Research

A protein’s life trajectory is the path that it chooses from synthesis to degradation and a slight change in its life trajectory can lead to huge differences in its functional outcomes. To describe a protein’s life trajectory, we would ask: “When was it?”, “Where was it?”, “What was it doing?” and “Who did it meet?”. Such four dimensional information is critical for understanding a protein’s dynamic roles across its lifetime in the cellular society. Quantitative proteomics provides a versatile platform to systematically assess specific protein features, but typically report on only a single dimension of information. Many cutting-edge technologies have been developed for exploring each dimension, such as pulse-SILAC for the temporal dimension, proximity labeling (PL) for the spatial dimension and activity-based protein profiling for the functional dimension.

Our long-term research vision is to promote the revolution of proteomics from 1D to 4D, in order to describe each protein’s life trajectory in living cells. My lab will be focused on developing novel chemical and molecular tools, in combination with state-of-the-art proteomics, to simultaneously map dynamic timing, localization, function and interaction of proteomes, with the ultimate goal of better understanding essential mechanisms underlying the regulation of cellular physiology. Specifically, I have three major future directions to address different aspects of essential biological questions and lay the foundation for the eventual 4D proteomics.

Protein function is tightly regulated by its subcellular locations and dynamic movement between compartments. During my postdoc study, we have developed protein translocation profiling based on tandem proximity labeling. Although powerful, this technology requires two rounds of enrichment steps, which demand large starting materials and potentially sacrifice the sensitivity. We will further work on developing next-generation protein translocation profiling methods with higher efficiency.
On the other hand, the structure of a protein is intimately linked to its function. Global analysis of protein structures in living cells could serve a quantitative readout to capture most events that alter protein functional states. The global protein structural dynamics has been extensively investigated by a variety of proteomic methods, including crosslinking mass spectrometry, thermal proteome profiling and limited proteolysis-MS. However, current methods lack spatiotemporal resolution and are especially challenging when membranes and other cellular structures are still intact in living cells. We will further establish transformative approaches to analyze protein sturctural dynamics in living systems.

Cellular functions are tightly regulated by proteins, other biomolecules and their interactions, including protein–protein interactions (PPIs), protein–RNA/DNA interactions and protein–metabolite interactions. Such molecular interaction networks are central to most biological processes, while their dysregulation has been linked to a variety of human diseases including cancers, immune disorders and neurodegeneration. Methods enabling the large-scale discovery of molecular interactions in living cells have provided insights for biological exploration and therapeutic intervention. We aim to develop spatiotemporally-resolved proteomic methods to map diverse protein interactions and their dynamics. Meanwhile, we will further decipher functional protein interactions and understand their biological importance.

During bacterial infection, host cells recognize extracellular stimuli from invading pathogens and in response activate pro-inflammatory signals that protect the host. In the interface of host and pathogens, a variety of post-translational modifications (PTMs) are involved. For instance, many bacterial pathogens secrete virulence factors, also known as effector proteins, directly into host cells and a particularly interesting subset of effector post-translationally modify host proteins using novel chemistry that is not otherwise found in the mammalian proteome. The understanding of those functional PTMs in host-pathogen interface are largely impeded by the lack of tools to specifically label and manipulate those PTMs. We will work on developing new tools to understand how PTMs, including O-GlcNAcylation and itaconation, regulate pathogen infection and immune responses. We will also ultilize state-of-the-art computational proteomic approaches to discover novel PTMs in host-pathogen interface.