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Churchill ML, Holdsworth-Carson SJ, Cowley KJ, Luu J, Simpson KJ, Healey M, Rogers PAW, Donoghue JF. Using a Quantitative High-Throughput Screening Platform to Identify Molecular Targets and Compounds as Repurposing Candidates for Endometriosis. Biomolecules 2023; 13:965. [PMID: 37371546 DOI: 10.3390/biom13060965] [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: 03/27/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Endometriosis, defined as the growth of hormonally responsive endometrial-like tissue outside of the uterine cavity, is an estrogen-dependent, chronic, pro-inflammatory disease that affects up to 11.4% of women of reproductive age and gender-diverse people with a uterus. At present, there is no long-term cure, and the identification of new therapies that provide a high level of efficacy and favourable long-term safety profiles with rapid clinical access are a priority. In this study, quantitative high-throughput compound screens of 3517 clinically approved compounds were performed on patient-derived immortalized human endometrial stromal cell lines. Following assay optimization and compound criteria selection, a high-throughput screening protocol was developed to enable the identification of compounds that interfered with estrogen-stimulated cell growth. From these screens, 23 novel compounds were identified, in addition to their molecular targets and in silico cell-signalling pathways, which included the neuroactive ligand-receptor interaction pathway, metabolic pathways, and cancer-associated pathways. This study demonstrates for the first time the feasibility of performing large compound screens for the identification of new translatable therapeutics and the improved characterization of endometriosis molecular pathophysiology. Further investigation of the molecular targets identified herein will help uncover new mechanisms involved in the establishment, symptomology, and progression of endometriosis.
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Affiliation(s)
- Molly L Churchill
- Gynaecology Research Centre, Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, VIC 3052, Australia
| | - Sarah J Holdsworth-Carson
- Gynaecology Research Centre, Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, VIC 3052, Australia
- Julia Argyrou Endometriosis Centre, Epworth HealthCare, Richmond, VIC 3121, Australia
| | - Karla J Cowley
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Jennii Luu
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Martin Healey
- Gynaecology Research Centre, Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, VIC 3052, Australia
- Gynaecology Endometriosis and Pelvic Pain Unit, Royal Women's Hospital, Parkville, VIC 3052, Australia
| | - Peter A W Rogers
- Gynaecology Research Centre, Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, VIC 3052, Australia
| | - J F Donoghue
- Gynaecology Research Centre, Department of Obstetrics and Gynaecology, University of Melbourne and The Royal Women's Hospital, Parkville, VIC 3052, Australia
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Zink A, Conrad J, Telugu NS, Diecke S, Heinz A, Wanker E, Priller J, Prigione A. Assessment of Ethanol-Induced Toxicity on iPSC-Derived Human Neurons Using a Novel High-Throughput Mitochondrial Neuronal Health (MNH) Assay. Front Cell Dev Biol 2020; 8:590540. [PMID: 33224955 PMCID: PMC7674658 DOI: 10.3389/fcell.2020.590540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022] Open
Abstract
Excessive ethanol exposure can cause mitochondrial and cellular toxicity. In order to discover potential counteracting interventions, it is essential to develop assays capable of capturing the consequences of ethanol exposure in human neurons, and particularly dopaminergic neurons that are crucial for the development of alcohol use disorders (AUD). Here, we developed a novel high-throughput (HT) assay to quantify mitochondrial and neuronal toxicity in human dopaminergic neuron-containing cultures (DNs) from induced pluripotent stem cells (iPSCs). The assay, dubbed mitochondrial neuronal health (MNH) assay, combines live-cell measurement of mitochondrial membrane potential (MMP) with quantification of neuronal branching complexity post-fixation. Using the MNH assay, we demonstrated that chronic ethanol exposure in human iPSC-derived DNs decreases MMP and neuronal outgrowth in a dose-dependent manner. The toxic effect of ethanol on DNs was already detectable after 1 h of exposure, and occurred similarly in DNs derived from healthy individuals and from patients with AUD. We next used the MNH assay to carry out a proof-of-concept compound screening using FDA-approved drugs. We identified potential candidate compounds modulating acute ethanol toxicity in human DNs. We found that disulfiram and baclofen, which are used for AUD treatment, and lithium caused neurotoxicity also in the absence of ethanol, while the spasmolytic drug flavoxate positively influenced MNH. Altogether, we developed an HT assay to probe human MNH and used it to assess ethanol neurotoxicity and to identify modulating agents. The MNH assay represents an effective new tool for discovering modulators of MNH and toxicity in live human neurons.
