds of parameters are calculated from the images which deliver a phenotypic profile of the cell. It has been shown that compounds with similar modes of action deliver similar phenotypic profiles. Using a reference set of compounds with known modes of action, it is possible to assign probable modes of action to new compounds and to discover compounds with potentially new modes of action.Here we describe the cell painting assay as a screening tool using a hit identification workflow which has been implemented using open-source software.
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Affiliation(s)
- Axel Pahl
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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17
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Melillo B, Zoller J, Hua BK, Verho O, Borghs JC, Nelson SD, Maetani M, Wawer MJ, Clemons PA, Schreiber SL. Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds. J Am Chem Soc 2018; 140:11784-11790. [PMID: 30133283 DOI: 10.1021/jacs.8b07319] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Target- and phenotype-agnostic assessments of biological activity have emerged as viable strategies for prioritizing scaffolds, structural features, and synthetic pathways in screening sets, with the goal of increasing performance diversity. Here, we describe the synthesis of a small library of functionalized stereoisomeric azetidines and its biological annotation by "cell painting," a multiplexed, high-content imaging assay capable of measuring many hundreds of compound-induced changes in cell morphology in a quantitative and unbiased fashion. Using this approach, we systematically compare the degrees to which a core scaffold's biological activity, inferred from its effects on cell morphology, is affected by variations in stereochemistry and appendages. We show that stereoisomerism and appendage diversification can produce effects of similar magnitude, and that the concurrent use of these strategies results in a broader sampling of biological activity.
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Affiliation(s)
- Bruno Melillo
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Jochen Zoller
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Bruce K Hua
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Oscar Verho
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Jannik C Borghs
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States.,Institute of Organic Chemistry , RWTH Aachen University , 52074 Aachen , Germany
| | - Shawn D Nelson
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Micah Maetani
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , Cambridge , Massachusetts 02142 , United States.,Howard Hughes Medical Institute , Cambridge , Massachusetts 02138 , United States
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18
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Data-analysis strategies for image-based cell profiling. Nat Methods 2017; 14:849-863. [PMID: 28858338 PMCID: PMC6871000 DOI: 10.1038/nmeth.4397] [Citation(s) in RCA: 375] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/28/2017] [Indexed: 12/16/2022]
Abstract
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.
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19
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Gerry C, Hua BK, Wawer M, Knowles JP, Nelson Jr. SD, Verho O, Dandapani S, Wagner BK, Clemons PA, Booker-Milburn K, Boskovic ZV, Schreiber SL. Real-Time Biological Annotation of Synthetic Compounds. J Am Chem Soc 2016; 138:8920-7. [PMID: 27398798 PMCID: PMC4976700 DOI: 10.1021/jacs.6b04614] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 01/01/2023]
Abstract
Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in biological systems, and those that do are often tested long after the chemist can incorporate the results into synthetic planning. We propose the use of high-dimensional "multiplex" assays, which are capable of measuring thousands of cellular features in one experiment, to annotate rapidly and inexpensively the biological activities of newly synthesized compounds. This readily accessible and inexpensive "real-time" profiling method can be used in a prospective manner to facilitate, for example, the efficient construction of performance-diverse small-molecule libraries that are enriched in bioactives. Here, we demonstrate this concept by synthesizing ten triads of constitutionally isomeric compounds via complexity-generating photochemical and thermal rearrangements and measuring compound-induced changes in cellular morphology via an imaging-based "cell painting" assay. Our results indicate that real-time biological annotation can inform optimization efforts and library syntheses by illuminating trends relating to biological activity that would be difficult to predict if only chemical structure were considered. We anticipate that probe and drug discovery will benefit from the use of optimization efforts and libraries that implement this approach.
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Affiliation(s)
- Christopher
J. Gerry
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Bruce K. Hua
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Mathias
J. Wawer
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jonathan P. Knowles
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Shawn D. Nelson Jr.
