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Grafton F, Ho J, Ranjbarvaziri S, Farshidfar F, Budan A, Steltzer S, Maddah M, Loewke KE, Green K, Patel S, Hoey T, Mandegar MA. Deep learning detects cardiotoxicity in a high-content screen with induced pluripotent stem cell-derived cardiomyocytes. eLife 2021; 10:68714. [PMID: 34338636 PMCID: PMC8367386 DOI: 10.7554/elife.68714] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Drug-induced cardiotoxicity and hepatotoxicity are major causes of drug attrition. To decrease late-stage drug attrition, pharmaceutical and biotechnology industries need to establish biologically relevant models that use phenotypic screening to detect drug-induced toxicity in vitro. In this study, we sought to rapidly detect patterns of cardiotoxicity using high-content image analysis with deep learning and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). We screened a library of 1280 bioactive compounds and identified those with potential cardiotoxic liabilities in iPSC-CMs using a single-parameter score based on deep learning. Compounds demonstrating cardiotoxicity in iPSC-CMs included DNA intercalators, ion channel blockers, epidermal growth factor receptor, cyclin-dependent kinase, and multi-kinase inhibitors. We also screened a diverse library of molecules with unknown targets and identified chemical frameworks that show cardiotoxic signal in iPSC-CMs. By using this screening approach during target discovery and lead optimization, we can de-risk early-stage drug discovery. We show that the broad applicability of combining deep learning with iPSC technology is an effective way to interrogate cellular phenotypes and identify drugs that may protect against diseased phenotypes and deleterious mutations.
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Affiliation(s)
| | - Jaclyn Ho
- Tenaya Therapeutics, South San Francisco, United States
| | - Sara Ranjbarvaziri
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, United States
| | | | | | | | | | | | | | - Snahel Patel
- Tenaya Therapeutics, South San Francisco, United States
| | - Tim Hoey
- Tenaya Therapeutics, South San Francisco, United States
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Yan J, Sun CL, Shin S, Van Gilst M, Crowder CM. Effect of the mitochondrial unfolded protein response on hypoxic death and mitochondrial protein aggregation. Cell Death Dis 2021; 12:711. [PMID: 34267182 PMCID: PMC8282665 DOI: 10.1038/s41419-021-03979-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/23/2022]
Abstract
Mitochondria are the main oxygen consumers in cells and as such are the primary organelle affected by hypoxia. All hypoxia pathology presumably derives from the initial mitochondrial dysfunction. An early event in hypoxic pathology in C. elegans is disruption of mitochondrial proteostasis with induction of the mitochondrial unfolded protein response (UPRmt) and mitochondrial protein aggregation. Here in C. elegans, we screen through RNAis and mutants that confer either strong resistance to hypoxic cell death or strong induction of the UPRmt to determine the relationship between hypoxic cell death, UPRmt activation, and hypoxia-induced mitochondrial protein aggregation (HIMPA). We find that resistance to hypoxic cell death invariantly mitigated HIMPA. We also find that UPRmt activation invariantly mitigated HIMPA. However, UPRmt activation was neither necessary nor sufficient for resistance to hypoxic death and vice versa. We conclude that UPRmt is not necessarily hypoxia protective against cell death but does protect from mitochondrial protein aggregation, one of the early hypoxic pathologies in C. elegans.
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Affiliation(s)
- Junyi Yan
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Department of Anesthesiology, Central Hospital of Changdian, 118214, Dandong, Liaoning, China
| | - Chun-Ling Sun
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - Seokyung Shin
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Department of Anesthesiology and Pain Medicine, Anesthesia and Pain Research Institute Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Marc Van Gilst
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA.,Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, WA, 98109, USA
| | - C Michael Crowder
- Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, 98109, USA. .,Mitochondrial and Metabolism Center, University of Washington School of Medicine, Seattle, WA, 98109, USA. .,Department of Genome Science, University of Washington School of Medicine, Seattle, WA, 98109, USA.
