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  • Review Article
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Alternative splicing in neurodegenerative disease and the promise of RNA therapies

Abstract

Alternative splicing generates a myriad of RNA products and protein isoforms of different functions from a single gene. Dysregulated alternative splicing has emerged as a new mechanism broadly implicated in the pathogenesis of neurodegenerative diseases such as Alzheimer disease, amyotrophic lateral sclerosis, frontotemporal dementia, Parkinson disease and repeat expansion diseases. Understanding the mechanisms and functional outcomes of abnormal splicing in neurological disorders is vital in developing effective therapies to treat mis-splicing pathology. In this Review, we discuss emerging research and evidence of the roles of alternative splicing defects in major neurodegenerative diseases and summarize the latest advances in RNA-based therapeutic strategies to target these disorders.

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Fig. 1: Schematic representation of different patterns of alternative pre-mRNA splicing in eukaryotic genes.
Fig. 2: Alternative splicing is regulated by trans-acting splicing factors that bind to cis-sequence elements to promote or inhibit spliceosome assembly and activity at 3′-splice and 5′-splice sites.
Fig. 3: Splicing dysregulation in neurodegenerative disease.
Fig. 4: Alternative transcripts of neurodegenerative disease-linked genes.
Fig. 5: Upstream splicing factor sequestration and loss of function resulting in pathological target transcript dysregulation.
Fig. 6: Antisense oligonucleotide therapeutic mechanisms of action.

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References

  1. Chow, L. T., Gelinas, R. E., Broker, T. R. & Roberts, R. J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12, 1–8 (1977).

    CAS  PubMed  Google Scholar 

  2. Amara, S. G., Jonas, V., Rosenfeld, M. G., Ong, E. S. & Evans, R. M. Alternative RNA processing in calcitonin gene expression generates mRNAs encoding different polypeptide products. Nature 298, 240–244 (1982).

    CAS  PubMed  Google Scholar 

  3. Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413–1415 (2008).

    CAS  PubMed  Google Scholar 

  5. Yeo, G., Holste, D., Kreiman, G. & Burge, C. B. Variation in alternative splicing across human tissues. Genome Biol. 5, R74 (2004).

    PubMed  PubMed Central  Google Scholar 

  6. Barbosa-Morais, N. L. et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587–1593 (2012).

    CAS  PubMed  Google Scholar 

  7. Vuong, C. K., Black, D. L. & Zheng, S. The neurogenetics of alternative splicing. Nat. Rev. Neurosci. 17, 265–281 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Furlanis, E. & Scheiffele, P. Regulation of neuronal differentiation, function, and plasticity by alternative splicing. Annu. Rev. Cell Dev. Biol. 34, 451–469 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Ule, J. & Blencowe, B. J. Alternative splicing regulatory networks: functions, mechanisms, and evolution. Mol. Cell 76, 329–345 (2019).

    CAS  PubMed  Google Scholar 

  10. Zheng, S. Alternative splicing programming of axon formation. Wiley Interdiscip. Rev. RNA 11, e1585 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Traunmüller, L., Gomez, A. M., Nguyen, T.-M. & Scheiffele, P. Control of neuronal synapse specification by a highly dedicated alternative splicing program. Science 352, 982–986 (2016).

    PubMed  Google Scholar 

  12. Mauger, O. & Scheiffele, P. Beyond proteome diversity: alternative splicing as a regulator of neuronal transcript dynamics. Curr. Opin. Neurobiol. 45, 162–168 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhang, M. et al. Axonogenesis is coordinated by neuron-specific alternative splicing programming and splicing regulator PTBP2. Neuron 101, 690–706.e10 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Lin, L., Zhang, M., Stoilov, P., Chen, L. & Zheng, S. Developmental attenuation of neuronal apoptosis by neural-specific splicing of Bak1 microexon. Neuron 107, 1180–1196.e8 (2020). This study demonstrates that the neuronal splicing of a microexon in Bak1 reduces apoptosis competence and is necessary for supporting neuronal and animal survival, providing genetic evidence highlighting the essential role of neuronal splicing in brain development and organism survival.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Gonatopoulos-Pournatzis, T. & Blencowe, B. J. Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr. Opin. Genet. Dev. 65, 22–33 (2020).

