A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer
<strong>Background</strong> 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 therapeuti...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
BioMed Central
2022
|
| _version_ | 1826271556917002240 |
|---|---|
| author | Fletcher, CE Deng, L Orafidiya, F Yuan, W Lorentzen, MPGS Cyran, OW Varela-Carver, A Constantin, TA Leach, DA Dobbs, FM Figueiredo, I Gurel, B Parkes, E Bogdan, D Pereira, RR Zhao, SG Neeb, A Issa, F Hester, J Kudo, H Liu, Y Philippou, Y Bristow, R Knudsen, K Bryant, RJ Feng, FY Reed, SH Mills, IG de Bono, J Bevan, CL |
| author_facet | Fletcher, CE Deng, L Orafidiya, F Yuan, W Lorentzen, MPGS Cyran, OW Varela-Carver, A Constantin, TA Leach, DA Dobbs, FM Figueiredo, I Gurel, B Parkes, E Bogdan, D Pereira, RR Zhao, SG Neeb, A Issa, F Hester, J Kudo, H Liu, Y Philippou, Y Bristow, R Knudsen, K Bryant, RJ Feng, FY Reed, SH Mills, IG de Bono, J Bevan, CL |
| author_sort | Fletcher, CE |
| collection | OXFORD |
| description | <strong>Background</strong>
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.
<br>
<strong>Methods</strong>
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).
<br>
<strong>Results</strong>
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.
<br>
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.
<br>
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.
<br>
<strong>Conclusions</strong>
A balancing act between miR-346 and NORAD regulates DNA damage and repair in PC. miR-346 may be particularly effective as a therapeutic in the context of decreased NORAD observed in advanced PC, and in transcriptionally-hyperactive cancer cells. |
| first_indexed | 2024-03-06T21:58:31Z |
| format | Journal article |
| id | oxford-uuid:4dc8bbe1-dce0-4843-8877-e54e901ed4a3 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T21:58:31Z |
| publishDate | 2022 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:4dc8bbe1-dce0-4843-8877-e54e901ed4a32022-03-26T15:57:30ZA non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancerJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:4dc8bbe1-dce0-4843-8877-e54e901ed4a3EnglishSymplectic ElementsBioMed Central2022Fletcher, CEDeng, LOrafidiya, FYuan, WLorentzen, MPGSCyran, OWVarela-Carver, AConstantin, TALeach, DADobbs, FMFigueiredo, IGurel, BParkes, EBogdan, DPereira, RRZhao, SGNeeb, AIssa, FHester, JKudo, HLiu, YPhilippou, YBristow, RKnudsen, KBryant, RJFeng, FYReed, SHMills, IGde Bono, JBevan, CL<strong>Background</strong> 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. <br> <strong>Methods</strong> 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). <br> <strong>Results</strong> 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. <br> 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. <br> 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. <br> <strong>Conclusions</strong> A balancing act between miR-346 and NORAD regulates DNA damage and repair in PC. miR-346 may be particularly effective as a therapeutic in the context of decreased NORAD observed in advanced PC, and in transcriptionally-hyperactive cancer cells. |
| spellingShingle | Fletcher, CE Deng, L Orafidiya, F Yuan, W Lorentzen, MPGS Cyran, OW Varela-Carver, A Constantin, TA Leach, DA Dobbs, FM Figueiredo, I Gurel, B Parkes, E Bogdan, D Pereira, RR Zhao, SG Neeb, A Issa, F Hester, J Kudo, H Liu, Y Philippou, Y Bristow, R Knudsen, K Bryant, RJ Feng, FY Reed, SH Mills, IG de Bono, J Bevan, CL A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer |
| title | A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer |
| title_full | A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer |
| title_fullStr | A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer |
| title_full_unstemmed | A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer |
| title_short | A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer |
| title_sort | non coding rna balancing act mir 346 induced dna damage is limited by the long non coding rna norad in prostate cancer |
| work_keys_str_mv | AT fletcherce anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT dengl anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT orafidiyaf anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT yuanw anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT lorentzenmpgs anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT cyranow anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT varelacarvera anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT constantinta anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT leachda anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT dobbsfm anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT figueiredoi anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT gurelb anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT parkese anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bogdand anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT pereirarr anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT zhaosg anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT neeba anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT issaf anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT hesterj anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT kudoh anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT liuy anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT philippouy anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bristowr anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT knudsenk anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bryantrj anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT fengfy anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT reedsh anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT millsig anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT debonoj anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bevancl anoncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT fletcherce noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT dengl noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT orafidiyaf noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT yuanw noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT lorentzenmpgs noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT cyranow noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT varelacarvera noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT constantinta noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT leachda noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT dobbsfm noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT figueiredoi noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT gurelb noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT parkese noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bogdand noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT pereirarr noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT zhaosg noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT neeba noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT issaf noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT hesterj noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT kudoh noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT liuy noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT philippouy noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bristowr noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT knudsenk noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bryantrj noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT fengfy noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT reedsh noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT millsig noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT debonoj noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer AT bevancl noncodingrnabalancingactmir346induceddnadamageislimitedbythelongnoncodingrnanoradinprostatecancer |