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Habash SS, Brass HUC, Klein AS, Klebl DP, Weber TM, Classen T, Pietruszka J, Grundler FMW, Schleker ASS. Novel Prodiginine Derivatives Demonstrate Bioactivities on Plants, Nematodes, and Fungi. FRONTIERS IN PLANT SCIENCE 2020; 11:579807. [PMID: 33178246 PMCID: PMC7596250 DOI: 10.3389/fpls.2020.579807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/18/2020] [Indexed: 05/06/2023]
Abstract
Bacterial metabolites represent an invaluable source of bioactive molecules which can be used as such or serve as chemical frameworks for developing new antimicrobial compounds for various applications including crop protection against pathogens. Prodiginines are tripyrrolic, red-colored compounds produced by many bacterial species. Recently, due to the use of chemical-, bio-, or mutasynthesis, a novel group of prodiginines was generated. In our study, we perform different assays to evaluate the effects of prodigiosin and five derivatives on nematodes and plant pathogenic fungi as well as on plant development. Our results showed that prodigiosin and the derivatives were active against the bacterial feeding nematode Caenorhabditis elegans in a concentration- and derivative-dependent manner while a direct effect on infective juveniles of the plant parasitic nematode Heterodera schachtii was observed for prodigiosin only. All compounds were found to be active against the plant pathogenic fungi Phoma lingam and Sclerotinia sclerotiorum. Efficacy varied depending on compound concentration and chemical structure. We observed that prodigiosin (1), the 12 ring- 9, and hexenol 10 derivatives are neutral or even positive for growth of Arabidopsis thaliana depending on the applied compound concentration, whereas other derivatives appear to be suppressive. Our infection assays revealed that the total number of developed H. schachtii individuals on A. thaliana was decreased to 50% in the presence of compounds 1 or 9. Furthermore, female nematodes and their associated syncytia were smaller in size. Prodiginines seem to indirectly inhibit H. schachtii parasitism of the plant. Further research is needed to elucidate their mode of action. Our results indicate that prodiginines are promising metabolites that have the potential to be developed into novel antinematodal and antifungal agents.
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Affiliation(s)
- Samer S. Habash
- INRES Molecular Phytomedicine, University of Bonn, Bonn, Germany
- *Correspondence: Samer S. Habash, ; orcid.org/0000-0002-4493-1451
| | - Hannah U. C. Brass
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, Jülich, Germany
| | - Andreas S. Klein
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, Jülich, Germany
| | - David P. Klebl
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, Jülich, Germany
| | - Tim Moritz Weber
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, Jülich, Germany
| | - Thomas Classen
- IBG-1: Bioorganic Chemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Stetternicher Forst, Jülich, Germany
- IBG-1: Bioorganic Chemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - A. Sylvia S. Schleker
- INRES Molecular Phytomedicine, University of Bonn, Bonn, Germany
- A. Sylvia S. Schleker,
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Wang YT, Lim Y, McCall MN, Huang KT, Haynes CM, Nehrke K, Brookes PS. Cardioprotection by the mitochondrial unfolded protein response requires ATF5. Am J Physiol Heart Circ Physiol 2019; 317:H472-H478. [PMID: 31274354 PMCID: PMC6732477 DOI: 10.1152/ajpheart.00244.2019] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/21/2019] [Accepted: 06/09/2019] [Indexed: 11/22/2022]
Abstract
The mitochondrial unfolded protein response (UPRmt) is a cytoprotective signaling pathway triggered by mitochondrial dysfunction. UPRmt activation upregulates chaperones, proteases, antioxidants, and glycolysis at the gene level to restore proteostasis and cell energetics. Activating transcription factor 5 (ATF5) is a proposed mediator of the mammalian UPRmt. Herein, we hypothesized pharmacological UPRmt activation may protect against cardiac ischemia-reperfusion (I/R) injury in an ATF5-dependent manner. Accordingly, in vivo administration of the UPRmt inducers oligomycin or doxycycline 6 h before ex vivo I/R injury (perfused heart) was cardioprotective in wild-type but not global Atf5-/- mice. Acute ex vivo UPRmt activation was not cardioprotective, and loss of ATF5 did not impact baseline I/R injury without UPRmt induction. In vivo UPRmt induction significantly upregulated many known UPRmt-linked genes (cardiac quantitative PCR and Western blot analysis), and RNA-Seq revealed an UPRmt-induced ATF5-dependent gene set, which may contribute to cardioprotection. This is the first in vivo proof of a role for ATF5 in the mammalian UPRmt and the first demonstration that UPRmt is a cardioprotective drug target.NEW & NOTEWORTHY Cardioprotection can be induced by drugs that activate the mitochondrial unfolded protein response (UPRmt). UPRmt protection is dependent on activating transcription factor 5 (ATF5). This is the first in vivo evidence for a role of ATF5 in the mammalian UPRmt.
