Characterization of ELP1 as a novel SHH medulloblastoma predisposition gene

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PROJECT SUMMARY Medulloblastoma (MB) is among the most common malignant childhood brain tumors. Although aggressive treatments have improved outcomes, too many affected children still die of their disease, and survivors often suffer from severe long-term side effects of therapy. Extensive molecular and biological heterogeneity underlying MB has been described, culminating in the recognition of consensus molecular subgroups – WNT, SHH, Group 3, and Group 4 – each of which is associated with divergent genomic landscapes, patient demographics, and clinical outcomes. Although somatically altered genes and biological pathways are well annotated, comprehensive understanding of genetic predisposition to MB has lagged behind. We recently investigated germline loss-of-function (LoF) across all protein-coding genes in a series of >1,000 MB patients. This unbiased approach uncovered highly significant deleterious germline variants in ELP1 that were specific to childhood SHH-MB patients and twice as common as pathogenic variants affecting known MB-associated genes. ELP1 encodes a scaffolding subunit of Elongator, a multi-subunit protein complex (ELP1-6) that chemically modifies wobble U34 uridines in the anticodon loop of tRNAs to enable efficient translational elongation and maintenance of physiological protein folding dynamics. ELP1-associated tumors exhibited frequent co-occurrence of somatic PTCH1 mutations and amplifications of PPM1D and MDM4, suggesting germline ELP1 LoF variants cooperate with constitutive activation of SHH and/or TP53 signaling to promote MB development. ELP1-associated SHH-MBs were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis. Based on these findings, we hypothesize that ELP1 is a novel cancer predisposition gene and aim to functionally elucidate the developmental, biochemical, and molecular mechanisms by which pathogenic ELP1 LoF promotes SHH-MB. To test this hypothesis, we propose to (i) evaluate the requirement for Elp1 during cerebellar development; (ii) validate the tumor suppressive role of Elp1 in SHH-MB; and (iii) determine the impact of MB-associated Elp1 LoF on translation and the proteome. These studies will be conducted in a series of novel Elp1+/- transgenic mice, primary cells derived from the developing mouse cerebellum, and genetically faithful SHH-MB patient-derived xenografts. Successful execution of this research program will effectively link germline ELP1 LoF to the biochemical and molecular mechanisms governing SHH-MB pathogenesis. Outcomes of the proposed research will be of broad interest, extending to scientists and clinicians with an interest in cancer predisposition, as well as basic researchers studying the fundamentals of translational regulation and protein homeostasis and their role in human disease.