Motif neoepitopes for cancer immunotherapy

Abstract

Identifying immune checkpoint blockade (ICB) responsive cancer comprises sequencing nucleic acid from a biological sample; and identifying the cancer as ICB responsive when the sequencing detects a nucleic acid encoding a neoepitope that is a nonamer comprising a radical substitution in the second position. This enables the selection of a treatment strategy that improves the efficacy of ICB, based on the patient's profile. The patient can be treated with an agent that enhances responsiveness to ICB, by altering the subject's motif epitope profile or by administering a sensitizing agent. Treating can be with antigen presenting cells (APCs) trained with a neoepitope associated with the subject's cancer. For subjects expressing the HLA supertype B44, the radical substitution consists of a negatively charged amino acid, while for subjects expressing the HLA supertype B27, the radical substitution consists of a positively charged amino acid.

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