Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown efficacy

New strategies for cancer immunotherapy are needed since most solid tumors do not respond to current approaches. Here, we used EpCAM aptamer-linked small interfering RNAs (aptamer-siRNA chimeras (AsiCs)) to knockdown genes selectively in EpCAM+ tumors with the goal of making cancers more visible to the immune system to improve anti-tumor immunity. Gene targets were chosen whose knockdown was predicted to promote tumor neoantigen expression (Upf2 and Parp1), phagocytosis and antigen presentation (Cd47), or cause tumor cell death (Mcl1). Using scRNA-seq, we showed that knocking down the four targets simutaeoulsy potently improved the anti-tumor immunity mediated T cells and macrophage/monocytes, demonstrating the immunostimulatory capacity of EpCAM-AsiCs. Overall design: BALB/c mice were orthotopically implanted with ~105 4T1E cells/mouse. Three days post tumor challenge mice were treated with either EpCAM aptamer or EpCAM-AsiCs cocktail targeting Upf2, Parp1, Cd47 and Mcl1 by s.c. injection every third day. On day 14, CD45+ tumor infiltrating lymphocytes were enriched from tumors (two biological samples/group) for single cell encapsulation, RNA capture and libary construction.