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Loss of NPPA-AS1 promotes heart regeneration by stabilizing SFPQ–NONO heteromer-induced DNA repair

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Abstract

The role of long non-coding RNA (lncRNA) in endogenous cardiac regeneration remains largely elusive. The mammalian cardiomyocyte is capable of regeneration for a brief period after birth. This fact allows the exploration of the roles of critical lncRNAs in the regulation of cardiac regeneration. Through a cardiac regeneration model by apical resection (AR) of the left ventricle in neonatal mice, we identified an lncRNA named natriuretic peptide A antisense RNA 1 (NPPA-AS1), which negatively regulated cardiomyocyte proliferation. In neonates, NPPA-AS1 deletion did not affect heart development, but was sufficient to prolong the postnatal window of regeneration after AR. In adult mice, NPPA-AS1 deletion improved cardiac function and reduced infarct size after myocardial infarction (MI), associated with a significant improvement in cardiomyocyte proliferation. Further analysis showed that NPPA-AS1 interacted with DNA repair-related molecule splicing factor, proline- and glutamine-rich (SFPQ). A heteromer of SFPQ and non-POU domain-containing octamer-binding protein (NONO) was required for double-strand DNA break repair, but NPPA-AS1 was competitively bound with SFPQ due to the overlapped binding sites of SFPQ and NONO. NPPA-AS1 deletion promoted the binding of SFPQ–NONO heteromer, decreased DNA damage, and activated cardiomyocyte cell cycle re-entry. Together, loss of NPPA-AS1 promoted cardiomyocyte proliferation by stabilizing SFPQ–NONO heteromer-induced DNA repair and exerted a therapeutic effect against MI in adult mice. Consequently, NPPA-AS1 may be a novel target for stimulating cardiac regeneration to treat MI.

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Data availability

UCSC database (http://genome-asia.ucsc.edu/index.html) was used to determine the chromosomal location of targeted lncRNA. Through Coding Potential Assessment Tool (CPAT) database (http://lilab.research.bcm.edu/cpat/index.php), the coding potential of NPPA-AS1 was predicted. The cDNA sequences of human- and mouse-NPPA-AS1 were compared by Global Align tools: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=blastn&BLAST_SPEC=GlobalAln&LINK_LOC=BlastHomeLink. RNA structure analysis was predicted by RNA fold (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi) and Forna websites (http://rna.tbi.univie.ac.at/forna/forna.html). PanglaoDB (https://panglaodb.se) was used as a database to explore the cellular distribution of lncRNA when the protocol of single-cell RNA sequencing was SMART-seq2. We performed an enrichment analysis of signal pathways through Metascape (http://metascape.org/gp/index.html#/main/step1). The structure of SFPQ/NONO was referenced from the database of Protein Data Bank (https://www.rcsb.org/structure/4WIJ). The nucleotide-binding proteome of lncRNA was estimated via algorithms provided by catRAPID omics (http://service.tartaglialab.com/update_submission/274908/a801f9d744); RNA-binding regions of SFPQ proteins and NPPA-AS1 were predicted by catRAPID fragments (http://service.tartaglialab.com/update_submission/274910/fe4a85fb9e).

References

  1. Abbas N, Perbellini F, Thum T (2020) Non-coding RNAs: emerging players in cardiomyocyte proliferation and cardiac regeneration. Basic Res Cardiol 115:52. https://doi.org/10.1007/s00395-020-0816-0

    Article  CAS  Google Scholar 

  2. Ali M, Liccardo D, Cao T, Tian Y (2021) Natriuretic peptides and Forkhead O transcription factors act in a cooperative manner to promote cardiomyocyte cell cycle re-entry in the postnatal mouse heart. BMC Dev Biol 21:6. https://doi.org/10.1186/s12861-020-00236-y

    Article  CAS  Google Scholar 

  3. Andrin C, McDonald D, Attwood KM, Rodrigue A, Ghosh S, Mirzayans R, Masson JY, Dellaire G, Hendzel MJ (2012) A requirement for polymerized actin in DNA double-strand break repair. Nucleus 3:384–395. https://doi.org/10.4161/nucl.21055

    Article  Google Scholar 

  4. Bakkenist CJ, Kastan MB (2003) DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421:499–506. https://doi.org/10.1038/nature01368

    Article  CAS  Google Scholar 

  5. Bär C, Chatterjee S, Thum T (2016) Long noncoding RNAs in cardiovascular pathology, diagnosis, and therapy. Circulation 134:1484–1499. https://doi.org/10.1161/circulationaha.116.023686