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Affiliation(s)
- Annika Zink
- Department of Neuropsychiatry, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of General Pediatrics, Neonatology, and Pediatric Cardiology, Heinrich Heine University, Düsseldorf, Germany
| | - Josefin Conrad
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | | | - Andreas Heinz
- Department of Neuropsychiatry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Erich Wanker
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry, Charité - Universitätsmedizin Berlin, Berlin, Germany.,University of Edinburgh and UK Dementia Research Institute, Edinburgh, United Kingdom
| | - Alessandro Prigione
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of General Pediatrics, Neonatology, and Pediatric Cardiology, Heinrich Heine University, Düsseldorf, Germany
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Xie XP, Gan B, Yang W, Wang HQ. ctPath: Demixing pathway crosstalk effect from transcriptomics data for differential pathway identification. J Biomed Inform 2017; 73:104-114. [PMID: 28756161 DOI: 10.1016/j.jbi.2017.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022]
Abstract
Identifying differentially expressed pathways (DEPs) plays important roles in understanding tumor etiology and promoting clinical treatment of cancer or other diseases. By assuming gene expression to be a sparse non-negative linear combination of hidden pathway signals, we propose a pathway crosstalk-based transcriptomics data analysis method (ctPath) for identifying differentially expressed pathways. Biologically, pathways of different functions work in concert at the systematic level. The proposed method interrogates the crosstalks between pathways and discovers hidden pathway signals by mapping high-dimensional transcriptomics data into a low-dimensional pathway space. The resulted pathway signals reflect the activity level of pathways after removing pathway crosstalk effect and allow a robust identification of DEPs from inherently complex and noisy transcriptomics data. CtPath can also correct incomplete and inaccurate pathway annotations which frequently occur in public repositories. Experimental results on both simulation data and real-world cancer data demonstrate the superior performance of ctPath over other popular approaches. R code for ctPath is available for non-commercial use at the URL http://micblab.iim.ac.cn/Download/.
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Affiliation(s)
- Xin-Ping Xie
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, Anhui, China
| | - Bin Gan
- Biological Molecular Information System Lab., Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, Hefei, Anhui, China
| | - Wulin Yang
- Center for Medical Physics and Technology, Hefei Institutes of Physical Science, CAS, Hefei, Anhui, China; Cancer Hospital, CAS, Hefei, Anhui, China
| | - Hong-Qiang Wang
- Biological Molecular Information System Lab., Institute of Intelligent Machines, Hefei Institutes of Physical Science, CAS, Hefei, Anhui, China; Center for Medical Physics and Technology, Hefei Institutes of Physical Science, CAS, Hefei, Anhui, China; Cancer Hospital, CAS, Hefei, Anhui, China.
