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Nature DOI:10.1038/nature13437

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Publication TypeJournal Article
Year of Publication2014
AuthorsShalek, AK, Satija, R, Shuga, J, Trombetta, JJ, Gennert, D, Lu, D, Chen, P, Gertner, RS, Gaublomme, JT, Yosef, N, Schwartz, S, Fowler, B, Weaver, S, Wang, J, Wang, X, Ding, R, Raychowdhury, R, Friedman, N, Hacohen, N, Park, H, May, AP, Regev, A
Date Published2014 Jun 19
KeywordsAnimals, Antigens, Viral, Base Sequence, Cell Communication, Dendritic Cells, Gene Expression Profiling, Gene Expression Regulation, Immunity, Interferon-beta, Mice, Microfluidic Analytical Techniques, Paracrine Communication, Principal Component Analysis, RNA, Messenger, Single-Cell Analysis

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.


Alternate JournalNature
PubMed ID24919153
PubMed Central IDPMC4193940
Grant ListF32 HD075541 / HD / NICHD NIH HHS / United States
1F32HD075541-01 / HD / NICHD NIH HHS / United States
5DP1OD003893-03 / OD / NIH HHS / United States
U54 AI057159 / AI / NIAID NIH HHS / United States
DP1OD003958-01 / OD / NIH HHS / United States
DP1 CA174427 / CA / NCI NIH HHS / United States
DP2 OD002230 / OD / NIH HHS / United States
/ / Howard Hughes Medical Institute / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
DP1 OD003893 / OD / NIH HHS / United States
1P50HG006193-01 / HG / NHGRI NIH HHS / United States
DP1 OD003958 / OD / NIH HHS / United States