Cell-type-specific interpretation of pathogen information via single-cell NF-kappaB dynamics

Authors

• EW Martin
• A Pacholewska
• H Patel
• H Dashora
• MH Sung

Abstract

Activation of transcription factor (TF) signaling downstream of ligands binding to cell-surface receptors is a hallmark of cell biology. Yet, how cells utilize a relatively limited number of TF pathways to orchestrate diverse functional outputs in response to a multitude of unique inputs is not well-understood. To address this gap in scientific knowledge, we performed a systems-level investigation designed to elucidate how immune cells and non-immune cells utilize the NF-kappaB pathway to interpret and respond to different pathogenic stimuli. As the NF-kappaB pathway is the primary TF pathway activated in response pathogen exposure, macrophage and fibroblast cell lines stably-expressing fluorescent NF-kappaB fusion proteins were generated. The cells were treated with an array of pathogen-derived ligands known to stimulate the NF-kappaB pathway. Long-term, single-cell imaging was performed to capture the ligand-induced spatiotemporal dynamics of the NF-kappaB proteins. Quantitative image analysis revealed that different pathogenic stimuli can induce distinct NF-kappaB dynamics, and that cell-type-specific NF-kappaB dynamics seem to be a predominant feature of the inflammatory response. RNA-seq analysis was performed to explore the functional relevance of the NF-kappaB dynamics as reflected in global gene expression outcomes. The analysis revealed that relative to non-treated controls, expression of many genes was increased in cell-type- and ligand-specific manners. Moreover, a large proportion of the pathogen-induced changes in gene expression correlated with the quantitative characteristics of the observed NF-kappaB dynamics. The resulting experimental data delineate some of the dynamic features of NF-kappaB signaling which different cell-types utilize to process information during pathogen encounter.

Scientific Focus Area: Systems Biology

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