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

• Published in: Nature communications 2024-12, Vol.15 (1), p.10614-13
• Main Authors: Fulcher, James M., Markillie, Lye Meng, Mitchell, Hugh D., Williams, Sarah M., Engbrecht, Kristin M., Degnan, David J., Bramer, Lisa M., Moore, Ronald J., Chrisler, William B., Cantlon-Bruce, Joshua, Bagnoli, Johannes W., Qian, Wei-Jun, Seth, Anjali, Paša-Tolić, Ljiljana, Zhu, Ying
• Format: Article
• Language: English
• Subjects: 38/62; 38/91; 631/1647/296; 631/61/212/2019; 631/61/475; 639/638/92/612/1223; 82/58; Animals; CDC2 Protein Kinase - genetics; CDC2 Protein Kinase - metabolism; Cell cycle; Cyclin-dependent kinase; Cyclin-dependent kinases; Depth profiling; Gene Expression Profiling - methods; Gene sequencing; Humanities and Social Sciences; Humans; Islets of Langerhans - metabolism; Kinases; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; multidisciplinary; Peptide mapping; Proteins; Proteome - metabolism; Proteomes; Proteomics; Proteomics - methods; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Scientific imaging; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Splitting; Transcriptome; Transcriptomes; Transcriptomics
• ISSN: 2041-1723
• DOI: 10.1038/s41467-024-54099-z

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. Single-cell multiomics can provide broad insights into gene/protein regulatory networks and cellular diversity. Here, authors develop nanoSPLITS, a nanodroplet splitting approach for global profiling of the transcriptome and proteome from same single cells via RNA sequencing and mass spectrometry-based proteomics.