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DOE OSTI · 2480420

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

Fulcher, James M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000190333623)·Markillie, Lye Meng [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000182754882)·Mitchell, Hugh D. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000301438461)·Williams, Sarah M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)]·Engbrecht, Kristin M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)]·Degnan, David J. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000157377173)·Bramer, Lisa M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000283841926)·Moore, Ronald J. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000328062855)·Chrisler, William B. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)]·Cantlon-Bruce, Joshua [Scienion AG (Germany); Cellenion SASU, Lyon (France)]·Bagnoli, Johannes W. [Cellenion SASU, Lyon (France)]·Qian, Wei-Jun [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000253932827)·Seth, Anjali [Cellenion SASU, Lyon (France)]·Paša-Tolić, Ljiljana [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000198535457)·Zhu, Ying [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); Genentech Inc., South San Francisco, CA (United States)] (ORCID:0000000254160566)
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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.

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59 BASIC BIOLOGICAL SCIENCEScell-cycle proteinsmass spectrometryproteomicstranscriptomics

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Fulcher, James M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000190333623), Markillie, Lye Meng [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000182754882), Mitchell, Hugh D. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000301438461), Williams, Sarah M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)], Engbrecht, Kristin M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)], Degnan, David J. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000157377173), Bramer, Lisa M. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000283841926), Moore, Ronald J. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000328062855), Chrisler, William B. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)], Cantlon-Bruce, Joshua [Scienion AG (Germany); Cellenion SASU, Lyon (France)], Bagnoli, Johannes W. [Cellenion SASU, Lyon (France)], Qian, Wei-Jun [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)] (ORCID:0000000253932827), Seth, Anjali [Cellenion SASU, Lyon (France)], Paša-Tolić, Ljiljana [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)] (ORCID:0000000198535457), Zhu, Ying [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); Genentech Inc., South San Francisco, CA (United States)] (ORCID:0000000254160566). 2024-12-05. Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting. https://doi.org/10.1038/s41467-024-54099-z

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