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Serrano R, Feyen DAM, Bruyneel AAN, Hnatiuk AP, Vu MM, Amatya PL, Perea-Gil I, Prado M, Seeger T, Wu JC, Karakikes I, Mercola M. A deep learning platform to assess drug proarrhythmia risk. Cell Stem Cell 2023; 30:86-95.e4. [PMID: 36563695 PMCID: PMC9924077 DOI: 10.1016/j.stem.2022.12.002] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/25/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Drug safety initiatives have endorsed human iPSC-derived cardiomyocytes (hiPSC-CMs) as an in vitro model for predicting drug-induced cardiac arrhythmia. However, the extent to which human-defined features of in vitro arrhythmia predict actual clinical risk has been much debated. Here, we trained a convolutional neural network classifier (CNN) to learn features of in vitro action potential recordings of hiPSC-CMs that are associated with lethal Torsade de Pointes arrhythmia. The CNN classifier accurately predicted the risk of drug-induced arrhythmia in people. The risk profile of the test drugs was similar across hiPSC-CMs derived from different healthy donors. In contrast, pathogenic mutations that cause arrhythmogenic cardiomyopathies in patients significantly increased the proarrhythmic propensity to certain intermediate and high-risk drugs in the hiPSC-CMs. Thus, deep learning can identify in vitro arrhythmic features that correlate with clinical arrhythmia and discern the influence of patient genetics on the risk of drug-induced arrhythmia.
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Affiliation(s)
- Ricardo Serrano
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dries A M Feyen
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Arne A N Bruyneel
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Anna P Hnatiuk
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michelle M Vu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Prashila L Amatya
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Isaac Perea-Gil
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Maricela Prado
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Timon Seeger
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ioannis Karakikes
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Mark Mercola
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305, USA.
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Feyen DA, Perea-Gil I, Maas RG, Harakalova M, Gavidia AA, Ataam JA, Wu TH, Vink A, Pei J, Vadgama N, Suurmeijer AJ, te Rijdt WP, Vu M, Amatya PL, Prado M, Zhang Y, Dunkenberger L, Sluijter JP, Sallam K, Asselbergs FW, Mercola M, Karakikes I. Unfolded Protein Response as a Compensatory Mechanism and Potential Therapeutic Target in PLN R14del Cardiomyopathy. Circulation 2021; 144:382-392. [PMID: 33928785 PMCID: PMC8667423 DOI: 10.1161/circulationaha.120.049844] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Phospholamban (PLN) is a critical regulator of calcium cycling and contractility in the heart. The loss of arginine at position 14 in PLN (R14del) is associated with dilated cardiomyopathy with a high prevalence of ventricular arrhythmias. How the R14 deletion causes dilated cardiomyopathy is poorly understood, and there are no disease-specific therapies. METHODS We used single-cell RNA sequencing to uncover PLN R14del disease mechanisms in human induced pluripotent stem cells (hiPSC-CMs). We used both 2-dimensional and 3-dimensional functional contractility assays to evaluate the impact of modulating disease-relevant pathways in PLN R14del hiPSC-CMs. RESULTS Modeling of the PLN R14del cardiomyopathy with isogenic pairs of hiPSC-CMs recapitulated the contractile deficit associated with the disease in vitro. Single-cell RNA sequencing revealed the induction of the unfolded protein response (UPR) pathway in PLN R14del compared with isogenic control hiPSC-CMs. The activation of UPR was also evident in the hearts from PLN R14del patients. Silencing of each of the 3 main UPR signaling branches (IRE1, ATF6, or PERK) by siRNA exacerbated the contractile dysfunction of PLN R14del hiPSC-CMs. We explored the therapeutic potential of activating the UPR with a small molecule activator, BiP (binding immunoglobulin protein) inducer X. PLN R14del hiPSC-CMs treated with BiP protein inducer X showed a dose-dependent amelioration of the contractility deficit in both 2-dimensional cultures and 3-dimensional engineered heart tissues without affecting calcium homeostasis. CONCLUSIONS Together, these findings suggest that the UPR exerts a protective effect in the setting of PLN R14del cardiomyopathy and that modulation of the UPR might be exploited therapeutically.