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Oscar Verho
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Sivaraman Dandapani
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Bridget K. Wagner
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Paul A. Clemons
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Kevin
I. Booker-Milburn
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Zarko V. Boskovic
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Stuart L. Schreiber
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Center for the Science of Therapeutics and Howard Hughes Medical
Institute, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
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20
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Gingold JA, Coakley ES, Su J, Lee DF, Lau Z, Zhou H, Felsenfeld DP, Schaniel C, Lemischka IR. Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen. BMC Bioinformatics 2015. [PMID: 26198214 PMCID: PMC4511455 DOI: 10.1186/s12859-015-0636-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Chemical or small interfering (si) RNA screens measure the effects of many independent experimental conditions, each applied to a population of cells (e.g., all of the cells in a well). High-content screens permit a readout (e.g., fluorescence, luminescence, cell morphology) from each cell in the population. Most analysis approaches compare the average effect on each population, precluding identification of outliers that affect the distribution of the reporter in the population but not its average. Other approaches only measure changes to the distribution with a single parameter, precluding accurate distinction and clustering of interesting outlier distributions. Results We describe a methodology to identify outlier conditions by considering the cell-level measurements from each condition as a sample of an underlying distribution. With appropriate selection of a distance metric, all effects can be embedded in a fixed-dimensionality Euclidean basis, facilitating identification and clustering of biologically interesting outliers. We demonstrate that measurement of distances with the Hellinger distance metric offers substantial computational efficiencies over alternative metrics. We validate this methodology using an RNA interference (RNAi) screen in mouse embryonic stem cells (ESC) with a Nanog reporter. The methodology clusters effects of multiple control siRNAs into their true identities better than conventional approaches describing the median cell fluorescence or the commonly used Kolmogorov-Smirnov distance between the observed fluorescence distribution and the null distribution. It identifies outlier genes with effects on the reporter distribution that would have been missed by other methods. Among them, siRNA targeting Chek1 leads to a wider Nanog reporter fluorescence distribution. Similarly, siRNA targeting Med14 or Med27 leads to a narrower Nanog reporter fluorescence distribution. We confirm the roles of these three genes in regulating pluripotency by mRNA expression and alkaline phosphatase staining using independent short hairpin (sh) RNAs. Conclusions Using our methodology, we describe each experimental condition by a probability distribution. Measuring distances between probability distributions permits a multivariate rather than univariate readout. Clustering points derived from these distances allows us to obtain greater biological insight than methods based solely on single parameters. We find several outliers from a mouse ESC RNAi screen that we confirm to be pluripotency regulators. Many of these outliers would have been missed by other analysis methods. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0636-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julian A Gingold
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Ed S Coakley
- Program in Applied Mathematics, Yale University, New Haven, CT, 06511, USA.
| | - Jie Su
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Dung-Fang Lee
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zerlina Lau
- Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hongwei Zhou
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Dan P Felsenfeld
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Integrated Screening Core, Experimental Therapeutics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Christoph Schaniel
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Ihor R Lemischka
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. .,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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21
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Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Proc Natl Acad Sci U S A 2014; 111:10911-6. [PMID: 25024206 DOI: 10.1073/pnas.1410933111] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
High-throughput screening has become a mainstay of small-molecule probe and early drug discovery. The question of how to build and evolve efficient screening collections systematically for cell-based and biochemical screening is still unresolved. It is often assumed that chemical structure diversity leads to diverse biological performance of a library. Here, we confirm earlier results showing that this inference is not always valid and suggest instead using biological measurement diversity derived from multiplexed profiling in the construction of libraries with diverse assay performance patterns for cell-based screens. Rather than using results from tens or hundreds of completed assays, which is resource intensive and not easily extensible, we use high-dimensional image-based cell morphology and gene expression profiles. We piloted this approach using over 30,000 compounds. We show that small-molecule profiling can be used to select compound sets with high rates of activity and diverse biological performance.
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22
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Yatkin E, Polari L, Laajala TD, Smeds A, Eckerman C, Holmbom B, Saarinen NM, Aittokallio T, Mäkelä SI. Novel Lignan and stilbenoid mixture shows anticarcinogenic efficacy in preclinical PC-3M-luc2 prostate cancer model. PLoS One 2014; 9:e93764. [PMID: 24699425 PMCID: PMC3974786 DOI: 10.1371/journal.pone.0093764] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/08/2014] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer is the most common cancer of men in the Western world, and novel approaches for prostate cancer risk reduction are needed. Plant-derived phenolic compounds attenuate prostate cancer growth in preclinical models by several mechanisms, which is in line with epidemiological findings suggesting that consumption of plant-based diets is associated with low risk of prostate cancer. The objective of this study was to assess the effects of a novel lignan-stilbenoid mixture in PC-3M-luc2 human prostate cancer cells in vitro and in orthotopic xenografts. Lignan and stilbenoid –rich extract was obtained from Scots pine (Pinus sylvestris) knots. Pine knot extract as well as stilbenoids (methyl pinosylvin and pinosylvin), and lignans (matairesinol and nortrachelogenin) present in pine knot extract showed antiproliferative and proapoptotic efficacy at ≥40 μM concentration in vitro. Furthermore, pine knot extract derived stilbenoids enhanced tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induced apoptosis already at ≥10 μM concentrations. In orthotopic PC-3M-luc2 xenograft bearing immunocompromized mice, three-week peroral exposure to pine knot extract (52 mg of lignans and stilbenoids per kg of body weight) was well tolerated and showed anti-tumorigenic efficacy, demonstrated by multivariate analysis combining essential markers of tumor growth (i.e. tumor volume, vascularization, and cell proliferation). Methyl pinosylvin, pinosylvin, matairesinol, nortrachelogenin, as well as resveratrol, a metabolite of pinosylvin, were detected in serum at total concentration of 7−73 μM, confirming the bioavailability of pine knot extract derived lignans and stilbenoids. In summary, our data indicates that pine knot extract is a novel and cost-effective source of resveratrol, methyl pinosylvin and other bioactive lignans and stilbenoids. Pine knot extract shows anticarcinogenic efficacy in preclinical prostate cancer model, and our in vitro data suggests that compounds derived from the extract may have potential as novel chemosensitizers to TRAIL. These findings promote further research on health-related applications of wood biochemicals.