    CAS  PubMed  Google Scholar 

  16. Ha, K. C. H., Sterne-Weiler, T., Morris, Q., Weatheritt, R. J. & Blencowe, B. J. Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity. Nat. Commun. 12, 335 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Vuong, J. K., Ergin, V., Chen, L. & Zheng, S. Multilayered regulations of alternative splicing, NMD, and protein stability control temporal induction and tissue-specific expression of TRIM46 during axon formation. Nat. Commun. 13, 2081 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Zheng, S. et al. PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat. Neurosci. 15, 381–388 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhang, X. et al. Cell type-specific alternative splicing governs cell fate in the developing cerebral cortex. Cell 166, 1147–1162.e15 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Havens, M. A. & Hastings, M. L. Splice-switching antisense oligonucleotides as therapeutic drugs. Nucleic Acids Res. 44, 6549–6563 (2016).

    PubMed  PubMed Central  Google Scholar 

  21. Bennett, C. F., Krainer, A. R. & Cleveland, D. W. Antisense oligonucleotide therapies for neurodegenerative diseases. Annu. Rev. Neurosci. 42, 385–406 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M. & Gotoh, O. Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene 364, 53–62 (2005).

    CAS  PubMed  Google Scholar 

  23. Chen, M. & Manley, J. L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10, 741–754 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Garcia-Blanco, M. A., Baraniak, A. P. & Lasda, E. L. Alternative splicing in disease and therapy. Nat. Biotechnol. 22, 535–546 (2004).

    CAS  PubMed  Google Scholar 

  25. Ule, J. et al. An RNA map predicting Nova-dependent splicing regulation. Nature 444, 580–586 (2006).

    CAS  PubMed  Google Scholar 

  26. Wegener, M. & Müller-McNicoll, M. in The Biology of mRNA: Structure and Function (eds Oeffinger, M. & Zenklusen, D.) 83–112 (Springer International, 2019).

  27. Cáceres, J. F. & Kornblihtt, A. R. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 18, 186–193 (2002).

    PubMed  Google Scholar 

  28. Fu, X.-D. & Ares, M. Context-dependent control of alternative splicing by RNA-binding proteins. Nat. Rev. Genet. 15, 689–701 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Su, C.-H., Dhananjaya, D. & Tarn, W.-Y. Alternative splicing in neurogenesis and brain development. Front. Mol. Biosci. 5, 12 (2018).

    PubMed  PubMed Central  Google Scholar 

  30. Ohkura, N., Takahashi, M., Yaguchi, H., Nagamura, Y. & Tsukada, T. Coactivator-associated arginine methyltransferase 1, CARM1, affects pre-mRNA splicing in an isoform-specific manner. J. Biol. Chem. 280, 28927–28935 (2005).

    CAS  PubMed  Google Scholar 

  31. Cheng, D., Côté, J., Shaaban, S. & Bedford, M. T. The arginine methyltransferase CARM1 regulates the coupling of transcription and mRNA processing. Mol. Cell 25, 71–83 (2007).

    PubMed  Google Scholar 

  32. Chen, Y.-C. et al. Protein arginine methylation facilitates cotranscriptional recruitment of pre-mRNA splicing factors. Mol. Cell Biol. 30, 5245–5256 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Gunderson, F. Q. & Johnson, T. L. Acetylation by the transcriptional coactivator Gcn5 plays a novel role in co-transcriptional spliceosome assembly. PLoS Genet. 5, e1000682 (2009).

