Identification of lncMB3-dependent transcriptome in MYC-amplified D283 Med cells.

Medulloblastoma (MB) stands as the most prevalent malignant pediatric tumor affecting the central nervous system. Categorized into four primary subgroups, each with distinct biological and clinical features, MB presents unique therapeutic implications. Group 3 (G3) and 4 (G4) MBs collectively account for the majority of cases (60%) and exhibit the highest degree of aggressiveness. However, these subgroups remain poorly characterized from a biochemical perspective. Therefore, it is crucial to unveil the fundamental molecular mechanisms underlying G3 e G4 MBs to deepen our overall comprehension of these specific conditions and to pave the way for precision medicine-driven approaches. Compared to normal human cerebella, the MYC-dependent lncRNA MB3 was found to be induced in G3-derived cell lines expressing the proto-oncogene and upregulated in G3-MB primary tumors. Consistently, LncMB3 is downregulated upon MYC inhibition and in vitro studies reveal its potent anti-apoptotic activity. To dissect the molecular network through which LncMB3 operates in MB carcinogenesis, we initiated the identification of its target genes by analyzing through RNA-Sequencing the alteration of the transcriptome following LncMB3 knockdown in G3 MB cell lines, achieved through transfections of antisense Locked Nucleic Acid (LNA) oligonucleotides (GapmeRs). Here we provide the data of three polyA+ RNA samples derived from lncMB3 knockdown (KD) and 3 control samples from the MYC-amplified D283 Med cell line that were subjected to RNA-Seq analysis.