Targeting loss of heterozygosity for cancer-specific immunotherapy

Significance The lack of viable tumor-specific targets continues to thwart efforts to implement selective anticancer drugs in the clinic. Clonal loss of heterozygosity (LOH) occurs in the great majority of human tumors and represents an irreversible genetic alteration present in cancer cells that unequivocally distinguishes them from normal cells. Here, we report the development of NASCAR (Neoplasm-targeting Allele-Sensing CAR), a platform comprising pairwise chimeric receptors for detecting and targeting LOH events in cancer. As proof-of-concept, we demonstrate specific NASCAR T cell responses in models of HLA LOH in vitro and in vivo. This work lays the foundation for future exploration and exploitation of LOH-mediated vulnerabilities for precision cellular immunotherapy. Developing therapeutic agents with potent antitumor activity that spare normal tissues remains a significant challenge. Clonal loss of heterozygosity (LOH) is a widespread and irreversible genetic alteration that is exquisitely specific to cancer cells. We hypothesized that LOH events can be therapeutically targeted by “inverting” the loss of an allele in cancer cells into an activating signal. Here we describe a proof-of-concept approach utilizing engineered T cells approximating NOT-gate Boolean logic to target counterexpressed antigens resulting from LOH events in cancer. The NOT gate comprises a chimeric antigen receptor (CAR) targeting the allele of human leukocyte antigen (HLA) that is retained in the cancer cells and an inhibitory CAR (iCAR) targeting the HLA allele that is lost in the cancer cells. We demonstrate that engineered T cells incorporating such NOT-gate logic can be activated in a genetically predictable manner in vitro and in mice to kill relevant cancer cells. This therapeutic approach, termed NASCAR (Neoplasm-targeting Allele-Sensing CAR), could, in theory, be extended to LOH of other polymorphic genes that result in altered cell surface antigens in cancers.