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

James M. Fulcher (), Lye Meng Markillie, Hugh D. Mitchell, Sarah M. Williams, Kristin M. Engbrecht, David J. Degnan, Lisa M. Bramer, Ronald J. Moore, William B. Chrisler, Joshua Cantlon-Bruce, Johannes W. Bagnoli, Wei-Jun Qian, Anjali Seth, Ljiljana Paša-Tolić and Ying Zhu ()
Additional contact information
James M. Fulcher: Pacific Northwest National Laboratory
Lye Meng Markillie: Pacific Northwest National Laboratory
Hugh D. Mitchell: Pacific Northwest National Laboratory
Sarah M. Williams: Pacific Northwest National Laboratory
Kristin M. Engbrecht: Pacific Northwest National Laboratory
David J. Degnan: Pacific Northwest National Laboratory
Lisa M. Bramer: Pacific Northwest National Laboratory
Ronald J. Moore: Pacific Northwest National Laboratory
William B. Chrisler: Pacific Northwest National Laboratory
Joshua Cantlon-Bruce: Scienion AG
Johannes W. Bagnoli: Bâtiment BioSerra2
Wei-Jun Qian: Pacific Northwest National Laboratory
Anjali Seth: Bâtiment BioSerra2
Ljiljana Paša-Tolić: Pacific Northwest National Laboratory
Ying Zhu: Pacific Northwest National Laboratory

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. Here, we introduce nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells via RNA sequencing and mass spectrometry-based proteomics, respectively. Benchmarking of nanoSPLITS demonstrates high measurement precision with deep proteomic and transcriptomic profiling of single-cells. We apply nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing insights into cell cycle regulation. We extend nanoSPLITS to primary cells isolated from human pancreatic islets, introducing an efficient approach for facile identification of unknown cell types and their protein markers by mapping transcriptomic data to existing large-scale single-cell RNA sequencing reference databases. Accordingly, we establish nanoSPLITS as a multiomic technology incorporating global proteomics and anticipate the approach will be critical to furthering our understanding of biological systems.

Date: 2024
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DOI: 10.1038/s41467-024-54099-z

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