Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments.
Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differen...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2024-09-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1011806 |
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| author | Janice Yang Neil J Daily Taylor K Pullinger Tetsuro Wakatsuki Eric A Sobie |
| author_facet | Janice Yang Neil J Daily Taylor K Pullinger Tetsuro Wakatsuki Eric A Sobie |
| author_sort | Janice Yang |
| collection | DOAJ |
| description | Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differentiation methods produce cardiomyocytes with immature, fetal-like electrophysiological phenotypes, and the variety of maturation protocols in the literature results in phenotypic differences between labs. Heterogeneity of iPSC donor genetic backgrounds contributes to additional phenotypic variability. Several mathematical models of iPSC-CM electrophysiology have been developed to help to predict cell responses, but these models individually do not capture the phenotypic variability observed in iPSC-CMs. Here, we tackle these limitations by developing a computational pipeline to calibrate cell preparation-specific iPSC-CM electrophysiological parameters. We used the genetic algorithm (GA), a heuristic parameter calibration method, to tune ion channel parameters in a mathematical model of iPSC-CM physiology. To systematically optimize an experimental protocol that generates sufficient data for parameter calibration, we created in silico datasets by simulating various protocols applied to a population of models with known conductance variations, and then fitted parameters to those datasets. We found that calibrating to voltage and calcium transient data under 3 varied experimental conditions, including electrical pacing combined with ion channel blockade and changing buffer ion concentrations, improved model parameter estimates and model predictions of unseen channel block responses. This observation also held when the fitted data were normalized, suggesting that normalized fluorescence recordings, which are more accessible and higher throughput than patch clamp recordings, could sufficiently inform conductance parameters. Therefore, this computational pipeline can be applied to different iPSC-CM preparations to determine cell line-specific ion channel properties and understand the mechanisms behind variability in perturbation responses. |
| format | Article |
| id | doaj-art-0e07087b5ff44ebaaf53e12cb8627162 |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2024-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-0e07087b5ff44ebaaf53e12cb86271622025-08-20T02:45:06ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582024-09-01209e101180610.1371/journal.pcbi.1011806Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments.Janice YangNeil J DailyTaylor K PullingerTetsuro WakatsukiEric A SobieHuman induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differentiation methods produce cardiomyocytes with immature, fetal-like electrophysiological phenotypes, and the variety of maturation protocols in the literature results in phenotypic differences between labs. Heterogeneity of iPSC donor genetic backgrounds contributes to additional phenotypic variability. Several mathematical models of iPSC-CM electrophysiology have been developed to help to predict cell responses, but these models individually do not capture the phenotypic variability observed in iPSC-CMs. Here, we tackle these limitations by developing a computational pipeline to calibrate cell preparation-specific iPSC-CM electrophysiological parameters. We used the genetic algorithm (GA), a heuristic parameter calibration method, to tune ion channel parameters in a mathematical model of iPSC-CM physiology. To systematically optimize an experimental protocol that generates sufficient data for parameter calibration, we created in silico datasets by simulating various protocols applied to a population of models with known conductance variations, and then fitted parameters to those datasets. We found that calibrating to voltage and calcium transient data under 3 varied experimental conditions, including electrical pacing combined with ion channel blockade and changing buffer ion concentrations, improved model parameter estimates and model predictions of unseen channel block responses. This observation also held when the fitted data were normalized, suggesting that normalized fluorescence recordings, which are more accessible and higher throughput than patch clamp recordings, could sufficiently inform conductance parameters. Therefore, this computational pipeline can be applied to different iPSC-CM preparations to determine cell line-specific ion channel properties and understand the mechanisms behind variability in perturbation responses.https://doi.org/10.1371/journal.pcbi.1011806 |
| spellingShingle | Janice Yang Neil J Daily Taylor K Pullinger Tetsuro Wakatsuki Eric A Sobie Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. PLoS Computational Biology |
| title | Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. |
| title_full | Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. |
| title_fullStr | Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. |
| title_full_unstemmed | Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. |
| title_short | Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. |
| title_sort | creating cell specific computational models of stem cell derived cardiomyocytes using optical experiments |
| url | https://doi.org/10.1371/journal.pcbi.1011806 |
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