SMN2 as a therapeutic target in spinal muscular atrophy: advances in gene expression modulation

Abstract

Spinal muscular atrophy (SMA) is a progressive neuromuscular degenerative disorder caused by mutations in the survival motor neuron 1 (SMN1) gene, leading to insufficient production of the survival motor neuron (SMN) protein. The nearly identical SMN2 gene modifies disease severity but generates only limited amounts of functional SMN protein due to a C-to-T transition in exon 7 that disrupts proper splicing. This review summarizes advances in understanding SMN2 splicing regulation and post-transcriptional modification in SMA pathogenesis. It discusses the roles of cis- and trans-acting elements in exon 7 inclusion, as well as the impact of epigenetic mechanisms such as histone acetylation and DNA methylation on SMN2 expression. This review also examines available therapeutic strategies, including antisense oligonucleotides (Nusinersen), small-molecule splicing modulators (Risdiplam and Branaplam), and gene therapy (Onasemnogene abeparvovec). Emerging approaches such as CRISPR/Cas9 genome editing and nanotechnology-based delivery systems are also highlighted. In addition, this review explores translational research using animal models, iPSC-derived neurons, and multi-omics approaches. Finally, it emphasizes the need for integrated therapeutic strategies that address both SMN-dependent and -independent pathways to improve treatment outcomes.

Keywords

Spinal muscular atrophy / SMN2 splicing regulation / Nusinersen / Risdiplam / onasemnogene abeparvovec / gene and epigenetic modulation / translational models

References

[1] National Center for Biotechnology Information. Spinal muscular atrophy; 1998. Available from: https://www.ncbi.nlm.nih.gov/books/NBK22213/ [Last accessed on 22 Sep 2025]

[2] NishioH,SaitoT,TakeshimaY.Spinal muscular atrophy: the past, present, and future of diagnosis and treatment.Int J Mol Sci2023;24:11939 PMCID:PMC10418635

[3] VerhaartIEC,WilsonIJ.Prevalence, incidence and carrier frequency of 5q-linked spinal muscular atrophy - a literature review.Orphanet J Rare Dis2017;12:124 PMCID:PMC5496354

[4] LefebvreS,ReboulletS.Identification and characterization of a spinal muscular atrophy-determining gene.Cell1995;80:155-65

[5] PriorTW,FinangerEL. Spinal muscular atrophy; 2000. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1352/ [Last accessed on 22 Sep 2025]

[6] ButchbachME.Copy number variations in the survival motor neuron genes: implications for spinal muscular atrophy and other neurodegenerative diseases.Front Mol Biosci2016;3:7 PMCID:PMC4785180

[7] DubowitzV.Very severe spinal muscular atrophy (SMA type 0): an expanding clinical phenotype.Eur J Paediatr Neurol1999;3:49-51

[8] GilbreathHR.Common neuromuscular disorders in pediatrics.Phys Assist Clin2016;1:583-97

[9] PriorTW,FinangerEL. Spinal muscular atrophy, type II. Available from: https://www.ncbi.nlm.nih.gov/medgen/95975 [Last accessed on 22 Sep 2025]

[10] Salort-CampanaE.Clinical features of spinal muscular atrophy (SMA) type 3 (Kugelberg-Welander disease).Arch Pediatr2020;27:7S23-8

[11] WijngaardeCA,OttoLAM.Muscle strength and motor function in adolescents and adults with spinal muscular atrophy.Neurology2020;95:e1988-98

[12] TalbotK.The clinical landscape for SMA in a new therapeutic era.Gene Ther2017;24:529-33 PMCID:PMC5628264

[13] CalderAN,HodgettsKJ.Small molecules in development for the treatment of spinal muscular atrophy.J Med Chem2016;59:10067-83 PMCID:PMC5744254

[14] DhuriK,QuijanoE.Antisense oligonucleotides: an emerging area in drug discovery and development.J Clin Med2020;9:2004 PMCID:PMC7355792

[15] BowermanM,Yáñez-MuñozRJ.Therapeutic strategies for spinal muscular atrophy: SMN and beyond.Dis Model Mech2017;10:943-54 PMCID:PMC5560066

[16] SinghRN.Mechanism of splicing regulation of spinal muscular atrophy genes. In: Sattler R, Donnelly CJ, editors. RNA Metabolism in Neurodegenerative Diseases. Cham: Springer International Publishing; 2018. pp. 31-61.

