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McDiarmid AH, Gospodinova KO, Elliott RJR, Dawson JC, Graham RE, El-Daher MT, Anderson SM, Glen SC, Glerup S, Carragher NO, Evans KL. Morphological profiling in human neural progenitor cells classifies hits in a pilot drug screen for Alzheimer's disease. Brain Commun 2024; 6:fcae101. [PMID: 38576795 PMCID: PMC10994270 DOI: 10.1093/braincomms/fcae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
Alzheimer's disease accounts for 60-70% of dementia cases. Current treatments are inadequate and there is a need to develop new approaches to drug discovery. Recently, in cancer, morphological profiling has been used in combination with high-throughput screening of small-molecule libraries in human cells in vitro. To test feasibility of this approach for Alzheimer's disease, we developed a cell morphology-based drug screen centred on the risk gene, SORL1 (which encodes the protein SORLA). Increased Alzheimer's disease risk has been repeatedly linked to variants in SORL1, particularly those conferring loss or decreased expression of SORLA, and lower SORL1 levels are observed in post-mortem brain samples from individuals with Alzheimer's disease. Consistent with its role in the endolysosomal pathway, SORL1 deletion is associated with enlarged endosomes in neural progenitor cells and neurons. We, therefore, hypothesized that multi-parametric, image-based cell phenotyping would identify features characteristic of SORL1 deletion. An automated morphological profiling method (Cell Painting) was adapted to neural progenitor cells and used to determine the phenotypic response of SORL1-/- neural progenitor cells to treatment with compounds from a small internationally approved drug library (TargetMol, 330 compounds). We detected distinct phenotypic signatures for SORL1-/- neural progenitor cells compared to isogenic wild-type controls. Furthermore, we identified 16 compounds (representing 14 drugs) that reversed the mutant morphological signatures in neural progenitor cells derived from three SORL1-/- induced pluripotent stem cell sub-clones. Network pharmacology analysis revealed the 16 compounds belonged to five mechanistic groups: 20S proteasome, aldehyde dehydrogenase, topoisomerase I and II, and DNA synthesis inhibitors. Enrichment analysis identified DNA synthesis/damage/repair, proteases/proteasome and metabolism as key pathways/biological processes. Prediction of novel targets revealed enrichment in pathways associated with neural cell function and Alzheimer's disease. Overall, this work suggests that (i) a quantitative phenotypic metric can distinguish induced pluripotent stem cell-derived SORL1-/- neural progenitor cells from isogenic wild-type controls and (ii) phenotypic screening combined with multi-parametric high-content image analysis is a viable option for drug repurposing and discovery in this human neural cell model of Alzheimer's disease.
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Affiliation(s)
- Amina H McDiarmid
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Katerina O Gospodinova
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Richard J R Elliott
- Cancer Research UK Scotland Centre, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - John C Dawson
- Cancer Research UK Scotland Centre, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Rebecca E Graham
- Cancer Research UK Scotland Centre, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Marie-Therese El-Daher
- Medical Research Council Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Susan M Anderson
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Sophie C Glen
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Simon Glerup
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Neil O Carragher
- Cancer Research UK Scotland Centre, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Kathryn L Evans
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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2
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Baillache DJ, Valero T, Lorente-Macías Á, Bennett DJ, Elliott RJR, Carragher NO, Unciti-Broceta A. Discovery of pyrazolopyrimidines that selectively inhibit CSF-1R kinase by iterative design, synthesis and screening against glioblastoma cells. RSC Med Chem 2023; 14:2611-2624. [PMID: 38099057 PMCID: PMC10718585 DOI: 10.1039/d3md00454f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/09/2023] [Indexed: 12/17/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive type of brain cancer in adults, with an average life expectancy under treatment of approx. 15 months. GBM is characterised by a complex set of genetic alterations that results in significant disruption of receptor tyrosine kinase (RTK) signaling. We report here an exploration of the pyrazolo[3,4-d]pyrimidine scaffold in search for antiproliferative compounds directed to GBM treatment. Small compound libraries were synthesised and screened against GBM cells to build up structure-antiproliferative activity-relationships (SAARs) and inform further rounds of design, synthesis and screening. 76 novel compounds were generated through this iterative process that found low micromolar potencies against selected GBM lines, including patient-derived stem cells. Phenomics analysis demonstrated preferential activity against glioma cells of the mesenchymal subtype, whereas kinome screening identified colony stimulating factor-1 receptor (CSF-1R) as the lead's target, a RTK implicated in the tumourigenesis and progression of different cancers and the immunoregulation of the GBM microenvironment.
