UCSF

Cells are constantly encountering damaging reagents and undergoing damaging processes, all of which compromise the integrity of the cell. Luckily, our cells are equipped with repair mechanisms that can combat the damage and return the cell to a healthy state. However, these mechanisms are not fully efficient and over time cells will accumulate damage until they become pro-tumorigenic. These cells can then go on to become cancerous and lead to tumors. Fortunately, our cells have back up mechanisms to prevent these potentially cancerous cells from dividing, which ultimately manifest in a phenotype termed cellular senescence. Cells that have undergone senescence are put under permanent cell-cycle arrest, and secrete a number of factors to initiate removal through immune cell clearance. Yet, over time senescent cells will accumulate and with sustained secretion of inflammatory molecules drive a host of aging phenotypes. Therefore, discovering biomarkers for senescence that can be used to target senescent cells is important for both senescent cell identification and potential senolytic strategies. Monoclonal antibodies have been useful tools in distinguishing cell populations by binding to disease-associated extracellular biomarkers on the surface of cells. In this thesis, we look at a number of membrane proteins, in particular MHC-peptide complexes, that could serve as biomarkers for cellular senescence and those cells that have bypassed senescence to become cancer. In Chapter 1, we perform surface proteomics of senescent fibroblasts and identify the membrane protein GGT1 as a potential marker for senescence. In Chapter 2, we develop antibodies against MHC-peptide complexes containing the senescence-associated protein p16. 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 senescence and hypoxia. In Chapter 4, we use MEKi-modulation of the immunopeptidome in melanoma to identify targetable MHC-peptide complexes that can be leveraged to increase cytotoxicity of melanoma cells. In Chapter 5, we expand our antibody development into class II MHC-peptide complexes and engineer antibodies that can recognize MHC-peptide complexes with differential orientations in the peptide binding groove.