Background: Medulloblastoma (MB) is the most
common solid malignant pediatric brain neoplasm. Group 3 (G3) MB,
particularly MYC amplified G3 MB, is the most aggressive subgroup with the
highest frequency of children presenting with metastatic disease, and is
associated with a poor prognosis. To further our understanding of the role
of MSI1 in MYC amplified G3 MB, we performed an unbiased integrative
analysis of eCLIP binding sites, with changes observed at the transcriptome,
the translatome, and the proteome after shMSI1
inhibition. Methods: Primary human pediatric MBs,
SU_MB002 and HD-MB03 were kind gifts from Dr. Yoon-Jae Cho (Harvard, MS) and
Dr. Till Milde (Heidelberg) and cultured for in vitro and in vivo
experiments. eCLIP, RNA-seq, Polysome-seq, and TMT-MS were completed as
previously described.
Results:MSI1 is
overexpressed in G3 MB. shRNA Msi1 interference resulted in a reduction in
tumour burden conferring a survival advantage to mice injected with
shMSI1 G3MB cells. Robust ranked multiomic
analysis (RRA) identified an unconventional gene set directly perturbed by
MSI1 in G3 MB. Conclusions: Our robust unbiased
integrative analysis revealed a distinct role for MSI1 in the maintenance of
the stem cell state in G3 MB through post-transcriptional modification of
multiple pathways including identification of unconventional targets such as
HIPK1.