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Affiliation(s)
- Daniel J Baillache
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Teresa Valero
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | | | - Richard J R Elliott
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Neil O Carragher
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
| | - Asier Unciti-Broceta
- Edinburgh Cancer Research, Institute of Genetics & Cancer, University of Edinburgh Crewe Road South Edinburgh EH4 2XR UK
- Cancer Research UK Scotland Centre UK
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3
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Graham RE, Elliott RJR, Munro AF, Carragher NO. A cautionary note on the use of N-acetylcysteine as a reactive oxygen species antagonist to assess copper mediated cell death. PLoS One 2023; 18:e0294297. [PMID: 38079440 PMCID: PMC10712875 DOI: 10.1371/journal.pone.0294297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/29/2023] [Indexed: 12/18/2023] Open
Abstract
A new form of cell death has recently been proposed involving copper-induced cell death, termed cuproptosis. This new form of cell death has been widely studied in relation to a novel class of copper ionophores, including elesclomol and disulfiram. However, the exact mechanism leading to cell death remains contentious. The oldest and most widely accepted biological mechanism is that the accumulated intracellular copper leads to excessive build-up of reactive oxygen species and that this is what ultimately leads to cell death. Most of this evidence is largely based on studies using N-acetylcysteine (NAC), an antioxidant, to relieve the oxidative stress and prevent cell death. However, here we have demonstrated using inductively coupled mass-spectrometry, that NAC pretreatment significantly reduces intracellular copper uptake triggered by the ionophores, elesclomol and disulfiram, suggesting that reduction in copper uptake, rather than the antioxidant activity of NAC, is responsible for the diminished cell death. We present further data showing that key mediators of reactive oxygen species are not upregulated in response to elesclomol treatment, and further that sensitivity of cancer cell lines to reactive oxygen species does not correlate with sensitivity to these copper ionophores. Our findings are in line with several recent studies proposing the mechanism of cuproptosis is instead via copper mediated aggregation of proteins, resulting in proteotoxic stress leading to cell death. Overall, it is vital to disseminate this key piece of information regarding NAC's activity on copper uptake since new research attributing the effect of NAC on copper ionophore activity to quenching of reactive oxygen species is being published regularly and our studies suggest their conclusions may be misleading.
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Affiliation(s)
- Rebecca E. Graham
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard J. R. Elliott
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Alison F. Munro
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Neil O. Carragher
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
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4
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Smer-Barreto V, Quintanilla A, Elliott RJR, Dawson JC, Sun J, Campa VM, Lorente-Macías Á, Unciti-Broceta A, Carragher NO, Acosta JC, Oyarzún DA. Discovery of senolytics using machine learning. Nat Commun 2023; 14:3445. [PMID: 37301862 PMCID: PMC10257182 DOI: 10.1038/s41467-023-39120-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Cellular senescence is a stress response involved in ageing and diverse disease processes including cancer, type-2 diabetes, osteoarthritis and viral infection. Despite growing interest in targeted elimination of senescent cells, only few senolytics are known due to the lack of well-characterised molecular targets. Here, we report the discovery of three senolytics using cost-effective machine learning algorithms trained solely on published data. We computationally screened various chemical libraries and validated the senolytic action of ginkgetin, periplocin and oleandrin in human cell lines under various modalities of senescence. The compounds have potency comparable to known senolytics, and we show that oleandrin has improved potency over its target as compared to best-in-class alternatives. Our approach led to several hundred-fold reduction in drug screening costs and demonstrates that artificial intelligence can take maximum advantage of small and heterogeneous drug screening data, paving the way for new open science approaches to early-stage drug discovery.
