Yang H, Stebbeds W, Francis J, Pointon A, Obrezanova O, Beattie KA, Clements P, Harvey JS, Smith GF, Bender A. Deriving waveform parameters from calcium transients in human iPSC-derived cardiomyocytes to predict cardiac activity with machine learning.
Stem Cell Reports 2022;
17:556-568. [PMID:
35148844 PMCID:
PMC9039838 DOI:
10.1016/j.stemcr.2022.01.009]
[Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/24/2022] Open
Abstract
Human induced pluripotent stem cell-derived cardiomyocytes have been established to detect dynamic calcium transients by fast kinetic fluorescence assays that provide insights into specific aspects of clinical cardiac activity. However, the precise derivation and use of waveform parameters to predict cardiac activity merit deeper investigation. In this study, we derived, evaluated, and applied 38 waveform parameters in a novel Python framework, including (among others) peak frequency, peak amplitude, peak widths, and a novel parameter, shoulder-tail ratio. We then trained a random forest model to predict cardiac activity based on the 25 parameters selected by correlation analysis. The area under the curve (AUC) obtained for leave-one-compound-out cross-validation was 0.86, thereby replicating the predictions of conventional methods and outperforming fingerprint-based methods by a large margin. This work demonstrates that machine learning is able to automate the assessment of cardiovascular liability from waveform data, reducing any risk of user-to-user variability and bias.
An open-source algorithm was developed to derive parameters from waveform data
A machine learning model was trained to predict cardiac activity of compounds
Three parameters for peak width, height, and shape were found to be most predictive
The model can facilitate the assessment of cardiovascular liability
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