Paraspeckles are subnuclear organelles involved in the regulation of gene expression. NEAT1 is a long-non coding RNA required for paraspeckle formation that exists in two overlapping isoforms of sizes 3.7 kb and 23 kb, which are termed NEAT1_1 and NEAT1_2 respectively. NEAT1_2 is found to be the lncRNA back bone around which paraspeckles form, whereas NEAT1_1 can form paraspeckle-independent foci called microspeckles.
A clinical setting in which paraspeckle abundance may be important is the childhood brain cancer neuroblastoma, where changes in NEAT1 levels are correlated with patient outcome. Neuroblastoma is the most common infant cancer, ranging from low-risk, differentiated cancer cells to high-risk cells that maintain an undifferentiated, self-proliferative state. In this study, we show that paraspeckles may be implicated in the regulation of differentiation of high-risk neuroblastic cells, potentially reducing their self-proliferative capacity. We have developed antisense oligonucleotides that bind specific regions of NEAT1 RNA and induce the isoform switching of NEAT1_1 to NEAT1_2, thereby increasing paraspeckles in high risk neuroblastoma cell lines. Hence, these oligonucleotides have been dubbed Boost paraspeckle (PS) oligonucleotides. High-risk cells transfected with the oligonucleotides displayed reduced cell viability, and reduced cell confluence, indicating that reducing NEAT1_1 and increasing paraspeckle numbers may suppress proliferation. Accordingly, when we overexpressed NEAT1_1, cells had increased viability, suggesting microspeckles may have an oncogenic role in opposition to the suppressive paraspeckles. RNA-seq experiments with high-risk cells treated with Boost PS oligonucleotides show upregulation of differentiation pathways, which were further assessed studying RNA and protein levels. In summary, we have developed a method to transiently alter the formation of paraspeckles that may be useful in the clinical setting of high-risk neuroblastoma.