Automated workflow for the cell cycle analysis of non-adherent and adherent cells using a machine learning approach

Abstract

Understanding the details of the cell cycle at the level of individual cells is critical for both cellular biology and cancer research. While existing methods using specific fluorescent markers have advanced our ability to study the cell cycle in cells that adhere to surfaces, there is a clear gap when it comes to non-adherent cells. In this study, we combine a specialized surface to improve cell attachment, the genetically-encoded FUCCI(CA)2 sensor, an automated image processing and analysis pipeline, and a custom machine-learning algorithm. This combined approach allowed us to precisely measure the duration of different cell cycle phases in non-adherent, as well as adherent cells.Our method provided detailed information from hundreds of cells under different experimental conditions in a fully automated manner. We validated this approach in two different acute myeloid leukemia cell lines, NB4 and Kasumi-1, which have unique and distinct cell cycle characteristics. We also measured how drugs that influence cell cycle properties affect the duration of each phase in the cell cycles of these cell lines. Importantly, our cell cycle analysis system is freely available and has also been validated for use with adherent cells.In summary, this article introduces a comprehensive, automated method for studying the cell cycle in both non-adherent and adherent cells, offering a valuable tool for cellular biology, cancer research and drug development.