[17] BruceA,JulianL,KeithR. Proteins are made on polyribosomes; 2002. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26829/ [Last accessed on 22 Sep 2025]

[18] KissT.Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs.EMBO J2001;20:3617-22 PMCID:PMC125535

[19] WiseJA.Transcription | messenger RNA processing in eukaryotes. Encyclopedia of Biological Chemistry III. Elsevier; 2021. pp. 411-9.

[20] LodishHF. Molecular cell biology, 6th ed. United States: W.H. Freeman; 2008. Available from: https://books.google.com/books/about/Molecular_Cell_Biology.html?id=K3JbjG1JiUMC [Last accessed on 24 Sep 2025]

[21] WahlMC,LührmannR.The spliceosome: design principles of a dynamic RNP machine.Cell2009;136:701-18

[22] McManusCJ.RNA structure and the mechanisms of alternative splicing.Curr Opin Genet Dev2011;21:373-9 PMCID:PMC3149766

[23] PellizzoniL.Chaperoning ribonucleoprotein biogenesis in health and disease.EMBO Rep2007;8:340-5 PMCID:PMC1852756

[24] RopperAH,KleinJP. Adams and victor's principles of neurology, 11e. McGraw-Hill Education; 2019. Available from: https://neurology.mhmedical.com/content.aspx?bookid=1477&sectionid=215135193 [Last accessed on 24 Sep 2025]

[25] HassanHA,IssaMY,EssawiML.Genetic pattern of SMN1, SMN2, and NAIP genes in prognosis of SMA patients.Egypt J Med Hum Genet2020;21:44

[26] KernochanLE,WoodlingNS.The role of histone acetylation in SMN gene expression.Hum Mol Genet2005;14:1171-82

[27] CaoYY,HeSX.Association between SMN2 methylation and disease severity in Chinese children with spinal muscular atrophy.J Zhejiang Univ Sci B2016;17:76-82

[28] NarcísJO,TarabalO.Accumulation of poly(A) RNA in nuclear granules enriched in Sam68 in motor neurons from the SMNΔ7 mouse model of SMA.Sci Rep2018;8:9646 PMCID:PMC6018117

[29] EperonIC,MayedaA.Selection of alternative 5' splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1.Mol Cell Biol2000;20:8303-18 PMCID:PMC102138

[30] XueJ,ZhangX.TRA2: the dominant power of alternative splicing in tumors.Heliyon2023;9:e15516 PMCID:PMC10161706

[31] SinghNN,DiDonatoCJ.Mechanistic principles of antisense targets for the treatment of spinal muscular atrophy.Future Med Chem2015;7:1793-808 PMCID:PMC4660980

[32] FörchP,MartínezC,ValcárcelJ.The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5' splice sites.EMBO J2002;21:6882-92 PMCID:PMC139089

[33] BlencoweBJ.Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases.Trends Biochem Sci2000;25:106-10

[34] GorenA,AmitM.Comparative analysis identifies exonic splicing regulatory sequences-The complex definition of enhancers and silencers.Mol Cell2006;22:769-81

[35] MiyasoH,KondoS,MiyajimaH.An intronic splicing enhancer element in survival motor neuron (SMN) pre-mRNA.J Biol Chem2003;278:15825-31

[36] HanJ,ByeonCW.SR proteins induce alternative exon skipping through their activities on the flanking constitutive exons.Mol Cell Biol2011;31:793-802

[37] KashimaT,DavidCJ.hnRNP A1 functions with specificity in repression of SMN2 exon 7 splicing.Hum Mol Genet2007;16:3149-59

[38] MiyajimaH,OkumuraM,ImaizumiK.Identification of a cis-acting element for the regulation of SMN exon 7 splicing.J Biol Chem2002;277:23271-7

[39] PassmoreLA.Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression.Nat Rev Mol Cell Biol2022;23:93-106 PMCID:PMC7614307

[40] LiQ.Nusinersen as a therapeutic agent for spinal muscular atrophy.Yonsei Med J2020;61:273-83 PMCID:PMC7105407

