Jonne Rietdijk: Advances in Morphological Profiling of Cellular Responses to Environmental Stressors Using Cell Painting

Abstract

Humans are constantly exposed to stressors from natural sources, such as viruses and bacteria, and anthropogenic sources, including chemicals from consumer products and environmental pollution. The vast range and complexity of these exposures make it challenging to elucidate their potential adverse effects on human health. Morphological profiling has emerged as a powerful, scalable, and cost-effective approach for systematically studying diverse perturbations and their cellular responses. Cell Painting, an image-based assay for morphological profiling, measures global cellular responses through multiplexed staining of eight cellular components, high-content imaging, and multiparametric analysis. The resulting profiles capture subtle phenotypic changes, offering valuable insights into bioactivity and underlying biological mechanisms.

Among the diverse stressors humans face, emerging pathogenic viruses represent a particularly pressing global concern. To advance antiviral discovery, we adapted the Cell Painting assay by incorporating a virus-specific antibody, enabling simultaneous quantification of infection levels and in-depth characterization of host-cell responses. This approach offers clear advantages over conventional single-endpoint antiviral screens. Paper I investigated the effects of CoV-229E coronavirus infection on cell morphology and demonstrated the approach’s utility for antiviral compound screening. Paper II expanded this with a 5,275-compound drug repurposing screen, identifying drugs that reverse SARS-CoV-2-induced cell phenotypes while providing insights into host-targeted pathways and compound mechanisms of action.

While viral pathogens pose significant public health challenges, environmental pollution represents a more chronic threat, contributing to an estimated nine million deaths annually. Despite this burden, chemicals are often inadequately assessed for health effects and typically studied individually, overlooking potential combination effects from co-exposure. To address this gap, Paper III applied Cell Painting to study the morphological effects of chemical mixtures. Using three environmental compounds, we demonstrated that Cell Painting effectively characterizes dose- and combination-dependent cellular responses across biologically diverse cell lines. In Paper IV, we profiled 900 environmental chemicals across multiple human cell lines to assess their bioactivity and infer putative mechanisms of action by comparing them to reference chemicals with well-characterized toxicity mechanisms.

Together, these findings establish Cell Painting as a powerful tool for capturing complex cellular responses across diverse contexts, offering new avenues for antiviral discovery and environmental hazard assessment.