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Affiliation(s)
- Vanessa Smer-Barreto
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK.
| | - Andrea Quintanilla
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria-SODERCAN. C/ Albert Einstein 22, Santander, 39011, Spain
| | - Richard J R Elliott
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK
| | - Jiugeng Sun
- School of Informatics, University of Edinburgh, 10 Crichton St, Edinburgh, EH8 9AB, UK
| | - Víctor M Campa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria-SODERCAN. C/ Albert Einstein 22, Santander, 39011, Spain
| | - Álvaro Lorente-Macías
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK
| | - Asier Unciti-Broceta
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK
| | - Juan Carlos Acosta
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XR, UK.
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria-SODERCAN. C/ Albert Einstein 22, Santander, 39011, Spain.
| | - Diego A Oyarzún
- School of Informatics, University of Edinburgh, 10 Crichton St, Edinburgh, EH8 9AB, UK.
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK.
- The Alan Turing Institute, 96 Euston Road, London, NW1 2DB, UK.
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5
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Hughes R, Elliott RJR, Li X, Munro AF, Makda A, Carter RN, Morton NM, Fujihara K, Clemons NJ, Fitzgerald R, O’Neill JR, Hupp T, Carragher NO. Multiparametric High-Content Cell Painting Identifies Copper Ionophores as Selective Modulators of Esophageal Cancer Phenotypes. ACS Chem Biol 2022; 17:1876-1889. [PMID: 35696676 PMCID: PMC9295120 DOI: 10.1021/acschembio.2c00301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Esophageal adenocarcinoma is of increasing global concern due to increasing incidence, a lack of effective treatments, and poor prognosis. Therapeutic target discovery and clinical trials have been hindered by the heterogeneity of the disease, the lack of "druggable" driver mutations, and the dominance of large-scale genomic rearrangements. We have previously undertaken a comprehensive small-molecule phenotypic screen using the high-content Cell Painting assay to quantify the morphological response to a total of 19,555 small molecules across a panel of genetically distinct human esophageal cell lines to identify new therapeutic targets and small molecules for the treatment of esophageal adenocarcinoma. In this current study, we report for the first time the dose-response validation studies for the 72 screening hits from the target-annotated LOPAC and Prestwick FDA-approved compound libraries and the full list of 51 validated esophageal adenocarcinoma-selective small molecules (71% validation rate). We then focus on the most potent and selective hit molecules, elesclomol, disulfiram, and ammonium pyrrolidinedithiocarbamate. Using a multipronged, multitechnology approach, we uncover a unified mechanism of action and a vulnerability in esophageal adenocarcinoma toward copper-dependent cell death that could be targeted in the future.
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Affiliation(s)
- Rebecca
E. Hughes
- Cancer
Research UK Edinburgh Centre, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, U.K.
| | - Richard J. R. Elliott
- Cancer
Research UK Edinburgh Centre, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, U.K.
| | - Xiaodun Li
- MRC
Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, U.K.
| | - Alison F. Munro
- Cancer
Research UK Edinburgh Centre, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, U.K.
| | - Ashraff Makda
- Cancer
Research UK Edinburgh Centre, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, U.K.
| | - Roderick N. Carter
- Centre
for Clinical Brain Sciences, Chancellors Building, University of Edinburgh, Edinburgh EH16 4SB, U.K.
