TITLE: “Modeling the heterogenous NFκB dynamics of single immune cells.”
ABSTRACT: Macrophages function as immune sentinel cells, initiating appropriate and specialized immune responses to a great variety of pathogens. The transcription factor NFκB controls macrophage gene expression responses, and its temporal dynamics enable stimulus-specificity of these responses. Using a fluorescent reporter mouse our laboratory recently generated large amounts of single-cell NFκB dynamic data and identified dynamic features, termed ‘signaling codons’, that convey information to the nucleus about stimulus identity and dose. Here, we aimed to recapitulate the stimulus-specific but highly cell-to-cell heterogeneous NFκB dynamics with a mathematical model of the signaling network. The parameters that are subject to biological variation provide the potential to account for the heterogeneity in observed stimulus responses. We estimated parameter distributions using the Stochastic Approximation Expectation Maximization (SAEM) approach and then fit the individual cell data using Bayesian maximum a posteriori (MAP) estimation. Visual inspection revealed an excellent fit with the data. To quantitatively evaluate the fitting performance, we compared the experimental and predicted distributions of NFκB signaling codons. Further, we identified biochemical reactions that may account for the cellular heterogeneity in NFκB dynamics. We verified that the stimulus-specificity of the virtual macrophage NFκB responses was consistent with their live-cell counterparts, as assessed by mutual information and machine learning classification. Additionally, the mathematical model allowed us extend experimental dose response studies, revealing the doses that maximize information. Furthermore, the virtual NFκB macrophages enabled the exploration of individual cell responses to different ligands. Leveraging this capability, we made predictions regarding combinatorial ligands, that were then experimentally tested. Discrepancies between the experimental results and model predictions led to the identification of a competition mechanism between CpG and PolyIC for endosome trafficking, resulting in non-integrative responses behavior. Our results establish a mathematical modeling tool that may be used to study the molecular determinants of response specificity and dynamical coding in immune sentinel cells at the single cell level.
