MDB-05. Immunologically Targeting U1 Mutant Shh Medulloblastoma

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-delta 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 employing a loose threshold pipeline. In-house scripts were utilized for selecting for cryptic exons that are uniquely expressed in Shh-delta and Shh-alpha U1 snRNA mutant compared to wildtype (WT) Shh-gamma and beta 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 mutant samples to WT samples. Expressed exons were filtered to exclude known exons to identify cryptic exons that are not annotated in GENCODE. To select for U1 mutant induced cryptic exons, cryptic exons not identified in Shh U1 WT and included >10% percent spliced in (PSI) in U1 mutant samples were filtered. We identified 941 unannotated cryptic exons in the U1 mutant samples. Conclusion A 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.