Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

Area of Science:

• Single-cell biology
• Molecular biology
• Genomics

Background:

• Multimodal single-cell assays offer deep biological insights but are often limited to two data types.
• Existing methods restrict the simultaneous analysis of multiple cellular features.

Purpose of the Study:

• To introduce an expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq) method.
• To enable high-throughput characterization of at least five modalities from individual single cells.

Main Methods:

• Development and application of ECCITE-seq for simultaneous capture of transcriptome, surface proteins, and CRISPR-encoded genetic information.
• Integration of direct single-guide RNA capture for CRISPR screening.
• Application to clonotype-aware phenotyping of cancer samples.

Main Results:

• Demonstrated robust direct single-guide RNA capture for multimodal CRISPR screens.
• Successfully applied ECCITE-seq to clonotype-aware multimodal phenotyping of cancer samples.
• Enabled the simultaneous analysis of at least five modalities per cell.

Conclusions:

• ECCITE-seq significantly advances multimodal single-cell analysis capabilities.
• The method is versatile for applications ranging from CRISPR screens to cancer research.
• Provides a powerful tool for high-resolution characterization of complex cellular systems.