    Article  Google Scholar 

  6. Bassat E, Mutlak YE, Genzelinakh A, Shadrin IY, Baruch Umansky K, Yifa O, Kain D, Rajchman D, Leach J, Riabov Bassat D, Udi Y, Sarig R, Sagi I, Martin JF, Bursac N, Cohen S, Tzahor E (2017) The extracellular matrix protein agrin promotes heart regeneration in mice. Nature 547:179–184. https://doi.org/10.1038/nature22978

    Article  CAS  Google Scholar 

  7. Becker JR, Chatterjee S, Robinson TY, Bennett JS, Panáková D, Galindo CL, Zhong L, Shin JT, Coy SM, Kelly AE, Roden DM, Lim CC, MacRae CA (2014) Differential activation of natriuretic peptide receptors modulates cardiomyocyte proliferation during development. Development 141:335–345. https://doi.org/10.1242/dev.100370

    Article  CAS  Google Scholar 

  8. Bergmann O, Bhardwaj RD, Bernard S, Zdunek S, Barnabé-Heider F, Walsh S, Zupicich J, Alkass K, Buchholz BA, Druid H, Jovinge S, Frisén J (2009) Evidence for cardiomyocyte renewal in humans. Science 324:98–102. https://doi.org/10.1126/science.1164680

    Article  CAS  Google Scholar 

  9. Bladen CL, Udayakumar D, Takeda Y, Dynan WS (2005) Identification of the polypyrimidine tract binding protein-associated splicing factor.p54(nrb) complex as a candidate DNA double-strand break rejoining factor. J Biol Chem 280:5205–5210. https://doi.org/10.1074/jbc.M412758200

    Article  CAS  Google Scholar 

  10. Cahill TJ, Choudhury RP, Riley PR (2017) Heart regeneration and repair after myocardial infarction: translational opportunities for novel therapeutics. Nat Rev Drug Discov 16:699–717. https://doi.org/10.1038/nrd.2017.106

    Article  CAS  Google Scholar 

  11. Cai B, Ma W, Ding F, Zhang L, Huang Q, Wang X, Hua B, Xu J, Li J, Bi C, Guo S, Yang F, Han Z, Li Y, Yan G, Yu Y, Bao Z, Yu M, Li F, Tian Y, Pan Z, Yang B (2018) The Long Noncoding RNA CAREL Controls Cardiac Regeneration. J Am Coll Cardiol 72:534–550. https://doi.org/10.1016/j.jacc.2018.04.085

    Article  Google Scholar 

  12. Celik S, Sadegh MK, Morley M, Roselli C, Ellinor PT, Cappola T, Smith JG, Gidlöf O (2019) Antisense regulation of atrial natriuretic peptide expression. JCI Insight. https://doi.org/10.1172/jci.insight.130978

    Article  Google Scholar 

  13. de Silva HC, Lin MZ, Phillips L, Martin JL, Baxter RC (2019) IGFBP-3 interacts with NONO and SFPQ in PARP-dependent DNA damage repair in triple-negative breast cancer. Cell Mol Life Sci 76:2015–2030. https://doi.org/10.1007/s00018-019-03033-4

    Article  CAS  Google Scholar 

  14. He D, Wang J, Lu Y, Deng Y, Zhao C, Xu L, Chen Y, Hu YC, Zhou W, Lu QR (2017) lncRNA functional networks in oligodendrocytes reveal stage-specific myelination control by an lncOL1/Suz12 complex in the CNS. Neuron 93:362–378. https://doi.org/10.1016/j.neuron.2016.11.044

    Article  CAS  Google Scholar 

  15. Honkoop H, de Bakker DE, Aharonov A, Kruse F, Shakked A, Nguyen PD, de Heus C, Garric L, Muraro MJ, Shoffner A, Tessadori F, Peterson JC, Noort W, Bertozzi A, Weidinger G, Posthuma G, Grün D, van der Laarse WJ, Klumperman J, Jaspers RT, Poss KD, van Oudenaarden A, Tzahor E, Bakkers J (2019) Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart. Elife. https://doi.org/10.7554/eLife.50163

    Article  Google Scholar 

  16. Jaafar L, Li Z, Li S, Dynan WS (2017) SFPQ•NONO and XLF function separately and together to promote DNA double-strand break repair via canonical non-homologous end joining. Nucleic Acids Res 45:1848–1859. https://doi.org/10.1093/nar/gkw1209

