Systems biology explores the emergent property of living systems by combining biological experimentation, mathematical modeling, and computer simulation. Such an emergent property mostly occurs when multiple components interact with each other in a nonlinear way. Cells have evolved a complicated signaling network to recognize external signals and produce appropriate responses for survival. We found that there are intriguing circuits in such a signaling network that were evolutionarily designed to elicit critical functions as an emergent property. In particular, we found that feedforward and feedback loops are essential in such circuits and that cellular dysfunctions related to complex human disease such as cancer can be caused by malfunctioning of these circuits. In this talk, I will introduce some case studies ranging from a small-scale signaling circuit to a large and complex molecular interaction network to discuss how the emergent properties of cellular functions can be induced by complicated interaction of multiple molecules and how we can control the cellular functions by perturbing some targeted molecules in the network, which leads to ‘network medicine’.

The dynamics of RNA - the synthesis, transport, and degradation - plays significant roles in a variety of neuronal processes. Abnormal mRNA processing and transport are implicated in neurological disorders such as autism and Alzheimer’s disease. However, understanding the mechanistic roles of RNA dynamics has been hampered by the lack of techniques to observe the endogenous molecules in the native tissue environment. Here I will describe a systems approach, combining single-particle tracking, genetic engineering, and intravital microscopy. Recently we have developed a new mouse model to fluorescently label endogenous Arc mRNA. The immediate early gene Arc (also known as Arg3.1) is highly involved in the formation of long-term memory. Expression of Arc is tightly coupled to the activity of the neuron; Arc mRNA is rapidly produced in response to neural activity and transported to distant dendrites. Based on our previous work to visualize single endogenous β-actin mRNA (Park et al., Science 343 (2014): 422-424), we generated Arc-PBS mouse by knocking in 24 tandem arrays of PP7 binding site (PBS) in the 3′ untranslated region (3′ UTR) of the Arc gene. Using this mouse model, we are studying activity-dependent transcription of Arc in live hippocampal neurons. By simultaneously imaging relative Ca2+ concentrations and Arc mRNA transcription, we are investigating the relationship between the activity of neurons and gene expression in a single cell level with single RNA resolution. The next step of our study is to image Arc mRNA in a more physiological condition such as in brain slices, or even in the brain of live mice using a two-photon microscope. Ultimately, our research will allow us to link behavior and gene expression in live animals in real time.

Some transmembrane proteins move in one membrane and bind other molecules in another membrane to facilitate cellular functions. For example, STIM1 (Ca2+ sensor in endoplasmic reticulum (ER)) diffuses in ER membrane and Orai1 (Ca2+ channel) diffuses in plasma membrane. After the depletion of Ca2+ store in ER, STIM1 translocate to ER-plasma junction and bind Orai1 to trigger store-operated Ca2+ entry. However, the motion of STIM1 and Orai1 before and after depletion of Ca2+ store has not been clearly understood yet. Here, we tracked the motion of single STIM1 and Orai1 particles in the ER and plasma membranes before and after the depletion and found anomalous diffusion of STIM1 and Orai1 before and after depletion. Using through analysis of the parameters of motions including radius of gyration, mean squared displacement and probability density function, we found that single STIM1 and Orai1 particle exhibits drastical change after the depletion. Probability density functions before the depletion are non-Gaussian but non-Gaussianity drastically increases after the depletion. Turning angle and simulation reveal that single STIM1 and Orai1 are confined in compartmentalized ER and plasma membrane before depletion and all the drastic change in the motion of STIM1 and Orai1 after depletion is caused by the drastic increase of confinement in ER-plasma junction. Our study presents the first report of drastic changes in the motion of two membrane particles in ER and plasma membrane by binding of two proteins in ER-plasma junctions, which is explained by the increased confinement in compartmentalized membrane.