Enabling drug discovery and development through single-cell imaging

ABSTRACT

Introduction: Single-cell imaging-based assays are an area of active and growing investment in drug discovery and development. This approach offers researchers the capability to interrogate rare subpopulations of cells with minimal sample consumption and multiplexed readouts. Recent technological advances in the optical interrogation and manipulation of single cells have substantially increased the throughput and sensitivity of these assays.

Areas covered: In this review, the authors focus on three classes of single-cell imaging-based analyses: single-cell microscopy combined with microfluidics, mass spectrometric imaging for subcellular compound localization, and imaging mass cytometry (IMC). They provide an overview of each technology and recent examples of their utility in advancing drug discovery, based on the potential for scalability, multiplexing, and capability to generate definitive data on cellular heterogeneity and target engagement.

Expert opinion: Understanding target engagement and heterogeneity at the single-cell level will enable the development of safer and more effective therapies, particularly for new modalities like CAR-T cell therapies and gene editing approaches (AAV, CRISPR). Successful adoption of new single-cell imaging-based approaches in drug discovery will require tandem investment in advanced computational analysis and bioinformatic approaches, due to the complexity and multivariate nature of single-cell imaging data.

KEYWORDS:

• Bioinformatics
• CAR-T
• fluorescence microscopy
• image analysis
• imaging mass cytometry
• imaging mass spectrometry
• immuno-oncology
• microfluidics
• multiplexing
• oncology
• tissue

Acknowledgments

The authors would like to acknowledge Markus Stoeckli and Alan Abrams for assistance with figure preparation and Catherine Jones for assistance with manuscript preparation.

Article highlights

• Optical microscopy is well suited for the characterization of single cells. This is due to alignment between typical length and temporal scales of interest for biological molecules and processes relevant to drug discovery and disease pathways, as well as the ability of imaging to interrogate complex biological systems in a quantitative and highly multiplexed manner.

• Cells themselves are now drug products (CAR-T cell therapies) that are revolutionizing immunotherapy. There is a critical need for single-cell assays to understand their safety, toxicity, and efficient methods of manufacturing.

• Highly multiplexed optical and imaging-guided assays such as imaging MS and IMC are critical for maximizing information on cell and subcellular target (e.g. protein or RNA) states, particularly for rare or difficult-to-culture cell types.

• Improvements in single-cell handling and manipulation with microfluidics and microdroplets have enabled the development of higher-throughput single-cell imaging assays.

• Advanced computational and bioinformatics methods are critical to address vast amounts of data and sample heterogeneity in a quantitative and unbiased manner.

This box summarizes key points contained in the article.

Declaration of interest

J.W. Fathman is an employee of the Genomics Institute of the Novartis Research Foundation with all remaining authors employees of the Novartis Institutes for BioMedical Research Inc. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Reviewer Disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

The authors are funded by the Novartis Institutes for Biomedical Research.