Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

Area of Science:

• Molecular Biology
• Genomics
• Immunology

Background:

• Single-cell measurements reveal cellular heterogeneity crucial for understanding differentiation, signaling responses, and disease.
• Paired protein and transcriptomic profiling advanced single-cell analysis, but lacked epigenetic insights into gene regulation.

Purpose of the Study:

• To develop novel multimodal single-cell assays integrating chromatin accessibility with protein and transcriptomic data.
• To establish a toolkit for linking cell phenotype to gene regulatory mechanisms.

Main Methods:

• Developed integrated cellular indexing of chromatin landscape and epitopes (ICICLE-seq) for paired cell surface marker and chromatin accessibility measurement.
• Extended ICICLE-seq to a trimodal assay (TEA-seq) using droplet-based multiomics for simultaneous transcriptomics, epitope, and chromatin accessibility profiling.
• Utilized human peripheral blood as a test case for assay development and validation.

Main Results:

• ICICLE-seq enhances signal-to-noise for paired measurement of chromatin accessibility and cell surface markers.
• TEA-seq enables simultaneous, high-throughput measurement of transcriptomics, epitopes, and chromatin accessibility from single cells.
• The assays provide a foundation for identifying type-specific gene regulation within phenotypically defined cell populations.

Conclusions:

• Multimodal single-cell assays like ICICLE-seq and TEA-seq offer a powerful toolkit for dissecting gene regulation.
• These methods bridge the gap between cell phenotype and epigenetic mechanisms driving cellular function and disease.
• The developed assays advance the study of cellular heterogeneity and gene expression in complex biological systems.