Achieving a Deeper Understanding of Drug Metabolism and Responses Using Single-Cell Technologies

Abstract

Recent advancements in single-cell technologies have enabled detection of RNA, proteins, metabolites, and xenobiotics in individual cells, and the application of these technologies has the potential to transform pharmacological research. Single-cell data has already resulted in the development of human and model species cell atlases, identifying different cell types within a tissue, further facilitating the characterization of tumor heterogeneity, and providing insight into treatment resistance. Research discussed in this review demonstrates that distinct cell populations express drug metabolizing enzymes to different extents, indicating there may be variability in drug metabolism not only between organs, but within tissue types. Additionally, we put forth the concept that single-cell analyses can be used to expose underlying variability in cellular response to drugs, providing a unique examination of drug efficacy, toxicity, and metabolism. We will outline several of these techniques: single-cell RNA-sequencing and mass cytometry to characterize and distinguish different cell types, single-cell proteomics to quantify drug metabolizing enzymes and characterize cellular responses to drug, capillary electrophoresis-ultrasensitive laser-induced fluorescence detection and single-probe single-cell mass spectrometry for detection of drugs, and others. Emerging single-cell technologies such as these can comprehensively characterize heterogeneity in both cell-type-specific drug metabolism and response to treatment, enhancing progress toward personalized and precision medicine. SIGNIFICANCE STATEMENT: Recent technological advances have enabled the analysis of gene expression and protein levels in single cells. These types of analyses are important to investigating mechanisms that cannot be elucidated on a bulk level, primarily due to the variability of cell populations within biological systems. Here, we summarize cell-type-specific drug metabolism and how pharmacologists can utilize single-cell approaches to obtain a comprehensive understanding of drug metabolism and cellular heterogeneity in response to drugs.

Fig. 1.

Three sample preparation strategies for single-cell proteomic analysis. (A) The nanoPOTS platform uses a nanoliter robotic pipetting to dispense cells and reagents onto microfabricated nanoarray chips (Zhu et al., 2018). (B) The ScoPE2 method uses TMT isobaric tags to label peptides of single cells and a 200-cell channel to boost protein sequence coverage (Petelski et al., 2021). (C) Whole-cell patch-clamp electrophysiology involves sample injection into a patch pipette, bottom-up proteomics on collected protein, and identification and quantification using a capillary electrophoresis electrospray ionization platform followed by high-resolution mass spectrometry (Choi et al., 2021).