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MESH Headings
- Activating Transcription Factors/deficiency
- Activating Transcription Factors/genetics
- Activating Transcription Factors/metabolism
- Animals
- Disease Models, Animal
- Doxycycline/pharmacology
- Female
- Gene Expression Regulation
- Isolated Heart Preparation
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Mitochondria, Heart/drug effects
- Mitochondria, Heart/genetics
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Myocardial Reperfusion Injury/genetics
- Myocardial Reperfusion Injury/metabolism
- Myocardial Reperfusion Injury/pathology
- Myocardial Reperfusion Injury/prevention & control
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Oligomycins/pharmacology
- Unfolded Protein Response/drug effects
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Affiliation(s)
- Yves T Wang
- Department of Anesthesiology, University of Rochester Medical Center, Rochester, New York
- Deaprtment of Medicine, University of Rochester Medical Center, Rochester, New York
| | - Yunki Lim
- Deaprtment of Medicine, University of Rochester Medical Center, Rochester, New York
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York
| | - Kai-Ting Huang
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York
| | - Cole M Haynes
- Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Keith Nehrke
- Deaprtment of Medicine, University of Rochester Medical Center, Rochester, New York
| | - Paul S Brookes
- Department of Anesthesiology, University of Rochester Medical Center, Rochester, New York
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5
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Zhang H, Gong G, Wang P, Zhang Z, Kolwicz SC, Rabinovitch PS, Tian R, Wang W. Heart specific knockout of Ndufs4 ameliorates ischemia reperfusion injury. J Mol Cell Cardiol 2018; 123:38-45. [PMID: 30165037 DOI: 10.1016/j.yjmcc.2018.08.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 12/22/2022]
Abstract
RATIONALE Ischemic heart disease (IHD) is a leading cause of mortality. The most effective intervention for IHD is reperfusion, which ironically causes ischemia reperfusion (I/R) injury mainly due to oxidative stress-induced cardiomyocyte death. The exact mechanism and site of reactive oxygen species (ROS) generation during I/R injury remain elusive. OBJECTIVE We aim to test the hypothesis that Complex I-mediated forward and reverse electron flows are the major source of ROS in I/R injury of the heart. METHODS AND RESULTS We used a genetic model of mitochondrial Complex I deficiency, in which a Complex I assembling subunit, Ndufs4 was knocked out in the heart (Ndufs4H-/-). The Langendorff perfused Ndufs4H-/- hearts exhibited significantly reduced infarct size (45.3 ± 5.5% in wild type vs 20.9 ± 8.1% in Ndufs4H-/-), recovered contractile function, and maintained mitochondrial membrane potential after no flow ischemia and subsequent reperfusion. In cultured adult cardiomyocytes from Ndufs4H-/- mice, I/R mimetic treatments caused minimal cell death. Reintroducing Ndufs4 in Ndufs4H-/- cardiomyocytes abolished the protection. Mitochondrial NADH declined much slower in Ndufs4H-/- cardiomyocytes during reperfusion suggesting decreased forward electron flow. Mitochondrial flashes, a marker for mitochondrial respiration, were inhibited in Ndufs4H-/- cardiomyocytes at baseline and during I/R, which was accompanied by preserved aconitase activity suggesting lack of oxidative damage. Finally, pharmacological blockade of forward and reverse electron flow at Complex I inhibited I/R-induced cell death. CONCLUSIONS These results provide the first genetic evidence supporting the central role of mitochondrial Complex I in I/R injury of mouse heart. The study also suggests that both forward and reverse electron flows underlie oxidative cardiomyocyte death during reperfusion.
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Affiliation(s)
- Huiliang Zhang
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Guohua Gong
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
| | - Pei Wang
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
| | - Zhen Zhang
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
| | - Stephen C Kolwicz
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Rong Tian
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
| | - Wang Wang
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
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