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A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer

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Title: A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer
Authors: Fletcher, C
Deng, L
Orafidiya, F
Yuan, W
Lorentzen, M
Cyran, O
Varela Carver, A
Constantin, T
Dobbs, F
Figueiredo, I
Gurel, B
Parkes, E
Bogdan, D
Pereira, R
Zhao, S
Neeb, A
Issa, F
Hester, J
Kudo, H
Liu, Y
Philippou, Y
Bristow, R
Knudsen, K
Bryant, R
Feng, F
Reed, S
Mills, I
De Bono, J
Bevan, C
Item Type: Journal Article
Abstract: Background: miR‑346 was identified as an activator of Androgen Receptor (AR) signalling that associates with DNA damage response (DDR)‑linked transcripts in prostate cancer (PC). We sought to delineate the impact of miR‑346 on DNA damage, and its potential as a therapeutic agent. Methods: RNA‑IP, RNA‑seq, RNA‑ISH, DNA fibre assays, in vivo xenograft studies and bioinformatics approaches were used alongside a novel method for amplification‑free, single nucleotide‑resolution genome‑wide mapping of DNA breaks (INDUCE‑seq). Results: miR‑346 induces rapid and extensive DNA damage in PC cells ‑ the first report of microRNA‑induced DNA damage. Mechanistically, this is achieved through transcriptional hyperactivation, R‑loop formation and replication stress, leading to checkpoint activation and cell cycle arrest. miR‑346 also interacts with genome‑protective lncRNA NORAD to disrupt its interaction with PUM2, leading to PUM2 stabilisation and its increased turnover of DNA damage response (DDR) transcripts. Confirming clinical relevance, NORAD expression and activity strongly correlate with poor PC clinical outcomes and increased DDR in biopsy RNA‑seq studies. In contrast, miR‑346 is associated with improved PC survival. INDUCE‑seq reveals that miR‑346‑induced DSBs occur preferentially at binding sites of the most highly‑transcriptionally active transcription factors in PC cells, including c‑Myc, FOXA1, HOXB13, NKX3.1, and importantly, AR, resulting in target transcript downregulation. Further, RNA‑seq reveals widespread miR‑346 and shNORAD dysregulation of DNA damage, replication and cell cycle processes. NORAD drives target‑directed miR decay (TDMD) of miR‑346 as a novel genome protection mechanism: NORAD silencing increases mature miR‑346 levels by several thousand‑fold, and WT but not TDMD‑mutant NORAD rescues miR‑346‑induced DNA damage. Importantly, miR‑346 sensitises PC cells to DNA‑damaging drugs including PARP inhibitor and chemotherapy, and induces tumour regression as a monotherapy in vivo, indicating that targeting miR‑346:NORAD balance is a valid therapeutic strategy.
Issue Date: 22-Mar-2022
Date of Acceptance: 10-Feb-2022
URI: http://hdl.handle.net/10044/1/95759
DOI: 10.1186/s12943-022-01540-w
ISSN: 1476-4598
Publisher: BioMed Central
Journal / Book Title: Molecular Cancer
Volume: 21
Copyright Statement: © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativeco mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Sponsor/Funder: Prostate Cancer Foundation
Prostate Cancer Foundation
Imperial College London
Prostate Cancer UK
AstraZeneca UK Limited
Imperial College Healthcare NHS Trust- BRC Funding
Prostate Cancer Foundation
Rosetrees Trust
Rosetrees Trust
Prostate Cancer UK
Funder's Grant Number: 20160119
53789
8300290964
RDB01
18CHAL06
N/A
A1209
DCSJDBAHK
Keywords: DNA damage
Long non-coding RNA
Non-coding RNA
Prostate cancer
Replication stress
Target-directed microRNA decay
cancer
microRNA
Oncology & Carcinogenesis
1112 Oncology and Carcinogenesis
Publication Status: Published
Online Publication Date: 2022-03-22
Appears in Collections:Department of Metabolism, Digestion and Reproduction
Department of Surgery and Cancer
Chemistry
Biological and Biophysical Chemistry
Faculty of Medicine
Faculty of Natural Sciences



This item is licensed under a Creative Commons License Creative Commons