Phospho-proteomic analysis of CAR-T cell signaling following activation by antigen-presenting cancer cells

Abstract Chimeric antigen receptors (CARs) are synthetic biomolecules comprised of an extracellular antigen recognition domain and intracellular signaling domains. When expressed in immune cells, CARs direct their host cells to kill diseased cells expressing the antigen recognized by the CAR. Although signaling pathways downstream of CAR activation control the cytotoxic function of CAR-expressing cells, phospho-proteomic studies of CAR signaling have been limited. Most approaches have used antibodies or soluble ligands, rather than cell-displayed antigens, to activate CAR signaling. Here, we demonstrate an efficient and cost-effective label-free phospho-proteomic approach to analyze CAR signaling in immune cells stimulated with antigen-presenting cancer cells. Following co-culture of CAR-T cells with cancer cells, we first preserve phospho-signaling by cross-linking proteins with formalin. Then, we use magnet-activated cell sorting (MACS) to isolate CAR-T cells from the co-culture. Validation experiments demonstrated that formalin fixation did not alter the phospho-proteome and that MACS achieved >90% CAR-T cell purity. Next, we compared the phospho-proteome in CAR-T cells stimulated with either CD19-expressing or non-CD19-expressing SKOV3 ovarian cancer cells. This analysis revealed that CAR signaling activated known pathways including the mitogen- activated protein kinases (MAPKs) ERK1/2. Bioinformatic approaches further showed that CAR activation induced other signaling pathways including the MAPK p38α, protein kinase A, and checkpoint kinase 1 (CHK1). Taken together, this work presents an easy and inexpensive method to better understand CAR immunotherapy by label-free phospho-proteomic analysis of CAR signaling in immune cells stimulated by antigen- presenting cancer cells.