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

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.
Competing Interests: Competing interests: J.C.B., J.W.B, and A.S. are employees of Scienion/Cellenion. Y.Z. is an employee of Genentech Inc. and shareholder of Roche Group. Battelle Memorial Institute has submitted a U.S. patent application for the design of nanoSPLITS devices and the associated operation methods (Application number: 17/954,834, filed 09/28/2022; Inventors: Y.Z., J.M.F., L.M.M., and L.P.T.; Status of application: Pending). Other authors declare no other competing interests.
(© 2024. Battelle Memorial Institute, Scienion US Inc. and Cellenion SASU 2024.)