Integrating live-cell imaging approaches with single-cell sequencing technologies

Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disputed. Here, Stanford University bioengineers explore these questions by integrating live-cell imaging approaches with single-cell sequencing technologies. They used this approach to measure both the dynamics of lipopolysaccharide-induced NF-κB activation and the global transcriptional response in the same individual cell. Their results identify multiple, distinct cytokine expression patterns that are correlated with NF-κB activation dynamics, establishing a functional role for NF-κB dynamics in determining cellular phenotypes. Applications of this approach to other model systems and single-cell sequencing technologies have significant potential for discovery, as it is now possible to trace cellular behavior from the initial stimulus, through the signaling pathways, down to genome-wide changes in gene expression, all inside of a single cell.

rna-seq

  • A microfluidic platform for measuring NF-κB dynamics and RNA-seq in the same cell
  • Dual clustering analysis shows a strong link between NF-κB dynamics and gene expression
  • The researchers link imaging and single-cell genomics technologies using experiment and computation
Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe’er D, Boutet SC, Covert MW. (2017) Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. Cell Syst S2405-4712(17)30132-1. [abstract]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.