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Affiliation(s)
- Dries A.M. Feyen
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Isaac Perea-Gil
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Renee G.C. Maas
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Alexandra A. Gavidia
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer Arthur Ataam
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ting-Hsuan Wu
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Jiayi Pei
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Nirmal Vadgama
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Albert J. Suurmeijer
- Deptment of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wouter P. te Rijdt
- Netherlands Heart Institute, Utrecht, The Netherlands,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michelle Vu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Prashila L. Amatya
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maricela Prado
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuan Zhang
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Logan Dunkenberger
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joost P.G. Sluijter
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Karim Sallam
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom,Health Data Research UK and Institute of Health Informatics, University College London, London, United Kingdom
| | - Mark Mercola
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA,Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA,Address for Correspondence: Ioannis Karakikes, PhD, Stanford University School of Medicine, Department of Cardiothoracic Surgery, 300 Pasteur Dr, Suite 1347, Stanford, California 94305, USA. Telephone: 650-721-0784,
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Feyen DAM, McKeithan WL, Bruyneel AAN, Spiering S, Hörmann L, Ulmer B, Zhang H, Briganti F, Schweizer M, Hegyi B, Liao Z, Pölönen RP, Ginsburg KS, Lam CK, Serrano R, Wahlquist C, Kreymerman A, Vu M, Amatya PL, Behrens CS, Ranjbarvaziri S, Maas RGC, Greenhaw M, Bernstein D, Wu JC, Bers DM, Eschenhagen T, Metallo CM, Mercola M. Metabolic Maturation Media Improve Physiological Function of Human iPSC-Derived Cardiomyocytes. Cell Rep 2021; 32:107925. [PMID: 32697997 PMCID: PMC7437654 DOI: 10.1016/j.celrep.2020.107925] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/15/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have enormous potential for the study of human cardiac disorders. However, their physiological immaturity severely limits their utility as a model system and their adoption for drug discovery. Here, we describe maturation media designed to provide oxidative substrates adapted to the metabolic needs of human iPSC (hiPSC)-CMs. Compared with conventionally cultured hiPSC-CMs, metabolically matured hiPSC-CMs contract with greater force and show an increased reliance on cardiac sodium (Na+) channels and sarcoplasmic reticulum calcium (Ca2+) cycling. The media enhance the function, long-term survival, and sarcomere structures in engineered heart tissues. Use of the maturation media made it possible to reliably model two genetic cardiac diseases: long QT syndrome type 3 due to a mutation in the cardiac Na+ channel SCN5A and dilated cardiomyopathy due to a mutation in the RNA splicing factor RBM20. The maturation media should increase the fidelity of hiPSC-CMs as disease models. Physiological immaturity of iPSC-derived cardiomyocytes limits their fidelity as disease models. Feyen et al. developed a low glucose, high oxidative substrate media that increase maturation of ventricular-like hiPSC-CMs in 2D and 3D cultures relative to standard protocols. Improved characteristics include a low resting Vm, rapid depolarization, and increased Ca2+ dependence and force generation.
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Affiliation(s)
- Dries A M Feyen
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wesley L McKeithan
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Arne A N Bruyneel
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sean Spiering
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Larissa Hörmann
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bärbel Ulmer
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hui Zhang
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Francesca Briganti
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michaela Schweizer
- Electron Microscopy Unit, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bence Hegyi
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
| | - Zhandi Liao
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
| | | | - Kenneth S Ginsburg
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
| | - Chi Keung Lam
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Serrano
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Christine Wahlquist
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Alexander Kreymerman
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michelle Vu
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Prashila L Amatya
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Charlotta S Behrens
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sara Ranjbarvaziri
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Renee G C Maas
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthew Greenhaw
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel Bernstein
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joseph C Wu
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Donald M Bers
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Mark Mercola
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA 94305, USA; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA.
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Chen M, Cooper VI, Deng J, Amatya PL, Ambrus D, Dong S, Stalker N, Nadeau-Bonilla C, Patel J. Occurrence of Pharmaceuticals in Calgary's Wastewater and Related Surface Water. Water Environ Res 2015; 87:414-424. [PMID: 26460461 DOI: 10.2175/106143015x14212658614199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The influents/effluents from Calgary's water resource recovery facilities and the surface water were analyzed for pharmaceuticals in the present study. The median concentrations in the effluents for the 15 targeted pharmaceuticals were within the range of 0.006 to 3.32 ppb. Although the wastewater treatment facilities were not designed to remove pharmaceuticals, this study indicates that the wastewater treatment processes are effective in removing some of the pharmaceuticals from the aqueous phase. The removal rate estimated can be 99.5% for caffeine, whereas little or no removal was observed for carbamazepine. Biodegradation, chemical degradation, and sorption could be some of the mechanisms responsible for the removal of pharmaceuticals. The drug residues in downstream surface water could be associated with incomplete removal of pharmaceuticals during the treatment process and may lead to concerns in terms of potential impacts on the aquatic ecosystem. However, this study does not indicate any immediate risks to the downstream aquatic environment.
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