Quantifying HiPSC-CM structural organization at scale with deep learning-enhanced SarcGraph

Abstract

In cardiac cells, structural organization is an important indicator of cell maturity and healthy function. Healthy and mature cardiomyocytes exhibit a highly organized structure, characterized by well-aligned almost crystalline morphology with densely packed and organized sarcomeres. Immature and/or diseased cardiomyocytes typically lack this highly organized structure. Critically, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer a valuable model for studying human cardiac cells in a controlled, patient-specific, and minimally invasive manner. However, these cells often exhibit a disorganized and difficult to quantify structure both in their immature form and as disease models. In this work, we extend the SarcGraph computational framework-designed specifically to assess the structural and functional behavior of hiPSC-CMs-to better accommodate the structural features of immature cells. There are two key enhancements: (1) incorporating a deep learning-based z-disc classifier, and (2) introducing a novel ensemble graph-scoring approach. These modification significantly reduced false positive sarcomere detections, particularly in immature cells, and improved the detection of longer myofibrils in mature samples. With this enhanced framework, we analyze an open-source dataset published by the Allen Institute for Cell Science, where, for the first time, we are able to extract key structural features from these data using information from each individually detected sarcomere. Not only are we able to use these structural features to predict expert scores, but we are also able to use these structural features to identify bias in expert scoring and offer an alternative unsupervised learning approach based on explainable clustering. These results demonstrate the efficacy of our modified SarcGraph algorithm in extracting biologically meaningful structural features, enabling a deeper understanding of hiPSC-CM structural integrity. By making our code and tools open-source, we aim to empower the broader cardiac research community and foster further development of computational tools for cardiac tissue analysis.