NEAT1 polyA-modulating antisense oligonucleotides reveal opposing functions for both long non-coding RNA isoforms in neu
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Cellular and Molecular Life Sciences
ORIGINAL ARTICLE
NEAT1 polyA‑modulating antisense oligonucleotides reveal opposing functions for both long non‑coding RNA isoforms in neuroblastoma Alina Naveed1 · Jack A. Cooper1 · Ruohan Li1 · Alysia Hubbard2 · Jingwei Chen3,4 · Tao Liu3,4 · Steve D. Wilton5 · Sue Fletcher5,6 · Archa H. Fox1 Received: 1 May 2020 / Revised: 28 July 2020 / Accepted: 26 August 2020 © Springer Nature Switzerland AG 2020
Abstract Many long non-coding RNAs (lncRNA) are highly dysregulated in cancer and are emerging as therapeutic targets. One example is NEAT1, which consists of two overlapping lncRNA isoforms, NEAT1_1 (3.7 kb) and NEAT1_2 (23 kb), that are functionally distinct. The longer NEAT1_2 is responsible for scaffolding gene-regulatory nuclear bodies termed paraspeckles, whereas NEAT1_1 is involved in paraspeckle-independent function. The NEAT1 isoform ratio is dependent on the efficient cleavage and polyadenylation of NEAT1_1 at the expense of NEAT1_2. Here, we developed a targeted antisense oligonucleotide (ASO) approach to sterically block NEAT1_1 polyadenylation processing, achieving upregulation of NEAT1_2 and abundant paraspeckles. We have applied these ASOs to cells of the heterogeneous infant cancer, neuroblastoma, as we found higher NEAT1_1:NEAT1_2 ratio and lack of paraspeckles in high-risk neuroblastoma cells. These ASOs decrease NEAT1_1 levels, increase NEAT1_2/paraspeckles and concomitantly reduce cell viability in high-risk neuroblastoma specifically. In contrast, overexpression of NEAT1_1 has the opposite effect, increasing cell proliferation. Transcriptomic analyses of highrisk neuroblastoma cells with altered NEAT1 ratios and increased paraspeckle abundance after ASO treatment showed an upregulation of differentiation pathways, as opposed to the usual aggressive neuroblastic phenotype. Thus, we have developed potential anti-cancer ASO drugs that can transiently increase growth-inhibiting NEAT1_2 RNA at the expense of growth-promoting NEAT1_1 RNA. These ASOs, unlike others that degrade lncRNAs, provide insights into the importance of altering lncRNA polyadenylation events to suppress tumorigenesis as a strategy to combat cancer. Keywords RNA therapeutics · NONO · Biomolecular condensates · Super resolution · MYCN Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00018-020-03632-6) contains supplementary material, which is available to authorized users. * Archa H. Fox [email protected] 1
School of Human Sciences and School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
2
Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Crawley, WA 6009, Australia
3
Children’s Cancer Institute Australia, Randwick, NSW 2031, Australia
4
Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW 2052, Australia
5
Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia
6
Cent
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