Surfaceomic technologies and antibodies to probe cell surface proteomes and their interactomes at unprecedented small scale and high-resolution

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Title: Surfaceomic technologies and antibodies to probe cell surface proteomes and their interactomes at unprecedented small scale and high-resolution Project summary The cell surfaceome is the primary hub that allows cells to sense and respond to changes in their environment, yet only a minority of the estimated 4000-5000 plasma membrane and secreted proteins have been functionally characterized. We understand even less about coordinate regulation of the surfaceome, and specifically how the composition, complexes, distribution, and function of membrane proteins are altered to collectively mediate changes to cellular phenotypes. Our long-range goal is to systematically understand how cells remodel their membrane proteome (surfaceome) in health and disease, and to develop antibodies that probe and modulate these processes. With the support of the R35 MIRA in the last five years, we have extensively characterized the surfaceome changes induced by oncogene transformation leading to discovery of new biomarkers, cancer drug targets, and generation of highly specific antibodies. In the next five years, we will develop new surfaceome technologies for small scale analysis of cell populations, particularly in neurodegeneration using iPSC derived models and patient-derived samples. We will define the cell surface protein complexes and interactomes using a high-resolution proximity labeling method enabled by Dexter Energy Transfer (DET). We plan to interrogate the interactome of EGFR family receptors in i ii iii cancer, and cytokine receptors in T-cell Ir activation. We believe the technologies for small scale surfaceomics and interactomics will dramatically improve our abilities to map cell surfaces and their intreactomes in diseases ranging from cancer, immunology, neurology, and more. We have produced recombinant Figure 1. Overview of development of surfaceomics technologies. antibodies to 100s of cell surface proteins using phage, yeast, and mammalian display, and we anticipate the expanded efforts in understanding the surfaceome will advance the development of highly selective antibodies that probe and modulate cellular states. We began this vision in our first R35 grant by defining the surfaceomes induced by specific oncogenes in cancer. Next, we will greatly expand surfaceomics science to much smaller scales of specialized and primary cells, and much higher resolution analysis of signaling interactomes.