DEPICT-seq: Single-Cell Transcriptomic Analysis of Rare Cell Subsets Isolated via Nucleic Acid Cytometry

Area of Science:

• Single-cell biology
• Genomics
• Molecular biology

Background:

• Identifying rare cell populations is crucial for understanding tissue function and disease.
• Single-cell RNA sequencing (scRNA-seq) identifies new cell subtypes by transcriptomic markers.
• Current methods for retrieving cells based on nucleic acid markers are limited.

Purpose of the Study:

• To introduce DEPICT-seq, a novel high-throughput droplet nucleic acid cytometry method.
• To enable precise isolation and transcriptomic analysis of rare cells based on nucleic acid markers.
• To demonstrate the application of DEPICT-seq for isolating engineered T cells and paired TCR sequencing.

Main Methods:

• DEPICT-seq integrates batch cell fixation, double emulsion digital PCR-based cell sorting, and full-length transcriptomic analysis.
• The method targets specific nucleic acid markers for cell isolation.
• A variation incorporates RNase H-dependent PCR for enriched full-length TCR sequencing.

Main Results:

• DEPICT-seq successfully isolates and characterizes T cell receptor (TCR)-engineered T cells from mixed populations.
• The workflow allows for paired single-cell TCR sequencing and transcriptomic profiling.
• The method provides in-depth transcriptomic analysis at single-cell resolution.

Conclusions:

• DEPICT-seq offers a powerful new approach for rare cell isolation and analysis.
• This method advances the ability to study cell populations defined by specific nucleic acid markers.
• DEPICT-seq has broad applications in immunology, cancer research, and other fields requiring precise cell characterization.