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Wali R, Xu H, Cheruiyot C, Saleem HN, Janshoff A, Habeck M, Ebert A. Integrated machine learning and multimodal data fusion for patho-phenotypic feature recognition in iPSC models of dilated cardiomyopathy. Biol Chem 2024; 0:hsz-2024-0023. [PMID: 38651266 DOI: 10.1515/hsz-2024-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Integration of multiple data sources presents a challenge for accurate prediction of molecular patho-phenotypic features in automated analysis of data from human model systems. Here, we applied a machine learning-based data integration to distinguish patho-phenotypic features at the subcellular level for dilated cardiomyopathy (DCM). We employed a human induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) model of a DCM mutation in the sarcomere protein troponin T (TnT), TnT-R141W, compared to isogenic healthy (WT) control iPSC-CMs. We established a multimodal data fusion (MDF)-based analysis to integrate source datasets for Ca2+ transients, force measurements, and contractility recordings. Data were acquired for three additional layer types, single cells, cell monolayers, and 3D spheroid iPSC-CM models. For data analysis, numerical conversion as well as fusion of data from Ca2+ transients, force measurements, and contractility recordings, a non-negative blind deconvolution (NNBD)-based method was applied. Using an XGBoost algorithm, we found a high prediction accuracy for fused single cell, monolayer, and 3D spheroid iPSC-CM models (≥92 ± 0.08 %), as well as for fused Ca2+ transient, beating force, and contractility models (>96 ± 0.04 %). Integrating MDF and XGBoost provides a highly effective analysis tool for prediction of patho-phenotypic features in complex human disease models such as DCM iPSC-CMs.
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Affiliation(s)
- Ruheen Wali
- Department of Cardiology and Pneumology, Heart Research Center, University Medical Center, 27177 Göttingen University , Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
- Partner Site Göttingen, DZHK (German Center for Cardiovascular Research), Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Hang Xu
- Department of Cardiology and Pneumology, Heart Research Center, University Medical Center, 27177 Göttingen University , Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
- Partner Site Göttingen, DZHK (German Center for Cardiovascular Research), Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Cleophas Cheruiyot
- Department of Cardiology and Pneumology, Heart Research Center, University Medical Center, 27177 Göttingen University , Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
- Partner Site Göttingen, DZHK (German Center for Cardiovascular Research), Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Hafiza Nosheen Saleem
- Department of Cardiology and Pneumology, Heart Research Center, University Medical Center, 27177 Göttingen University , Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
- Partner Site Göttingen, DZHK (German Center for Cardiovascular Research), Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Andreas Janshoff
- Institute for Physical Chemistry, Göttingen University, Tammannstraße 6, D-37077 Göttingen, Germany
| | - Michael Habeck
- Microscopic Image Analysis, 39065 Jena University Hospital , Kollegiengasse 10, D-07743 Jena, Germany
| | - Antje Ebert
- Department of Cardiology and Pneumology, Heart Research Center, University Medical Center, 27177 Göttingen University , Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
- Partner Site Göttingen, DZHK (German Center for Cardiovascular Research), Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
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Dai Y, Ignatyeva N, Xu H, Wali R, Toischer K, Brandenburg S, Lenz C, Pronto J, Fakuade FE, Sossalla S, Zeisberg EM, Janshoff A, Kutschka I, Voigt N, Urlaub H, Rasmussen TB, Mogensen J, Lehnart SE, Hasenfuss G, Ebert A. An Alternative Mechanism of Subcellular Iron Uptake Deficiency in Cardiomyocytes. Circ Res 2023; 133:e19-e46. [PMID: 37313752 DOI: 10.1161/circresaha.122.321157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Systemic defects in intestinal iron absorption, circulation, and retention cause iron deficiency in 50% of patients with heart failure. Defective subcellular iron uptake mechanisms that are independent of systemic absorption are incompletely understood. The main intracellular route for iron uptake in cardiomyocytes is clathrin-mediated endocytosis. METHODS We investigated subcellular iron uptake mechanisms in patient-derived and CRISPR/Cas-edited induced pluripotent stem cell-derived cardiomyocytes as well as patient-derived heart tissue. We used an integrated platform of DIA-MA (mass spectrometry data-independent acquisition)-based proteomics and signaling pathway interrogation. We employed a genetic induced pluripotent stem cell model of 2 inherited mutations (TnT [troponin T]-R141W and TPM1 [tropomyosin 1]-L185F) that lead to dilated cardiomyopathy (DCM), a frequent cause of heart failure, to study the underlying molecular dysfunctions of DCM mutations. RESULTS We identified a druggable molecular pathomechanism of impaired subcellular iron deficiency that is independent of systemic iron metabolism. Clathrin-mediated endocytosis defects as well as impaired endosome distribution and cargo transfer were identified as a basis for subcellular iron deficiency in DCM-induced pluripotent stem cell-derived cardiomyocytes. The clathrin-mediated endocytosis defects were also confirmed in the hearts of patients with DCM with end-stage heart failure. Correction of the TPM1-L185F mutation in DCM patient-derived induced pluripotent stem cells, treatment with a peptide, Rho activator II, or iron supplementation rescued the molecular disease pathway and recovered contractility. Phenocopying the effects of the TPM1-L185F mutation into WT induced pluripotent stem cell-derived cardiomyocytes could be ameliorated by iron supplementation. CONCLUSIONS Our findings suggest that impaired endocytosis and cargo transport resulting in subcellular iron deficiency could be a relevant pathomechanism for patients with DCM carrying inherited mutations. Insight into this molecular mechanism may contribute to the development of treatment strategies and risk management in heart failure.
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Affiliation(s)
- Yuanyuan Dai
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Nadezda Ignatyeva
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Hang Xu
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Ruheen Wali
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Karl Toischer
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Sören Brandenburg
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Christof Lenz
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Department of Clinical Chemistry, University Medical Center Goettingen, (C.L., H.U.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen (C.L., H.U.)
| | - Julius Pronto
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
| | - Funsho E Fakuade
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Samuel Sossalla
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
- Department for Internal Medicine II, University Medical Center Regensburg (S.S.)
| | - Elisabeth M Zeisberg
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
| | - Andreas Janshoff
- Institute for Physical Chemistry (A.J.), University of Goettingen, Germany
| | - Ingo Kutschka
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Department of Thoracic and Cardiovascular Surgery, University Medical Center Göttingen (I.K.)
| | - Niels Voigt
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen, (J.P., F.E.F., N.V.), University of Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Goettingen, (C.L., H.U.), University of Goettingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen (C.L., H.U.)
| | | | - Jens Mogensen
- Department of Cardiology, Aalborg University Hospital, Denmark (J.M.)
| | - Stephan E Lehnart
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC; C.L., F.E.F., N.V., S.E.L.), University of Goettingen, Germany
| | - Gerd Hasenfuss
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
- Heart Center, Clinic for Cardiology and Pneumology, University Medical Center Goettingen (K.T., S.B., S.S., G.H.), University of Goettingen, Germany
| | - Antje Ebert
- Heart Research Center Goettingen, Clinic for Cardiology and Pneumology, University Medical Center Goettingen, Georg-August University of Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., S.S., E.M.Z., S.E.L., G.H., A.E.)
- DZHK (German Center for Cardiovascular Research), partner site Goettingen, Germany (Y.D., N.I., H.X., R.W., K.T., S.B., C.L., J.P., F.E.F., E.M.Z., I.K., N.V., S.E.L., G.H., A.E.)
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