UCSF

With the advent of immunotherapy, identification and characterization of cancer-specific antigens is paramount to our ability to leverage this field towards the treatment of cancer. Pursuing the study of these cell surface antigens, especially in the context of cellular stress has become increasingly important. Low oxygen availability, or hypoxia, is a major environmental factor in solid tumors, which influences the metabolic, transcriptomic, and proteomic landscape of these cells. Hypoxia ultimately leads to poorer prognoses for patients with hypoxic solid tumors, and these hypoxia-specific effects suggest that tumor hypoxia can be leveraged for early stage diagnostics, as well as selective targeting of hypoxia-induced antigens in tumors. There are two main modes by which cell surface targets can be leveraged for the selective targeting of diseased cells, namely (1) through direct binding of a tumor cell surface antigen by antibodies and downstream activation of surrounding immune cells or (2) through the interaction of MHC-I peptide complexes with the native T-cell receptor (TCR). This work encompasses novel methods for the identification of both whole protein and MHC-peptide complexes in the context of hypoxic pancreatic cancer. As pancreatic cancer continues to lack tangible treatment options, it has become increasingly important to characterize these tumor types for new and selective therapeutic targets.

In Chapter 1, we perform cell surface proteomics on an array of basal and classical pancreatic adenocarcinoma (PDAC) cells in hypoxia and normal conditions and identify the membrane protein vasorin (VASN) as a potential marker for hypoxic PDAC. In Chapter 2, we develop a novel method for small-scale cell surface proteomics using membrane tethered forms of the promiscuous biotinylators APEX2 and HRP. In Chapter 3, we design a novel secreted HLA Fc-fusion construct that can be coupled with mass spectrometry to profile the immunopeptidome of disease-phenotypes, including hypoxia and senescence.