- Centre
for Cardiovascular Science, The Queen’s
Medical Research Institute, Edinburgh BioQuarter, Edinburgh EH16 4TJ, U.K.
| | - Nicholas M. Morton
- Centre
for Cardiovascular Science, The Queen’s
Medical Research Institute, Edinburgh BioQuarter, Edinburgh EH16 4TJ, U.K.
| | - Kenji Fujihara
- Gastrointestinal
Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Victoria, Australia
- Sir Peter
MacCallum Department of Oncology, The University
of Melbourne, Parkville 3010, Victoria, Australia
| | - Nicholas J. Clemons
- Gastrointestinal
Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Victoria, Australia
- Sir Peter
MacCallum Department of Oncology, The University
of Melbourne, Parkville 3010, Victoria, Australia
| | - Rebecca Fitzgerald
- Early
Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge CB2 0XZ, U.K.
| | - J. Robert O’Neill
- Cambridge
Oesophagogastric Centre, Cambridge University
Hospitals Foundation Trust, Cambridge CB2 2QQ, U.K.
| | - Ted Hupp
- Cancer
Research UK Edinburgh Centre, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, U.K.
| | - Neil O. Carragher
- Cancer
Research UK Edinburgh Centre, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XR, U.K.
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6
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Marwick JA, Elliott RJR, Longden J, Makda A, Hirani N, Dhaliwal K, Dawson JC, Carragher NO. Application of a High-Content Screening Assay Utilizing Primary Human Lung Fibroblasts to Identify Antifibrotic Drugs for Rapid Repurposing in COVID-19 Patients. SLAS Discov 2021; 26:1091-1106. [PMID: 34078171 PMCID: PMC8458684 DOI: 10.1177/24725552211019405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lung imaging and autopsy reports among COVID-19 patients show elevated lung scarring (fibrosis). Early data from COVID-19 patients as well as previous studies from severe acute respiratory syndrome, Middle East respiratory syndrome, and other respiratory disorders show that the extent of lung fibrosis is associated with a higher mortality, prolonged ventilator dependence, and poorer long-term health prognosis. Current treatments to halt or reverse lung fibrosis are limited; thus, the rapid development of effective antifibrotic therapies is a major global medical need that will continue far beyond the current COVID-19 pandemic. Reproducible fibrosis screening assays with high signal-to-noise ratios and disease-relevant readouts such as extracellular matrix (ECM) deposition (the hallmark of fibrosis) are integral to any antifibrotic therapeutic development. Therefore, we have established an automated high-throughput and high-content primary screening assay measuring transforming growth factor-β (TGFβ)-induced ECM deposition from primary human lung fibroblasts in a 384-well format. This assay combines longitudinal live cell imaging with multiparametric high-content analysis of ECM deposition. Using this assay, we have screened a library of 2743 small molecules representing approved drugs and late-stage clinical candidates. Confirmed hits were subsequently profiled through a suite of secondary lung fibroblast phenotypic screening assays quantifying cell differentiation, proliferation, migration, and apoptosis. In silico target prediction and pathway network analysis were applied to the confirmed hits. We anticipate this suite of assays and data analysis tools will aid the identification of new treatments to mitigate against lung fibrosis associated with COVID-19 and other fibrotic diseases.
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Affiliation(s)
- John A Marwick
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Richard J R Elliott
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James Longden
- Center for Clinical Brain Sciences, Chancellors Building, University of Edinburgh, Edinburgh, UK
| | - Ashraff Makda
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nik Hirani
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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7
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Hughes RE, Elliott RJR, Dawson JC, Carragher NO. High-content phenotypic and pathway profiling to advance drug discovery in diseases of unmet need. Cell Chem Biol 2021; 28:338-355. [PMID: 33740435 DOI: 10.1016/j.chembiol.2021.02.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/10/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Conventional thinking in modern drug discovery postulates that the design of highly selective molecules which act on a single disease-associated target will yield safer and more effective drugs. However, high clinical attrition rates and the lack of progress in developing new effective treatments for many important diseases of unmet therapeutic need challenge this hypothesis. This assumption also impinges upon the efficiency of target agnostic phenotypic drug discovery strategies, where early target deconvolution is seen as a critical step to progress phenotypic hits. In this review we provide an overview of how emerging phenotypic and pathway-profiling technologies integrate to deconvolute the mechanism-of-action of phenotypic hits. We propose that such in-depth mechanistic profiling may support more efficient phenotypic drug discovery strategies that are designed to more appropriately address complex heterogeneous diseases of unmet need.
