Investigating the signaling codes that specify immune responses by macrophages
Final Report Abstract
Macrophages are ubiquitous sentinel cells of the innate immune system with important functions in orchestrating local and systemic immune responses. Stimulus-specificity of their responses aids them in balancing high sensitivity to various types of pathogens and danger signals for sufficient responses with a tightly controllable, appropriate reaction to avoid pathological dysregulation. Macrophages sense stimuli through more than a dozen receptors, which converge on a limited number of signaling pathways. This specificity is thought to be achieved via temporal and combinatorial coding. In temporal coding, information about the stimulus can be encoded in the dynamics of a single signaling module, such as the transcription factor NFκB. In combinatorial coding, different pathways may be activated in stimulus-specific combinations through branching of the pathways. The overarching goal of my research project was to understand the dynamic and combinatorial signaling codes that specify innate immune responses by macrophages. In the first part of my project, I investigated the determinants of NFκB’s temporal code in response to TNF, a key inflammatory cytokine. Acute exposure to TNF activates characteristic oscillatory NFκB dynamics; these are distinct from the responses of cells directly exposed to pathogen-associated molecular patterns (PAMPs). I demonstrated that tonic TNF safeguards the oscillations in TNF-induced NFκB responses by subtly affecting TNFR levels, thus decreasing TNFR signaling strength such that IKK activity does not neutralize the IκBα feedback loop. I showed that macrophage conditioning by tonic, physiological levels of TNF safeguards the specificity of gene expression and epigenomic integrity in response to acute TNF exposure, ensuring that the responses to this host cytokine are distinct from PAMP-induced signaling. In the second part of my project, I studied whether and how dynamic and combinatorial signaling by NFκB and p38, a key immuneresponsive MAP kinase, interface for increased information transmission on stimulus identity and dose. While the stimulusspecificity of NFκB dynamics is established, it was less clear how stimulus-specific p38 dynamics are. I generated and validated dualreporter macrophages to study p38 and NFκB activity dynamics by live cell microscopy in response to three PAMPs and TNF. Preliminary results of ongoing analyses showed that p38 dynamic features allowed prediction of stimulus molecular identity similar to NFκB features, that there is surprisingly little correlation between NFκB and p38 features, and that NFκB and p38 have differential dose responses to some, but not all stimuli. Information theoretic and machine learning analyses are currently being optimized to study the integration of combinatorial and dynamic signaling. The basis and consequence of this stimulus specificity is subject of ongoing investigation.
Publications
- Immune Sentinel Cells: Molecular Mechanisms for Combinatorial and Temporal Coding to Produce Stimulus-Appropriate Responses. Immunity. 2021; 54(9), 1915-1932
Luecke S, Sheu KM, Hoffmann A
(See online at https://doi.org/10.1016/j.immuni.2021.08.018) - Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Immunity. 2021; 54(5), 916-930
Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A
(See online at https://doi.org/10.1016/j.immuni.2021.04.011) - Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression. 2022
Osimiri LC, Bonny AR, Takagishi SR, Luecke S, Riehs N, Hoffmann A, El-Samad H
(See online at https://doi.org/10.1101/2022.08.03.502739)