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Silke J, Johnstone RW. In the Midst of Life-Cell Death: What Is It, What Is It Good for, and How to Study It. Cold Spring Harb Protoc 2016; 2016:2016/12/pdb.top070508. [PMID: 27934692 DOI: 10.1101/pdb.top070508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cell death, one of the most fundamental biological processes, has not made it into the public consciousness in the same way that genetic inheritance, cell division, or DNA replication has. Everyone knows they get their genes from their parents, but few would be aware that even before they were born a lot of essential cell death has shaped their development. The greater population, for the most part, is blissfully unaware that every day millions of their own cells die in a programmed way and that this is essential for normal human physiology-their well-being, in fact. Nowhere is the burial liturgy, "In the midst of life we are in death," more apt. Despite this public underappreciation, cell death research is a major industry. A search in PubMed for "apoptosis," a special form of cell death that is caused by caspases, returns approximately 280,000 hits. The intense research interest arises from the realization that abnormal cell death responses play an important role in two of the biggest killers in the western world: cancer and cardio/cerebrovascular disease. Furthermore, the manner in which cells die can also influence the development of autoimmune and autoinflammatory diseases. It is therefore of paramount importance to ensure that experiments accurately quantitate and correctly identify cell death in all its guises. That is the goal of this protocol collection.
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Affiliation(s)
- John Silke
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Parkville, Victoria 3050, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3052, Australia
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Thete D, Danthi P. Conformational changes required for reovirus cell entry are sensitive to pH. Virology 2015; 483:291-301. [PMID: 26004253 DOI: 10.1016/j.virol.2015.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/23/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022]
Abstract
During cell entry, reovirus particles disassemble to generate ISVPs. ISVPs undergo conformational changes to form ISVP(*) and this conversion is required for membrane penetration. In tissues where ISVP formation occurs within endosomes, ISVP-to-ISVP(*) conversion occurs at low pH. In contrast, in tissues where ISVP formation occurs extracellularly, ISVP-to-ISVP(*) transition occurs at neutral pH. Whether these two distinct pH environments influence the efficiency of cell entry is not known. In this study, we used Ouabain to lower the endosomal pH and determined its effect on reovirus infection. We found that Ouabain treatment blocks reovirus infection. In cells treated with Ouabain, virus attachment, internalization, and ISVP formation were unaffected but the efficiency of ISVP(*)s formation was diminished. Low pH also diminished the efficiency of ISVP-to-ISVP(*) conversion in vitro. Thus, the pH of the compartment where ISVP-to-ISVP(*) conversion takes place may dictate the efficiency of reovirus infection.
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Affiliation(s)
- Deepti Thete
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Pranav Danthi
- Department of Biology, Indiana University, Bloomington, IN 47405, United States.
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Falkenberg KJ, Saunders DN, Simpson KJ. A high-throughput, multiplex cell death assay using an RNAi screening approach. Cold Spring Harb Protoc 2014; 2014:663-76. [PMID: 24890208 DOI: 10.1101/pdb.prot080267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This protocol outlines a high-throughput, multiplex cell death assay and its use in conjunction with a genome-scale siRNA screen to identify genes that cooperate with a drug to induce apoptosis. The assay, ApoLive-Glo (Promega), measures viability of drug-treated, reverse-transfected cells via the fluorescent CellTiter-Fluor reagent, which includes a substrate that is cleaved by a live cell protease. ApoLive-Glo also quantitates cell death by the amount of cleaved caspases 3 and 7 using a luminescent Caspase-Glo 3/7 caspase activation assay. The advantage of the multiplex assay is that it distinguishes rapid cell death from the slower activation of caspase activity, permitting measurement of different stages of cell death in the same sample at a single time point. In parallel, a high-content imaging protocol involving 4',6-diamidino-2-phenylindole-stained nuclei is used as a cost-effective way to quantitate viability of vehicle-treated control cells. Automation and robotic liquid handling are built into the protocol to increase speed of workflow and improve reproducibility. A screen using these assays will identify gene targets that are essential for viability irrespective of drug treatment and gene targets that cause a synergistic enhancement of cell death in the presence of drug. Candidate target activity can then be validated by conventional flow cytometry-based assays.
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Affiliation(s)
- Katrina J Falkenberg
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Department of Pathology, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Darren N Saunders
- Cancer Research Program, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales Medicine, Sydney, New South Wales 2000, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia Department of Pathology, The University of Melbourne, Parkville, Victoria 3052, Australia Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria 3052, Australia
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