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Affiliation(s)
- Rebecca E Hughes
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Richard J R Elliott
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - John C Dawson
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK.
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8
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Hughes RE, Elliott RJR, Munro AF, Makda A, O’Neill JR, Hupp T, Carragher NO. High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery. SLAS Discov 2020; 25:770-782. [PMID: 32441181 PMCID: PMC7372582 DOI: 10.1177/2472555220917115] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/26/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022]
Abstract
Esophageal adenocarcinoma (EAC) is a highly heterogeneous disease, dominated by large-scale genomic rearrangements and copy number alterations. Such characteristics have hampered conventional target-directed drug discovery and personalized medicine strategies, contributing to poor outcomes for patients. We describe the application of a high-content Cell Painting assay to profile the phenotypic response of 19,555 compounds across a panel of six EAC cell lines and two tissue-matched control lines. We built an automated high-content image analysis pipeline to identify compounds that selectively modified the phenotype of EAC cell lines. We further trained a machine-learning model to predict the mechanism of action of EAC selective compounds using phenotypic fingerprints from a library of reference compounds. We identified a number of phenotypic clusters enriched with similar pharmacological classes, including methotrexate and three other antimetabolites that are highly selective for EAC cell lines. We further identify a small number of hits from our diverse chemical library that show potent and selective activity for EAC cell lines and that do not cluster with the reference library of compounds, indicating they may be selectively targeting novel esophageal cancer biology. Overall, our results demonstrate that our EAC phenotypic screening platform can identify existing pharmacologic classes and novel compounds with selective activity for EAC cell phenotypes.
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Affiliation(s)
- Rebecca E. Hughes
- MRC Institute of Genetics &
Molecular Medicine, The University of Edinburgh, Western General Hospital,
Edinburgh, UK
| | - Richard J. R. Elliott
- MRC Institute of Genetics &
Molecular Medicine, The University of Edinburgh, Western General Hospital,
Edinburgh, UK
| | - Alison F. Munro
- MRC Institute of Genetics &
Molecular Medicine, The University of Edinburgh, Western General Hospital,
Edinburgh, UK
| | - Ashraff Makda
- MRC Institute of Genetics &
Molecular Medicine, The University of Edinburgh, Western General Hospital,
Edinburgh, UK
| | - J. Robert O’Neill
- Cambridge Oesophagogastric Centre,
Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire,
UK
| | - Ted Hupp
- MRC Institute of Genetics &
Molecular Medicine, The University of Edinburgh, Western General Hospital,
Edinburgh, UK
| | - Neil O. Carragher
- MRC Institute of Genetics &
Molecular Medicine, The University of Edinburgh, Western General Hospital,
Edinburgh, UK
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9
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Elliott RJR, Jarvis A, Rajasekaran MB, Menon M, Bowers L, Boffey R, Bayford M, Firth-Clark S, Key R, Aqil R, Kirton SB, Niculescu-Duvaz D, Fish L, Lopes F, McLeary R, Trindade I, Vendrell E, Munkonge F, Porter R, Perrior T, Springer C, Oliver AW, Pearl LH, Ashworth A, Lord CJ. Design and discovery of 3-aryl-5-substituted-isoquinolin-1-ones as potent tankyrase inhibitors. Med Chem Commun 2015. [DOI: 10.1039/c5md00210a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The tankyrase proteins (TNKS, TNKS2) are attractive anti-cancer drug targets, particularly as inhibition of their catalytic activity has been shown to antagonise oncogenic WNT signalling.
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