Deciphering dynamic signals in control of cell fate decisions

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PROJECT SUMMARY In the long-term, our goal is to understand how single cells integrate and process information to make irreversible decisions such as whether to proliferate, differentiate or die. Inflammatory factors that participate in many normal and diseased cell fate decisions initiate signals by dynamically re-organizing proteins within the cell. For example, ligand-bound TNF receptors transiently organize large protein complexes near the plasma membrane, and these are visible within the cell as discrete punctate structures, whereas other proteins translocate between cellular compartments such as the cytoplasm and the nucleus. It is an emerging principle that dynamic properties of molecules within signal transduction circuits provide temporal codes (including rate of change, amplitude, duration or frequency among others) that are critical to each cell’s response to stimulus. Given that there is substantial cell-to-cell heterogeneity, even in clonal cell lines, static measurements at fixed time points cannot reveal the mechanisms of dynamic information processing. We hypothesize that components of the same signaling pathway are deterministically linked to one another in a single cell, even though there is substantial heterogeneity between cells. Here, we propose to multiplex expression of live-cell fluorescent reporters for up- and down-stream components of the same signaling pathway in the same cell, and correlate time-varying signals from live-cell microscopy data. Using a hybrid of quantitative imaging, microfluidics and computational techniques we will extract time-varying data from 100s-1000s of single cells in each experimental condition, and compare them across several different cell lines. We will also compare cellular responses across different inflammatory factors that share signaling modules and converge on the NF-κB transcriptional system, such as TNF, LPS or IL-1 among others. Using a rich single-cell dataset, we will use transfer entropy to measure mutual information between features of time-varying signals in the same pathway, and infer mechanisms of signal transduction in addition to correlations with cell fate. Data from live-cell experiments will be incorporated into mechanistic models to formalize our understanding of how information is relayed through the signaling network into transcription, and suggest perturbations to test predicted mechanisms. We anticipate that increasingly accurate models may lead to non-intuitive strategies to manipulate decisions in single cells. Through a detailed understanding of how dynamic molecular signals encode, process, and decode information, we have the potential to understand biological problems that are deeply rooted in disease, and use this knowledge to rationally design therapies that impact cell fate decisions.