Transcriptomic and phosphoproteomic characterization of CAR-NK signaling (#246)
Chimeric antigen receptor (CAR) therapy is a form of cancer immunotherapy in which immune cells are engineered to express a synthetic receptor that recognizes tumor associated antigens. Upon antigen binding, the stimulatory and co-stimulatory domains of the CAR initiate signaling leading to immune activation and anti-tumor cytotoxicity. Historically designed for T cells, the protein domains incorporated into CARs are largely based on our understanding of T cell activation and utilize endogenous T cell receptor and co-receptor domains such as CD3z, CD28, and 41BB. Translation of CAR therapy into NK cells has primarily relied on intuitive protein engineering principles rather than a mechanistic understanding of the proteomic and transcriptomic signaling events different protein domains initiate and the effector functions they activate. We aimed to characterize the signaling of CAR-NK cells and hypothesized that CAR-NK cells exhibit NK-specific signaling which is distinct from CAR-T cell signaling. We performed proteomic and transcriptomic analysis of an anti-Her2 CAR incorporating a CD3z stimulatory domain and CD28 costimulatory domain to decipher NK-specific signaling networks. We generated donor-matched primary CAR-NK and CAR-T cells using CRISPR-AAV6 site-directed insertion into the AAVS1 safe harbor locus and induced CAR activation using recombinant Her2 protein. Through mass spectrometry-based phosphoproteomics, we detected phosphorylation changes at 726 phosphotyrosine sites and 7678 phosphoserine, threonine, and tyrosine sites in stimulated CAR-NK cells versus control. We show that CAR stimulation results in weaker tyrosine phosphorylation in NK cells compared to donor-matched CAR-T cells despite similar kinetics. Transcriptomically, CAR signaling results in a shared inflammatory transcriptional program in NK and T cells. However, we observe that CAR signaling uniquely and paradoxically activates Tcf-7 transcription in NK cells which is typically repressed upon lymphocyte activation to enable mature effector functions. Together, this work illustrates NK-specific CAR signaling and avenues for tailoring signaling to improve CAR-NK therapeutic efficacy.