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

Abstract

Significance Immunotherapy benefits some aggressive breast cancers, but many breast tumors do not respond to checkpoint blockade. Novel strategies to increase breast cancer immunogenicity are needed to improve immunotherapy. Here, we used epithelial cell adhesion molecule (EpCAM) aptamer-linked small-interfering RNA chimeras (AsiC) to selectively knock down genes in mouse breast cancers to induce tumor neoantigens or overcome immune evasion. Individual gene knockdown markedly delayed tumor growth and enhanced antitumor immunity. Cd47 and Parp1 AsiCs outperformed anti-CD47 antibody and the PARP1 inhibitor Olaparib, respectively. Combining EpCAM-AsiCs targeting multiple pathways worked better than single agents and enhanced tumor inhibition by a checkpoint inhibitor. EpCAM-AsiCs have the potential to boost immunity to tumors that are poorly responsive to checkpoint blockade. New strategies for cancer immunotherapy are needed since most solid tumors do not respond to current approaches. Here we used epithelial cell adhesion molecule EpCAM (a tumor-associated antigen highly expressed on common epithelial cancers and their tumor-initiating cells) aptamer-linked small-interfering RNA chimeras (AsiCs) to knock down genes selectively in EpCAM+ tumors with the goal of making cancers more visible to the immune system. Knockdown of genes that function in multiple steps of cancer immunity was evaluated in aggressive triple-negative and HER2+ orthotopic, metastatic, and genetically engineered mouse breast cancer models. Gene targets were chosen whose knockdown was predicted to promote tumor neoantigen expression (Upf2, Parp1, Apex1), phagocytosis, and antigen presentation (Cd47), reduce checkpoint inhibition (Cd274), or cause tumor cell death (Mcl1). Four of the six AsiC (Upf2, Parp1, Cd47, and Mcl1) potently inhibited tumor growth and boosted tumor-infiltrating immune cell functions. AsiC mixtures were more effective than individual AsiC and could synergize with anti–PD-1 checkpoint inhibition.