[41] HoySM.Nusinersen: a review in 5q spinal muscular atrophy.CNS Drugs2021;35:1317-28 PMCID:PMC8709816

[42] U.S. Food and Drug Administration. SPINRAZA (Nusinersen) injection, for intrathecal use: highlights of prescribing information; 2016. Available from: https://www.accessdata.fda.gov/drugsatfda_docs/label/2016/209531lbl.pdf [Last accessed on 22 Sep 2025]

[43] NeilEE.Nusinersen: a novel antisense oligonucleotide for the treatment of spinal muscular atrophy.J Pediatr Pharmacol Ther2019;24:194-203 PMCID:PMC6510522

[44] FinkelRS,DarrasBT.Nusinersen versus Sham control in infantile-onset spinal muscular atrophy.N Engl J Med2017;377:1723-32

[45] MercuriE,ChiribogaCA.Nusinersen versus Sham control in later-onset spinal muscular atrophy.N Engl J Med2018;378:625-35

[46] RatniH,StephanAH.Risdiplam, the first approved small molecule splicing modifier drug as a blueprint for future transformative medicines.ACS Med Chem Lett2021;12:874-7 PMCID:PMC8201486

[47] BaranelloG,DayJW.Risdiplam in type 1 spinal muscular atrophy.N Engl J Med2021;384:915-23

[48] SturmS,JaberB.A phase 1 healthy male volunteer single escalating dose study of the pharmacokinetics and pharmacodynamics of risdiplam (RG7916, RO7034067), a SMN2 splicing modifier.Br J Clin Pharmacol2019;85:181-93 PMCID:PMC6303280

[49] MassonR,RoseK.Safety and efficacy of risdiplam in patients with type 1 spinal muscular atrophy (FIREFISH part 2): secondary analyses from an open-label trial.Lancet Neurol2022;21:1110-9

[50] OskouiM,DeconinckN.Correction to: Two-year efficacy and safety of risdiplam in patients with type 2 or non-ambulant type 3 spinal muscular atrophy (SMA).J Neurol2023;270:2547-9 PMCID:PMC10129951

[51] CheungAK,KerriganR.Discovery of small molecule splicing modulators of survival motor neuron-2 (SMN2) for the treatment of spinal muscular atrophy (SMA).J Med Chem2018;61:11021-36

[52] KellerCG,MonteysAM.An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion.Nat Commun2022;13:1150

[53] TheilD,BreesD.Neurofilament light chain: a translational safety biomarker for drug-induced peripheral neurotoxicity.Toxicol Pathol2023;51:135-47

[54] YeoCJJ.Overturning the Paradigm of spinal muscular atrophy as just a motor neuron disease.Pediatr Neurol2020;109:12-9

[55] HaqueUS.Recent progress in gene-targeting therapies for spinal muscular atrophy: promises and challenges.Genes2024;15:999 PMCID:PMC11353366

[56] DayJW,ChiribogaCA.Onasemnogene abeparvovec gene therapy for symptomatic infantile-onset spinal muscular atrophy in patients with two copies of SMN2 (STR1VE): an open-label, single-arm, multicentre, phase 3 trial.Lancet Neurol2021;20:284-93

[57] MercuriE,BaranelloG.Onasemnogene abeparvovec gene therapy for symptomatic infantile-onset spinal muscular atrophy type 1 (STR1VE-EU): an open-label, single-arm, multicentre, phase 3 trial.Lancet Neurol2021;20:832-41

[58] StraussKA,MuntoniF.Onasemnogene abeparvovec for presymptomatic infants with three copies of SMN2 at risk for spinal muscular atrophy: the Phase III SPR1NT trial.Nat Med2022;28:1390-7 PMCID:PMC9205287

[59] MendellJR,LehmanKJ.Five-year extension results of the phase 1 START trial of onasemnogene abeparvovec in spinal muscular atrophy.JAMA Neurol2021;78:834-41 PMCID:PMC8129901

[60] MuntoniF,ComiG.Long-term follow-up of patients with type 2 and non-ambulant type 3 spinal muscular atrophy (SMA) treated with olesoxime in the OLEOS trial.Neuromuscul Disord2020;30:959-69

