RT Journal Article
SR Electronic
T1 Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 665307
DO 10.1101/665307
A1 Harrison Specht
A1 Edward Emmott
A1 Aleksandra A. Petelski
A1 R. Gray Huffman
A1 David H. Perlman
A1 Marco Serra
A1 Peter Kharchenko
A1 Antonius Koller
A1 Nikolai Slavov
YR 2020
UL http://biorxiv.org/content/early/2020/10/04/665307.abstract
AB The fate and physiology of individual cells are controlled by proteins. Yet, our ability to quantitatively analyze proteins in single cells has remained limited. To overcome this barrier, we developed SCoPE2. It substantially increases quantitative accuracy and throughput while lowering cost and hands-on time by introducing automated and miniaturized sample preparation. These advances enabled us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiated into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantified over 3,042 proteins in 1,490 single monocytes and macrophages in ten days of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Furthermore, the data uncovered a continuous gradient of proteome states for the macrophage-like cells, suggesting that macrophage heterogeneity may emerge even in the absence of polarizing cytokines. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that our measurements sampled 20-fold more protein copies than RNA copies per gene, and thus SCoPE2 supports quantification with improved count statistics. Joint analysis of the data illustrates how variability across single cells can reveal transcriptional and post-transcriptional gene regulation. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass-spectrometry.Competing Interest StatementThe authors have declared no competing interest.