    Article  CAS  Google Scholar 

  17. Kimura W, Xiao F, Canseco DC, Muralidhar S, Thet S, Zhang HM, Abderrahman Y, Chen R, Garcia JA, Shelton JM, Richardson JA, Ashour AM, Asaithamby A, Liang H, Xing C, Lu Z, Zhang CC, Sadek HA (2015) Hypoxia fate mapping identifies cycling cardiomyocytes in the adult heart. Nature 523:226–230. https://doi.org/10.1038/nature14582

    Article  CAS  Google Scholar 

  18. Kozlov SV, Graham ME, Peng C, Chen P, Robinson PJ, Lavin MF (2006) Involvement of novel autophosphorylation sites in ATM activation. Embo J 25:3504–3514. https://doi.org/10.1038/sj.emboj.7601231

    Article  CAS  Google Scholar 

  19. Leach JP, Heallen T, Zhang M, Rahmani M, Morikawa Y, Hill MC, Segura A, Willerson JT, Martin JF (2017) Hippo pathway deficiency reverses systolic heart failure after infarction. Nature 550:260–264. https://doi.org/10.1038/nature24045

    Article  CAS  Google Scholar 

  20. Lee M, Sadowska A, Bekere I, Ho D, Gully BS, Lu Y, Iyer KS, Trewhella J, Fox AH, Bond CS (2015) The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation. Nucleic Acids Res 43:3826–3840. https://doi.org/10.1093/nar/gkv156

    Article  CAS  Google Scholar 

  21. Li S, Li Z, Shu FJ, Xiong H, Phillips AC, Dynan WS (2014) Double-strand break repair deficiency in NONO knockout murine embryonic fibroblasts and compensation by spontaneous upregulation of the PSPC1 paralog. Nucleic Acids Res 42:9771–9780. https://doi.org/10.1093/nar/gku650

    Article  CAS  Google Scholar 

  22. Li X, He X, Wang H, Li M, Huang S, Chen G, Jing Y, Wang S, Chen Y, Liao W, Liao Y, Bin J (2018) Loss of AZIN2 splice variant facilitates endogenous cardiac regeneration. Cardiovasc Res 114:1642–1655. https://doi.org/10.1093/cvr/cvy075

    Article  CAS  Google Scholar 

  23. Lin Z, Pu WT (2014) Strategies for cardiac regeneration and repair. Sci Transl Med. https://doi.org/10.1126/scitranslmed.3006681

    Article  Google Scholar 

  24. Mahmoud AI, Porrello ER, Kimura W, Olson EN, Sadek HA (2014) Surgical models for cardiac regeneration in neonatal mice. Nat Protoc 9:305–311. https://doi.org/10.1038/nprot.2014.021

    Article  CAS  Google Scholar 

  25. Porrello ER, Mahmoud AI, Simpson E, Hill JA, Richardson JA, Olson EN, Sadek HA (2011) Transient regenerative potential of the neonatal mouse heart. Science 331:1078–1080. https://doi.org/10.1126/science.1200708

    Article  CAS  Google Scholar 

  26. Porrello ER, Mahmoud AI, Simpson E, Johnson BA, Grinsfelder D, Canseco D, Mammen PP, Rothermel BA, Olson EN, Sadek HA (2013) Regulation of neonatal and adult mammalian heart regeneration by the miR-15 family. Proc Natl Acad Sci U S A 110:187–192. https://doi.org/10.1073/pnas.1208863110

    Article  Google Scholar 

  27. Puente BN, Kimura W, Muralidhar SA, Moon J, Amatruda JF, Phelps KL, Grinsfelder D, Rothermel BA, Chen R, Garcia JA, Santos CX, Thet S, Mori E, Kinter MT, Rindler PM, Zacchigna S, Mukherjee S, Chen DJ, Mahmoud AI, Giacca M, Rabinovitch PS, Aroumougame A, Shah AM, Szweda LI, Sadek HA (2014) The oxygen-rich postnatal environment induces cardiomyocyte cell-cycle arrest through DNA damage response. Cell 157:565–579. https://doi.org/10.1016/j.cell.2014.03.032

    Article  CAS  Google Scholar 

  28. Rizki G, Boyer LA (2015) Lncing epigenetic control of transcription to cardiovascular development and disease. Circ Res 117:192–206. https://doi.org/10.1161/circresaha.117.304156

