Valid-NEO: A Multi-Omics Platform for Neoantigen Detection and Quantification from Limited Clinical Samples

SIMPLE SUMMARY: Neoantigens have emerged as highly personalized cancer therapeutic targets in recent years. Numerous studies have reported phenomenal therapeutic efficacy through treatments targeting cancer patient-specific neoantigens. Despite the growing interests, to identify druggable neoantigens is still largely dependent on genomic sequencing and AI algorithm-based prediction, which have been proven to be error-prone. Numerous reported mass spectrometry-based neoantigen assays utilized multi-gram levels of the tumor tissues, required invasive procedures, and were not practically feasible for most cancer patients, particularly patients that were non-operable or with early diseases, who may benefit most from immunotherapeutic approaches. Here we reported an integrated pipeline that can detect and quantify patient-specific neoantigens from a very limited amount of patient samples through a variety of innovative designs and optimizations. It may enable neoantigen-based therapeutics to benefit a broader spectrum of cancer and non-cancer patients. ABSTRACT: The presentation of neoantigens on the cell membrane is the foundation for most cancer immunotherapies. Due to their extremely low abundance, analyzing neoantigens in clinical samples is technically difficult, hindering the development of neoantigen-based therapeutics for more general use in the treatment of diverse cancers worldwide. Here, we describe an integrated system, “Valid-NEO”, which reveals patient-specific cancer neoantigen therapeutic targets from minute amounts of clinical samples through direct observation, without computer-based prediction, in a sensitive, rapid, and reproducible manner. The overall four-hour procedure involves mass spectrometry analysis of neoantigens purified from tumor samples through recovery of HLA molecules with HLA antibodies. Valid-NEO could be applicable to the identification and quantification of presented neoantigens in cancer patients, particularly when only limited amounts of sample are available.