Phd in GENETICS AND MOLECULAR BIOLOGY

Thesis title: Identification of long noncoding RNAs underlying Group 3 Medulloblastoma

Long noncoding RNAs (lncRNAs) play a crucial role in the multi-layered regulation of physiological and disease-related gene expression, showing a particular significance in shaping the central nervous system (CNS) complexity. Dysregulated lncRNA expression has been reported in several human cancers, and their tissue-specificity makes them promising candidates as diagnostic/prognostic biomarkers and/or therapeutic targets. Medulloblastoma (MB) is one of the most aggressive pediatric brain tumours; the currently therapeutic approaches cause long-term secondary effects, which could be avoided by using more targeted therapies. Recently, the refinement of high-throughput analyses revealed the existence of four MB subgroups (WNT, SHH, Group 3 and Group 4), each molecularly distinct. Their further classification in 12 subtypes paved the way to the design of specific targets to improve treatment efficacy. In this regard, while protein-coding genes aberrantly expressed have been thoroughly investigated, the contribute of the “noncoding side” to MB tumorigenesis remains still unexplored. In this direction, our work contributed to unveil novel lncRNA species underlying G3 MB, the most aggressive and less known MB subgroup, harbouring a MYC-amplified signature. To this aim, we perturbed MYC function in a G3-derived cell line (D283 Med) and performed a transcriptome analysis that revealed 205 differentially expressed lncRNAs regulated by MYC. Upon stringent filtering criteria, we selected three lncRNAs, namely AC116407.1, AC091182.1 and AC010998.3 which are upregulated in G3-derived cells compared to normal human cerebella, suggesting a putative oncogenic role in G3 MB. Accordingly, their knock down negatively impacts on the viable cell number. Preliminary experiments suggested for AC116407.1 a role as a negative translational regulator of its antisense gene RHOT1. AC091182.1 showed, instead, a role as a positive cis regulator of the expression of its flanking genes, the oncogene ZNF703 and the CNS angiogenesis regulator ADGRA2. Finally, AC010998.3 displayed a striking effect as a repressor of D283 Med cell apoptosis; based on this role, it was renamed MyRACL (MYc-Regulated Apoptosis Counteracting LncRNA). This study represents the first experimental analysis uncovering MYC-regulated lncRNAs in G3 MB and identify for some of them a role as potential oncogenes and novel biomarkers in MYC-driven MB.