CNSC-12. IMMUNOLOGICALLY TARGETING U1 MUTANT SHH MEDULLOBLASTOMA

Abstract

Abstract OBJECTIVES Medulloblastoma (MB) is the most common malignant pediatric brain tumor representing a significant burden of morbidity and mortality in the US. MB is comprised of four subgroups: Wnt, Shh, Group 3, and Group 4. Shh tumors represent 25% of cases and subdivides into Shh-beta and Shh-gamma, Shh-alpha, and Shh-delta. Half of Shh MB carry an identical somatic point mutation in a non-coding small nuclear RNA (snRNA) called U1 (r.3A>G) which is found in 97% of Shh-d tumors, and in most Shh-alpha tumors with TP53 mutations. Current therapies for patients with TP53 and U1 mutant Shh-alpha MB observe rare survivors, and adult Shh-delta patients continue to experience significant morbidity and mortality calling for urgent prioritization of these tumors for targeted therapy. METHODS Cryptic exons were identified in both Shh-delta U1 snRNA mutant samples and Shh-delta U1 wildtype (WT) samples using CryEx pipeline. In-house scripts were utilized for selecting for cryptic exons that are uniquely expressed in Shh-delta U1 snRNA mutant compared to wildtype (WT) samples. RESULTS Analyzing 180 Shh MB RNA-seq samples, we identified 23% Shh-alpha, no Shh-beta, 97% of Shh-delta and 3% Shh-gamma harbored the U1 mutation. The splicing landscape was then interrogated comparing Shh-delta U1 snRNA mutant samples to WT samples. Expressed exons were filtered to exclude known exons to identify novel or cryptic exons. To select for Shh-delta U1 snRNA mutant induced cryptic exons, CryEx arising from introns, not identified in Shh-delta U1 WT and included >10% of their inclusion rates measured by percent spliced in (PSI) in Shh-delta U1 snRNA mutant samples were filtered. Of the middle CryEx, we identified 43,188 that were U1 mutant induced. Further filtering for cell surface Middle CryEx, three of the 75 middle CryEx overlapped. CONCLUSION The PTCH1 neoantigen formed from the CryEx insertion translates a protein that is unique to the tumor cells (i.e., not in normal tissue) was identified as a juxtamembrane for therapeutic drug discovery.