Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting.

Area of Science:

• Molecular Biology
• Genomics
• Proteomics

Background:

• Single-cell multiomics is crucial for understanding complex biological systems.
• Existing methods face challenges in comprehensive profiling of both transcriptome and proteome from the same cell.
• Advanced techniques are needed to integrate transcriptomic and proteomic data at the single-cell level.

Purpose of the Study:

• To introduce nanoSPLITS, an integrated platform for simultaneous transcriptome and proteome profiling of single cells.
• To demonstrate the capability of nanoSPLITS for deep and precise multiomic measurements.
• To apply nanoSPLITS for investigating cell cycle regulation and identifying cell types in primary tissues.

Main Methods:

• nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples) platform.
• RNA sequencing for global transcriptome profiling.
• Mass spectrometry-based proteomics for global proteome profiling.
• Application to cyclin-dependent kinase 1 inhibited cells and human pancreatic islets.

Main Results:

• nanoSPLITS achieves high measurement precision for deep proteomic and transcriptomic profiling of single cells.
• Phospho-signaling events were quantified alongside global protein and mRNA in CDK1 inhibited cells, revealing cell cycle regulation insights.
• nanoSPLITS enabled efficient identification of unknown cell types and protein markers in human pancreatic islets by mapping transcriptomic data.

Conclusions:

• nanoSPLITS is established as a powerful multiomic technology integrating global proteomics and transcriptomics.
• The platform provides critical insights into cellular mechanisms, including signaling pathways and cell identity.
• nanoSPLITS is anticipated to be vital for advancing the understanding of biological systems through comprehensive single-cell analysis.