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Affiliation(s)
- Emrah Yatkin
- Functional Foods Forum, University of Turku, Turku, Finland
- Turku Center for Disease Modeling (TCDM), Institute of Biomedicine, University of Turku, Turku, Finland
| | - Lauri Polari
- Functional Foods Forum, University of Turku, Turku, Finland
- Turku Center for Disease Modeling (TCDM), Institute of Biomedicine, University of Turku, Turku, Finland
| | - Teemu D. Laajala
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Annika Smeds
- Åbo Akademi University, Process Chemistry Centre, Laboratory of Wood and Paper Chemistry, Turku, Finland
| | - Christer Eckerman
- Åbo Akademi University, Process Chemistry Centre, Laboratory of Wood and Paper Chemistry, Turku, Finland
| | - Bjarne Holmbom
- Åbo Akademi University, Process Chemistry Centre, Laboratory of Wood and Paper Chemistry, Turku, Finland
| | - Niina M. Saarinen
- Functional Foods Forum, University of Turku, Turku, Finland
- Turku Center for Disease Modeling (TCDM), Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tero Aittokallio
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sari I. Mäkelä
- Functional Foods Forum, University of Turku, Turku, Finland
- Turku Center for Disease Modeling (TCDM), Institute of Biomedicine, University of Turku, Turku, Finland
- * E-mail:
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23
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Abraham Y, Zhang X, Parker CN. Multiparametric Analysis of Screening Data: Growing Beyond the Single Dimension to Infinity and Beyond. ACTA ACUST UNITED AC 2014; 19:628-39. [PMID: 24598104 DOI: 10.1177/1087057114524987] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 01/14/2014] [Indexed: 11/16/2022]
Abstract
Advances in instrumentation now allow the development of screening assays that are capable of monitoring multiple readouts such as transcript or protein levels, or even multiple parameters derived from images. Such advances in assay technologies highlight the complex nature of biology and disease. Harnessing this complexity requires integration of all the different parameters that can be measured rather than just monitoring a single dimension as is commonly used. Although some of the methods used to combine multiple measurements, such as principal component analysis, are commonly used for microarray analysis, biologists are not yet using many of the tools that have been developed in other fields to address such issues. Visualization of multiparametric data sets is one of the major challenges in this field, and a depiction of the results in a manner that can be readily interpreted is essential. This article describes a number of assay systems being used to generate such data sets en masse, and the methods being applied to their visualization and analysis. We also discuss some of the challenges of applying methods developed in other fields to biology.
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Affiliation(s)
- Yann Abraham
- Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Xian Zhang
- Novartis Institute for Biomedical Research, Basel, Switzerland
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24
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Isherwood BJ, Walls RE, Roberts ME, Houslay TM, Brave SR, Barry ST, Carragher NO. High-content analysis to leverage a robust phenotypic profiling approach to vascular modulation. ACTA ACUST UNITED AC 2013; 18:1246-59. [PMID: 24108119 DOI: 10.1177/1087057113499775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Phenotypic screening seeks to identify substances that modulate phenotypes in a desired manner with the aim of progressing first-in-class agents. Successful campaigns require physiological relevance, robust screening, and an ability to deconvolute perturbed pathways. High-content analysis (HCA) is increasingly used in cell biology and offers one approach to prosecution of phenotypic screens, but challenges exist in exploitation where data generated are high volume and complex. We combine development of an organotypic model with novel HCA tools to map phenotypic responses to pharmacological perturbations. We describe implementation for angiogenesis, a process that has long been a focus for therapeutic intervention but has lacked robust models that recapitulate more completely mechanisms involved. The study used human primary endothelial cells in co-culture with stromal fibroblasts to model multiple aspects of angiogenic signaling: cell interactions, proliferation, migration, and differentiation. Multiple quantitative descriptors were derived from automated microscopy using custom-designed algorithms. Data were extracted using a bespoke informatics platform that integrates processing, statistics, and feature display into a streamlined workflow for building and interrogating fingerprints. Ninety compounds were characterized, defining mode of action by phenotype. Our approach for assessing phenotypic outcomes in complex assay models is robust and capable of supporting a range of phenotypic screens at scale.
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