[61] BertiniE,MercuriE.Safety and efficacy of olesoxime in patients with type 2 or non-ambulatory type 3 spinal muscular atrophy: a randomised, double-blind, placebo-controlled phase 2 trial.Lancet Neurol2017;16:513-22

[62] VillanovaM.Allogeneic mesenchymal stem cell therapy outcomes for three patients with spinal muscular atrophy type 1.Am J Phys Med Rehabil2015;94:410-5

[63] MireaA,AxenteM.Combination therapy with nusinersen and onasemnogene abeparvovec-xioi in spinal muscular atrophy type I.J Clin Med2021;10:5540 PMCID:PMC8658131

[64] ZhangW,YangD.Comprehensive analysis of adverse events associated with onasemnogene abeparvovec (Zolgensma) in spinal muscular atrophy patients: insights from FAERS database.Front Pharmacol2024;15:1475884 PMCID:PMC11747325

[65] WaldropMA,StoreyMA.Gene therapy for spinal muscular atrophy: safety and early outcomes.Pediatrics2020;146:e20200729

[66] KotulskaK,JedrzejowskaM.Newborn screening and gene therapy in SMA: challenges related to vaccinations.Front Neurol2022;13:890860 PMCID:PMC9727226

[67] SleighJN,TalbotK.The contribution of mouse models to understanding the pathogenesis of spinal muscular atrophy.Dis Model Mech2011;4:457-67 PMCID:PMC3124050

[68] KrayKM,ChughD,BurghesAHM.Dual SMN inducing therapies can rescue survival and motor unit function in symptomatic ∆7SMA mice.Neurobiol Dis2021;159:105488 PMCID:PMC8502210

[69] ZhaoX,LingKK.Pharmacokinetics, pharmacodynamics, and efficacy of a small-molecule SMN2 splicing modifier in mouse models of spinal muscular atrophy.Hum Mol Genet2016;25:1885-99 PMCID:PMC5062580

[70] SeoJ,OttesenEW,ShishimorovaM.Oxidative stress triggers body-wide skipping of multiple exons of the spinal muscular atrophy gene.PLoS One2016;11:e0154390 PMCID:PMC4844106

[71] BaenasN.Drosophila melanogaster as an alternative model organism in nutrigenomics.Genes Nutr2019;14:14 PMCID:PMC6501408

[72] PraveenK,MateraAG.A Drosophila model of spinal muscular atrophy uncouples snRNP biogenesis functions of survival motor neuron from locomotion and viability defects.Cell Rep2012;1:624-31 PMCID:PMC3405901

[73] SpringAM,HamiltonCD,MateraAG.Comprehensive modeling of spinal muscular atrophy in drosophila melanogaster.Front Mol Neurosci2019;12:113 PMCID:PMC6532329

[74] GonzalezD,LunaA.Modeling spinal muscular atrophy in zebrafish: current advances and future perspectives.Int J Mol Sci2024;25:1962 PMCID:PMC10888324

[75] McWhorterML,BurghesAH.Knockdown of the survival motor neuron (Smn) protein in zebrafish causes defects in motor axon outgrowth and pathfinding.J Cell Biol2003;162:919-31 PMCID:PMC1761110

[76] CerneckisJ,ShiY.Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications.Signal Transduct Target Ther2024;9:112 PMCID:PMC11053163

[77] Bautista CM, Sterneckert J. Progress and challenges in directing the differentiation of human iPSCs into spinal motor neurons.Front Cell Dev Biol2022;10:1089970 PMCID:PMC9849822

[78] PagliariE,ManziniP.Targeting STMN2 for neuroprotection and neuromuscular recovery in Spinal Muscular Atrophy: evidence from in vitro and in vivo SMA models.Cell Mol Life Sci2024;82:29 PMCID:PMC11671459

[79] OhuchiK,KatoZ.Established stem cell model of spinal muscular atrophy is applicable in the evaluation of the efficacy of thyrotropin-releasing hormone analog.Stem Cells Transl Med2016;5:152-63 PMCID:PMC4729546

[80] WangJ,JohnsonKA.Mechanistic studies of a small-molecule modulator of SMN2 splicing.Proc Natl Acad Sci USA2018;115:E4604-12 PMCID:PMC5960314

