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.
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.
1. Novel methods for spatiotemporally-resolved profiling of dynamic protein events.
Protein function is tightly regulated by its subcellular locations and dynamic movement between compartments. 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.
2. Novel methods for spatiotemporally-resolved profiling of molecular interactions.
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.
3. Discovery of functional protein PTMs in host-pathogen interface.
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 utilize state-of-the-art computational proteomic approaches to discover novel PTMs in host-pathogen interface.
