Two Single-Cell RNA-seq Papers This Week

Just when you thought you finished reading an interesting single-cell RNA-seq paper, two more interesting papers come out on the same week: one in Nature and the other in Nature.

I am not even going to summarize the papers now, other than saying that the Nature paper looks at single-cell RNA-seq data from over 1700 single-cell samples from mouse under three different conditiona and four time points.  The Science paper looks at single-cell RNA-seq data from  430 cells from five primary glioblastomas.  Aviv Regev from Broad Institute is one of the corresponding authors in both the papers.

Here you go and have fun!

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

by Alex K. Shalek,Rahul Satija, Joe Shuga, John J. Trombetta, Dave Gennert, Diana Lu, Peilin Chen, Rona S. Gertner,Jellert T. Gaublomme, Nir Yosef, Schraga Schwartz, Brian Fowler, Suzanne Weaver, Jing Wang, Xiaohui Wang, Ruihua Ding, Raktima Raychowdhury, Nir Friedman, Nir Hacohen, Hongkun Park, Andrew P. May & Aviv Regev

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.

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Anoop P. Patel*, Itay Tirosh*, John J. Trombetta, Alex K. Shalek, Shawn M. Gillespie, Hiroaki Wakimoto, Daniel P. Cahill, Brian V. Nahed, William T. Curry, Robert L. Martuza, David N. Louis, Orit Rozenblatt-Rosen, Mario L. Suvà, Aviv Regev, Bradley E. Bernstein

Human cancers are complex ecosystems composed of cells with distinct phenotypes, genotypes, and epigenetic states, but current models do not adequately reflect tumor composition in patients. We used single-cell RNA sequencing (RNA-seq) to profile 430 cells from five primary glioblastomas, which we found to be inherently variable in their expression of diverse transcriptional programs related to oncogenic signaling, proliferation, complement/immune response, and hypoxia. We also observed a continuum of stemness-related expression states that enabled us to identify putative regulators of stemness in vivo. Finally, we show that established glioblastoma subtype classifiers are variably expressed across individual cells within a tumor and demonstrate the potential prognostic implications of such intratumoral heterogeneity. Thus, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.


  1. […] rheumatoid arthritis or ulcerative colitis. The paper has been picked up by a couple of blogs: NextGenSeek describes it alongside another single cell paper, and the RNASeqBlog describes the main […]

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