[81] ZheleznyakovaGY,KiselevAV.Genome-wide analysis shows association of epigenetic changes in regulators of Rab and Rho GTPases with spinal muscular atrophy severity.Eur J Hum Genet2013;21:988-93 PMCID:PMC3746269

[82] ZwartkruisMM,GommersD.Comprehensive analysis across SMN2 excludes DNA methylation as an epigenetic biomarker for spinal muscular atrophy.iScience2025;28:112461 PMCID:PMC12084074

[83] RedmanM,WatsonC.What is CRISPR/Cas9?.Arch Dis Child Educ Pract Ed2016;101:213-5 PMCID:PMC4975809

[84] LiJJ,TangC.Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice.Natl Sci Rev2020;7:92-101 PMCID:PMC8446915

[85] KariyawasamDST,LinC,FarrarMA.Biomarkers and the development of a personalized medicine approach in spinal muscular atrophy.Front Neurol2019;10:898 PMCID:PMC6709682

[86] BurghesAH.Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick?.Nat Rev Neurosci2009;10:597-609 PMCID:PMC2853768

[87] DarrasBT,FinkelRS.Neurofilament as a potential biomarker for spinal muscular atrophy.Ann Clin Transl Neurol2019;6:932-44 PMCID:PMC6530526

[88] VirataMCA,LippiG.Neurofilament light chain: a biomarker at the crossroads of clarity and confusion for gene-directed therapies.Neurodegener Dis Manag2024;14:227-39 PMCID:PMC11703492

[89] RutkoveSB,DarrasBT.Electrical impedance myography in spinal muscular atrophy: a longitudinal study.Muscle Nerve2012;45:642-7

[90] HuangY,HuY.Muscular MRI and magnetic resonance neurography in spinal muscular atrophy.Clin Radiol2024;79:673-80

[91] GlanzmanAM,MainM.The children's hospital of philadelphia infant test of neuromuscular disorders (CHOP INTEND): test development and reliability.Neuromuscul Disord2010;20:155-61 PMCID:PMC3260046

[92] NelsonLL.Clinical outcome assessments in Duchenne muscular dystrophy and spinal muscular atrophy: past, present and future.Neuromuscul Disord2021;31:1028-37

[93] BishopKM,FinkelRS.Motor milestone assessment of infants with spinal muscular atrophy using the hammersmith infant neurological exam-part 2: experience from a nusinersen clinical study.Muscle Nerve2018;57:142-6

[94] MainM,MercuriE.The Hammersmith functional motor scale for children with spinal muscular atrophy: a scale to test ability and monitor progress in children with limited ambulation.Eur J Paediatr Neurol2003;7:155-9

[95] RamseyD,MayhewA.Revised hammersmith scale for spinal muscular atrophy: a SMA specific clinical outcome assessment tool.PLoS One2017;12:e0172346 PMCID:PMC5319655

[96] WolfeA,RamseyD.Disease trajectories in the revised hammersmith scale in a cohort of untreated patients with spinal muscular atrophy types 2 and 3.J Neuromuscul Dis2024;11:665-77

[97] KrosschellKJ,MaczulskiJA,ReynaSP.Project Cure SMAReliability of the modified hammersmith functional motor scale in young children with spinal muscular atrophy.Muscle Nerve2011;44:246-51 PMCID:PMC3136587

[98] ErdosJ.Mid- and long-term (at least 12 months) follow-up of patients with spinal muscular atrophy (SMA) treated with nusinersen, onasemnogene abeparvovec, risdiplam or combination therapies: a systematic review of real-world study data.Eur J Paediatr Neurol2022;39:1-10

[99] MotylAAL,GroenEJN.Pre-natal manifestation of systemic developmental abnormalities in spinal muscular atrophy.Hum Mol Genet2020;29:2674-83 PMCID:PMC7530529

[100] HatanakaF,ShojimaK.Therapeutic strategy for spinal muscular atrophy by combining gene supplementation and genome editing.Nat Commun2024;15:6191 PMCID:PMC11269569

[101] NguyenTT,VoTK.Nanotechnology-based drug delivery for central nervous system disorders.Biomed Pharmacother2021;143:112117

[102] SinghNN,SinghRN.Chapter 5 - Transcriptional and splicing regulation of spinal muscular atrophy genes.Spinal Muscular Atrophy2017;75-97