Abstract IA014: Mass spectrometry and RNAseq based discovery of frameshift neoantigens and cryptic neoantigens from malignant peripheral nerve sheath tumors for prophylactic vaccines


 Neurofibromatosis type 1 (NF1) syndrome is an autosomal, dominant tumor predisposition syndrome caused by loss-of-function mutations of NF1 gene encoding neurofibromin. Loss of the non-mutant allele of NF1 in a rare Schwann cell or precursor leads to benign plexiform neurofibromas. The main cause of death among NF1 patients is the malignant peripheral nerve sheath tumor (MPNST), a highly aggressive soft tissue sarcoma that most likely develops from plexiform neurofibroma, in particular the so-called “atypical” plexiform neurofibroma. Approximately half of MPNSTs are NF1-associated, and NF1 patients have ~15% lifetime risk of developing this terrible cancer. NF1 patients could greatly benefit from prophylactic vaccination that would prevent the malignant transformation to MPNSTs. We hypothesize that malignant transformation leads to the expression of recurrent alternately processed transcripts, such as transcriptionally-induced chimeras, that could express neoantigens and be used as targets for prophylactic vaccines. Such transcripts can be translated to produce novel peptides downstream of frameshift mutations caused by coding exon read-through into introns, mis-splicing from a coding exon to a non-canonical splice acceptors or splice acceptors in other genes. In most cases, a premature termination codon (PTC) will be rapidly encountered by the ribosome translating such transcripts. Therefore, we furthermore hypothesize that these alternately processed transcripts can express what we call “cryptic” neoantigens when treated with drugs that suppress utilization of premature codons such as Ataluren or gentamicin. In such a way, we could administer a prophylactic vaccine and induce conditionally active immune response that would eliminate nascent tumors only when drug treatment is used. We have developed a PTC suppression read-through reporter which results in presentation of the SIINFEKL peptide on C57BL6/J tumor cells. We developed a bioinformatic algorithm that takes deep RNA-seq data and identifies candidate neoepitopes encoded by non-normally processed or mutant mRNAs called Identifying and Verifying Immunogenic Neoepitopes and Neojunctions (IVINN). We have also achieved successful purification of human HLA Class I complex using an anti-pan HLA antibody column, and bound peptides have been isolated and identified by liquid chromatography tandem mass spectrometry (LC-MS/MS). We plan to utilize these approaches for mouse model and human MPNST patient derived xenografts.
 Citation Format: David A. Largaespada. Mass spectrometry and RNAseq based discovery of frameshift neoantigens and cryptic neoantigens from malignant peripheral nerve sheath tumors for prophylactic vaccines [abstract]. In: Proceedings of the Second Biennial NCI Meeting: Translational Advances in Cancer Prevention Agent Development (TACPAD); 2022 Sep 7-9. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_2): Abstract nr IA014.