Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells

Abstract

Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mechanisms that control this process are poorly understood. Here we report on a droplet-based microfluidic platform to investigate type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNFα production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. Combining single-cell cytokine analysis with single-cell RNA-seq profiling reveals no evidence for a pre-existing subset of type I IFN-producing pDCs. By modulating the droplet microenvironment, we demonstrate that vigorous pDC population responses are driven by a type I IFN amplification loop. Our study highlights the significance of stochastic gene regulation and suggests strategies to dissect the characteristics of immune responses at the single-cell level.

Miniaturization technologies for cost-effective AmpliSeq library preparation for next generation sequencing

“…Miniaturization seemed to make the protocol easier to be influenced by environmental factors. This is the first application of the Mosquito HTS for the AmpliSeq ultra-multiplex PCR protocol and adds to other existing protocols for NGS library preparation [8][9][10][11][12]. However, there are two limitations of this Mosquito protocol.…”

The how and why of lncRNA function: An innate immune perspective

“…For more information on specific lncRNAs that are involved in innate immunity we direct you to the following recent reviews on this topic [42,47,63]. In addition to these bulk RNA sequencing studies, a small number of single cell RNA sequencing studies have been performed in both human and mouse that can be utilized to examine differential expression of lncRNAs in basal versus treatment conditions or between cell types [64][65][66][67][68]. Numerous RNA-seq (both bulk and single cell) datasets are available for a variety of primary cells, cell lines or tissues of interest either basally or under a multitude of inflammatory or cellular differentiation treatments.…”

Massively parallel encapsulation of single cells with structured microparticles and secretion-based flow sorting

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