UCSF

Immunotherapies such as adoptive cell therapies and checkpoint inhibitors are curing previously lethal cancers, however only a small fraction of patients are responsive. A major predictor of the response to immunotherapy is the extent of tumor infiltrating lymphocytes (TILs) in the tumor microenvironment. Unfortunately, most solid tumors exclude TILs through various immunosuppressive mechanisms and are classified as immune ‘cold’ tumors. In this thesis research, we studied how the expression of dominant oncogenes broadly modulates immune evasion phenotypes across cancer models. We translated those findings into therapeutic antibodies that stimulate innate immune pathways to turn immune ‘cold’ tumors ‘hot’ and improve response rates to immunotherapies.In Chapter 1 we used discovery proteomics to characterize isogenic models of driver oncogenes (Myc, KRAS, BRAF, MEK, AKT, HER2, EGFR) and identify common axes of dysregulation. From an unbiased approach, the most ubiquitous and dramatic molecular and functional phenotype across oncogenes was the suppression of proteins regulated by type 1 interferon, particularly antiviral dsRNA sensors. These effects were validated in patient- and cancer-derived tumor cells driven by KRAS and/or Myc oncogenes. These results have broad implications for standard therapies like radiation, epigenetic and cytotoxic drugs, and immunotherapies that require type 1 interferon and antiviral pathways for their cytotoxic effects, and suggest opportunities for oncolytic and gene-therapy viruses. In Chapter 2 we used in vitro display technologies and protein engineering to build therapeutic antibodies that re-activate innate immune signaling in the tumor microenvironment. ENPP1 is an extracellular phosphodiesterase that hydrolyzes cGAMP, an immunostimulant that is transported between cells to activate type 1 interferon. ENPP1 is frequently up-regulated on tumor cells, and small molecule drugs have shown inhibiting ENPP1 stimulates type 1 interferon signaling and sensitizes immune ‘cold’ tumors to radiation and immunotherapy. Here, we generated first-in-class variable heavy (VH) single-domain antibodies that bind and allosterically inhibit ENPP1. The VH domains were recombinantly engineered into multivalent formats and immunotherapies that improved their selectivity and potency. A cryo-EM structure of the VH-ENPP1 complex revealed its allosteric inhibitory epitope and a novel mechanism of substrate-selective inhibition.