Research Interests

My research integrates computational modeling and experimental methodologies to analyze the homeostatic and dynamic behavior of the IKK:IkB:NF-kB signaling network. Most cellular stresses that activate NF-kB do so via activation of the IkB kinase (IKK) that targets IkB proteins to the proteasome and thus allows NF-kB to translocate to the nucleus. A great deal of combinatorial (multiple isoforms of IkB, NF-kB, etc) and temporal complexity (diverse range of IKK dynamics) complicates our understanding of how NF-kB activation is controlled.

A computational model was built and validated against experimental results to help explain how the network transduces signals [Hoffmann et al. Science 2002]. The computational model uses mass action kinetics to calculate the time-dependent changes in concentrations of proteins and mRNA in a network that contains IKK (the input to the model), NF-kB (the output of the model), and the IkB proteins that inhibit NF-kB activation. It includes reactions that describe IkB:NF-kB:IKK association and dissociation, synthesis and degradation of IkBs, and cellular localization.

Specifically, I have expanded this initial model to examine the interplay between multiple negative feedback loops and the impact on the network. Initially, I discovered experimentally that IkBepsilon, a little-appreciated IkB isoform, provides delayed negative feedback. Inclusion of this feedback mechanism in the model revealed that delayed IkBepsilon feedback counteracts the oscillations in NF-kB activity driven by the immediate IkBalpha-mediated negative feedback [Kearns et al. JCB 2006].

In collaboration with a post-doctoral fellow in the lab (Dr. Soumen Basak), I expanded the model to include a fourth IkB isoform, IkBdelta, and a second IKK isoform, IKKalpha, which is activated via developmental cues [Basak et al. Cell 2007]. IkBalpha, IkBbeta, and IkBepsilon are degraded via IKKbeta while IkBdelta is degraded via IKKalpha. I validated the model against his experimental data and then used the model to predict that IkBdelta mediates crosstalk between inflammatory (IKKbeta) and developmental (IKKalpha) signaling. This prediction was confirmed in cells pre-challenged with inflammatory IKKbeta stimulation (thus increasing the amount of IkBdelta) followed by developmental IKKalpha stimulation. Cells that were pre-challenged showed markedly increased NF-kB activation in response to subsequent developmental challenge.

More recently, I have continued the theme of comparing/contrasting negative feedback regulators by examining the roles of IkBalpha and the A20 deubiquitinase [Werner and Kearns et al. G&D 2008]. Both proteins are strongly induced by NF-kB activation with similar temporal profiles, but function at different locations in the signaling network. IkBalpha directly inhibits NF-kB while A20 functions upstream to deactivate the TNFR signaling complex. Naively, these negative feedbacks should be redundant, but via simulations of a model that includes the upstream TNF pathway and experimental analyses (Shannon L. Werner), we found that they are in fact non-overlapping and provide different regulatory functions.

Publications