Research and Projects

Our lab takes a chemical biology approach to studying the innate immune system and covalent inhibitor development. Our research is divided into three main foci:

1. Leveraging chemical proteomic technologies for the development of covalent inhibitors
2. Discovering new ‘don’t eat me’ signal ligands encoded by pathogens
3. Understanding the etiology of the tumor associated macrophage

1. Leveraging chemical proteomic technologies for the development of covalent inhibitors

Covalent inhibitors have emerged as promising therapeutics, oftentimes demonstrating improved selectivity and potency compared to traditional, reversible inhibitors. The presence of an electrophilic moiety on small molecule scaffolds endow these inhibitors with the ability to covalently engage a nucleophilic residue on a protein of interest. However, designing selective covalent inhibitors and evaluating their selectivity in a comprehensive manner remains a challenge in the field. Our lab seeks to harness recent advances in chemical proteomics to develop new tools and approaches to optimize the discovery and design of covalent inhibitors. In particular, our aim is to identify unique physicochemical features on proteins which can be exploited during the design stage of covalent inhibitor development to improve selectivity. Through the development of these tools, we hope to identify highly selective compounds that can pave the way for next-generation covalent inhibitors.

2. Discovering new ‘don’t eat me’ signal ligands encoded by pathogens

‘Don’t eat me’ signaling axes are ligand-receptor interactions utilized by the innate immune system to recognize healthy self cells and prevent their phagocytosis by macrophages. The most-widely studied axis is between the ligand CD47 and the receptor SIRPɑ. Surprisingly, while there is little population-wide diversity in the gene encoding CD47, the gene encoding SIRPɑ is polymorphic in the CD47-binding region. These polymorphisms are associated with geography and are implicated in infectious disease and therapeutic outcomes. Sites of strong positive selection are found in exon encoding the CD47-binding region. This is particularly surprising given that CD47 is the only reported ligand of SIRPɑ, prompting us to ask what could be driving high-frequency sequence variation. We hypothesize that pathogens have evolved to express surface proteins that engage self-recognition receptors, specifically SIRPɑ, thus evading the innate immune system through pathways once thought to be distinctly-mammalian. This may have broad reaching implications for human biology. In support of our theory, we recently discovered a mimic of CD47 on the surface of the bacteria Borrelia burgdorferi, the causative agent of Lyme Disease, called P66. Loss of P66 increases phagocytosis of the bacteria by macrophages. Our lab is now actively engaged in research to dissect the biology of this new ‘don’t eat me’ signal ligand mimic, to develop novel therapeutics targeting P66 for the treatment of Lyme Disease, and to discover more mimics encoded by pathogens.

3. Understanding the etiology of the tumor associated macrophage

Macrophages clear exhausted, damaged, and sick cells in our bodies, as well as exogenous pathogens, cellular debris, and atherosclerotic plaques. They recognize and engulf their targets prior to destruction in the lysosome. Phagocytosis is a vital process in our innate immune system and is altered in diseases, including cancer. Between 15-70% of solid tumor bulk consists of tumor-associated macrophages. These macrophages are no longer capable of phagocytosis, and their relative contribution to tumor bulk often is associated with poor disease outcome. As a result, tumor associated macrophages are emerging as a focus of tumor immunology studies. Transcriptomic analyses demonstrate that tumor associated macrophages are unequivocally different than a normal healthy macrophage, but they have revealed little as to how these cells have become so dysfunction. We hypothesize that these changes are, in fact, post-transcriptional and that a proteomic understanding of how macrophages change during the process of cancer cell phagocytosis may provide a deeper understanding of mechanisms at play in cancer, and perhaps more-broadly across macrophage function. To this end we have developed a novel proteomics platform to uncover key mechanisms in macrophage and tumor biology that we are actively validating in the lab.

Commitment to collaboration

Work in the Zaro lab leverages novel biochemical, mass spectrometry and chemical proteomics techniques to answer long-standing biological questions, with a focus on immunology and cancer biology. However, we also collaborate with investigators across our scientific community to apply state-of-the-art proteomic techniques to biological systems understudied with such approaches. For example, we merged mass spectrometry and Cryo-EM to elucidate the role of the endoplasmic reticulum membrane protein complex in membrane protein biogenesis. We also developed new surface protein enrichment methodologies to discover novel RNA-binding proteins on the cell surface. For a complete list of publications, please see our Publications page.