    Article  CAS  Google Scholar 

  29. Salton M, Lerenthal Y, Wang SY, Chen DJ, Shiloh Y (2010) Involvement of Matrin 3 and SFPQ/NONO in the DNA damage response. Cell Cycle 9:1568–1576. https://doi.org/10.4161/cc.9.8.11298

    Article  CAS  Google Scholar 

  30. Schipke J, Roloff K, Kuhn M, Mühlfeld C (2015) Systemic, but not cardiomyocyte-specific, deletion of the natriuretic peptide receptor guanylyl cyclase A increases cardiomyocyte number in neonatal mice. Histochem Cell Biol 144:365–375. https://doi.org/10.1007/s00418-015-1337-z

    Article  CAS  Google Scholar 

  31. Scully R, Xie A (2013) Double strand break repair functions of histone H2AX. Mutat Res 750:5–14. https://doi.org/10.1016/j.mrfmmm.2013.07.007

    Article  CAS  Google Scholar 

  32. Senyo SE, Steinhauser ML, Pizzimenti CL, Yang VK, Cai L, Wang M, Wu TD, Guerquin-Kern JL, Lechene CP, Lee RT (2013) Mammalian heart renewal by pre-existing cardiomyocytes. Nature 493:433–436. https://doi.org/10.1038/nature11682

    Article  CAS  Google Scholar 

  33. Shang Z, Yu J, Sun L, Tian J, Zhu S, Zhang B, Dong Q, Jiang N, Flores-Morales A, Chang C, Niu Y (2019) LncRNA PCAT1 activates AKT and NF-κB signaling in castration-resistant prostate cancer by regulating the PHLPP/FKBP51/IKKα complex. Nucleic Acids Res 47:4211–4225. https://doi.org/10.1093/nar/gkz108

    Article  CAS  Google Scholar 

  34. Shen W, Liang XH, Sun H, Crooke ST (2015) 2’-Fluoro-modified phosphorothioate oligonucleotide can cause rapid degradation of P54nrb and PSF. Nucleic Acids Res 43:4569–4578. https://doi.org/10.1093/nar/gkv298

    Article  CAS  Google Scholar 

  35. Takagawa J, Zhang Y, Wong ML, Sievers RE, Kapasi NK, Wang Y, Yeghiazarians Y, Lee RJ, Grossman W (1985) Springer ML (2007) Myocardial infarct size measurement in the mouse chronic infarction model: comparison of area- and length-based approaches. J Appl Physiol 102:2104–2111. https://doi.org/10.1152/japplphysiol.00033.2007

    Article  Google Scholar 

  36. Uryga A, Gray K, Bennett M (2016) DNA damage and repair in vascular disease. Annu Rev Physiol 78:45–66. https://doi.org/10.1146/annurev-physiol-021115-105127

    Article  CAS  Google Scholar 

  37. Viereck J, Thum T (2017) Long noncoding RNAs in pathological cardiac remodeling. Circ Res 120:262–264. https://doi.org/10.1161/circresaha.116.310174

    Article  CAS  Google Scholar 

  38. Wang WE, Li L, Xia X, Fu W, Liao Q, Lan C, Yang D, Chen H, Yue R, Zeng C, Zhou L, Zhou B, Duan DD, Chen X, Houser SR, Zeng C (2017) Dedifferentiation, proliferation, and redifferentiation of adult mammalian cardiomyocytes after ischemic injury. Circulation 136:834–848. https://doi.org/10.1161/circulationaha.116.024307

    Article  Google Scholar 

  39. Zhu W, Zhang E, Zhao M, Chong Z, Fan C, Tang Y, Hunter JD, Borovjagin AV, Walcott GP, Chen JY, Qin G, Zhang J (2018) Regenerative potential of neonatal porcine hearts. Circulation 138:2809–2816. https://doi.org/10.1161/circulationaha.118.034886

    Article  Google Scholar 

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Funding

This work was supported by grants from the National Science Foundation of China (81930008, U20A20344), Program of Innovative Research Team by National Natural Science Foundation (81721001, 81922005), National Key Research & Development Program of China (2018YFA0107403), and Chongqing Natural Science Foundation (cstc2020jcyj-jqX0016).

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Correspondence to Chunyu Zeng or Wei Eric Wang.

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Fu, W., Ren, H., Shou, J. et al. Loss of NPPA-AS1 promotes heart regeneration by stabilizing SFPQ–NONO heteromer-induced DNA repair. Basic Res Cardiol 117, 10 (2022). https://doi.org/10.1007/s00395-022-00921-y

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