Isoform balance of the long noncoding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts cell migration.

in The Journal of biological chemistry by Paul M Zakutansky, Li Ku, Guannan Zhang, Liang Shi, Yangping Li, Bing Yao, Gary J Bassell, Renee D Read, Yue Feng

TLDR

  • The study investigates the role of a type of RNA called NEAT1 in human cancers, specifically in glioblastoma multiforme (GBM) cells. The study found that there are two different versions of NEAT1, called NEAT1_1 and NEAT1_2, and that they are produced differently. The study also found that the NEAT1 proximal polyadenylation site (PAS) is important for controlling the production of these two versions of NEAT1. The study also found that changes in the levels of these two versions of NEAT1 can affect the way that cells move and the genes that are expressed in the cells. The study suggests that targeting the NEAT1 PAS could be a way to treat glioma.

Abstract

The long noncoding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) is involved in a variety of human cancers. Two overlapping NEAT1 isoforms, NEAT1_1 and NEAT1_2, are produced through mutually exclusive alternative 3' end formation. Previous studies extensively investigated NEAT1 dysregulation in tumors, but often failed to achieve distinct quantification of the two NEAT1 isoforms. Moreover, molecular mechanisms governing the biogenesis of NEAT1 isoforms and the functional impacts of their dysregulation in tumorigenesis remain poorly understood. In this study, we employed an isoform-specific quantification assay and found differential dysregulation of NEAT1 isoforms in patient-derived glioblastoma multiforme (GBM) cells. We further showed usage of the NEAT1 proximal polyadenylation site (PAS) is a critical mechanism that controls glioma NEAT1 isoform production. CRISPR-Cas9-mediated PAS deletion reduced NEAT1_1 and reciprocally increased NEAT1_2, which enhanced nuclear paraspeckle formation in human glioma cells. Moreover, the utilization of the NEAT1 PAS is facilitated by the RNA binding protein Quaking (QKI), which binds to the proximal QKI response elements (QREs). Functionally, we identified transcriptomic changes and altered biological pathways caused by NEAT1 isoform imbalance in glioma cells, including the pathway for the regulation of cell migration. Finally, we demonstrated the forced increase of NEAT1_2 upon NEAT1 PAS deletion is responsible for driving glioma cell migration and promoting the expression of genes implicated in the regulation of cell migration. Together, our studies uncovered a novel mechanism that regulates NEAT1 isoforms and their functional impacts on the glioma transcriptome, which affect pathological pathways of glioma, represented by migration.

Overview

  • The study investigates the role of the long noncoding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) in human cancers, specifically in glioblastoma multiforme (GBM) cells. The study aims to quantify the two NEAT1 isoforms, NEAT1_1 and NEAT1_2, and understand their biogenesis and functional impacts on tumorigenesis. The methodology used includes an isoform-specific quantification assay, CRISPR-Cas9-mediated PAS deletion, and transcriptomic analysis. The primary objective of the study is to identify the molecular mechanisms governing the biogenesis of NEAT1 isoforms and their functional impacts on the glioma transcriptome.

Comparative Analysis & Findings

  • The study found differential dysregulation of NEAT1 isoforms in patient-derived GBM cells. The utilization of the NEAT1 proximal polyadenylation site (PAS) is a critical mechanism that controls glioma NEAT1 isoform production. CRISPR-Cas9-mediated PAS deletion reduced NEAT1_1 and reciprocally increased NEAT1_2, which enhanced nuclear paraspeckle formation in human glioma cells. The study also identified transcriptomic changes and altered biological pathways caused by NEAT1 isoform imbalance in glioma cells, including the pathway for the regulation of cell migration. Finally, the forced increase of NEAT1_2 upon NEAT1 PAS deletion is responsible for driving glioma cell migration and promoting the expression of genes implicated in the regulation of cell migration.

Implications and Future Directions

  • The study's findings have significant implications for the field of research and clinical practice, as they uncover a novel mechanism that regulates NEAT1 isoforms and their functional impacts on the glioma transcriptome. The study identifies the NEAT1 PAS as a critical mechanism that controls glioma NEAT1 isoform production and highlights the importance of understanding the molecular mechanisms underlying NEAT1 dysregulation in tumors. The study also suggests future research directions, such as investigating the role of NEAT1 isoform imbalance in other cancers and exploring the potential of targeting the NEAT1 PAS as a therapeutic strategy for glioma.
Read Full Article