Massively multiplex chemical transcriptomics at single-cell resolution

Area of Science:

• Single-cell genomics
• Chemical biology
• Drug discovery

Background:

• Traditional high-throughput chemical screens offer limited insights into drug mechanisms and cellular responses.
• Understanding heterogeneous cellular responses to compounds is crucial for effective drug development.

Purpose of the Study:

• To introduce sci-Plex, a novel method for high-resolution analysis of transcriptional responses to chemical perturbations.
• To demonstrate the capability of sci-Plex in profiling large-scale single-cell transcriptomic data.

Main Methods:

• Development and application of sci-Plex, utilizing nuclear hashing for single-cell RNA sequencing.
• Screening of three cancer cell lines against 188 compounds, generating ~650,000 single-cell transcriptomes.
• Analysis of transcriptional profiles to identify compound-specific and family-related cellular responses.

Main Results:

• Sci-Plex enabled the profiling of ~5000 independent samples in a single experiment at single-cell resolution.
• Identified significant intercellular heterogeneity in cellular responses to individual compounds.
• Revealed commonalities in responses to compound families and differential effects within families.

Conclusions:

• Sci-Plex offers a powerful platform for dissecting complex cellular responses to chemical perturbations at unprecedented scale and resolution.
• The findings provide new insights into drug mechanisms, off-target effects, and personalized medicine.
• Results with histone deacetylase inhibitors suggest chromatin's role as an acetate reservoir in cancer cells.