    PubMed  PubMed Central  Google Scholar 

  34. Martinez, E. et al. Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol. Cell Biol. 21, 6782–6795 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Naftelberg, S., Schor, I. E., Ast, G. & Kornblihtt, A. R. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu. Rev. Biochem. 84, 165–198 (2015).

    CAS  PubMed  Google Scholar 

  36. Keren, H., Lev-Maor, G. & Ast, G. Alternative splicing and evolution: diversification, exon definition and function. Nat. Rev. Genet. 11, 345–355 (2010).

    CAS  PubMed  Google Scholar 

  37. Zhu, L.-Y., Zhu, Y.-R., Dai, D.-J., Wang, X. & Jin, H.-C. Epigenetic regulation of alternative splicing. Am. J. Cancer Res. 8, 2346–2358 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Luco, R. F., Allo, M., Schor, I. E., Kornblihtt, A. R. & Misteli, T. Epigenetics in alternative pre-mRNA splicing. Cell 144, 16–26 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Rahhal, R. & Seto, E. Emerging roles of histone modifications and HDACs in RNA splicing. Nucleic Acids Res. 47, 4911–4926 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Zhang, J., Zhang, Y.-Z., Jiang, J. & Duan, C.-G. The crosstalk between epigenetic mechanisms and alternative RNA processing regulation. Front. Genet. 11, 998 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Matthews, K. A. et al. Racial and ethnic estimates of Alzheimer’s disease and related dementias in the United States (2015–2060) in adults aged ≥65 years. Alzheimers Dement. 15, 17–24 (2019).

    PubMed  Google Scholar 

  42. Killin, L. O. J., Starr, J. M., Shiue, I. J. & Russ, T. C. Environmental risk factors for dementia: a systematic review. BMC Geriatr. 16, 175 (2016).

    PubMed  PubMed Central  Google Scholar 

  43. Ittner, L. M. & Götz, J. Amyloid-β and tau-a toxic pas de deux in Alzheimer’s disease. Nat. Rev. Neurosci. 12, 65–72 (2011).

    CAS  PubMed  Google Scholar 

  44. Love, J. E., Hayden, E. J. & Rohn, T. T. Alternative splicing in Alzheimer’s disease. J. Parkinsons Dis. Alzheimers Dis. 2, 6 (2015).

    PubMed  PubMed Central  Google Scholar 

  45. Hutton, M. et al. Association of missense and 5′-splice-site mutations in tau with the inherited dementia FTDP-17. Nature 393, 702–705 (1998). Together with Spillantini et al. (1998), this study reveals mutations in the splice sites of the MAPT gene causative for FTDP-17, which uncovered the key role of 3R-tau:4R-tau isoform balance in neurodegenerative pathology.

    CAS  PubMed  Google Scholar 

  46. Spillantini, M. G. et al. Mutation in the tau gene in familial multiple system tauopathy with presenile dementia. Proc. Natl Acad. Sci. USA 95, 7737–7741 (1998). Together with Hutton et al. (1998), this study reveals mutations in the splice sites of the MAPT gene causative for FTDP-17, which uncovered the key role of 3R-tau:4R-tau isoform balance in neurodegenerative pathology.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Poorkaj, P. et al. Tau is a candidate gene for chromosome 17 frontotemporal dementia. Ann. Neurol. 43, 815–825 (1998).

    CAS  PubMed  Google Scholar 

  48. Zhang, Y., Wu, K.-M., Yang, L., Dong, Q. & Yu, J.-T. Tauopathies: new perspectives and challenges. Mol. Neurodegener. 17, 28 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Strang, K. H., Golde, T. E. & Giasson, B. I. MAPT mutations, tauopathy, and mechanisms of neurodegeneration. Lab. Invest. 99, 912–928 (2019).

    PubMed  PubMed Central  Google Scholar 

  50. Liu, F. & Gong, C.-X. Tau exon 10 alternative splicing and tauopathies. Mol. Neurodegener. 3, 8 (2008).

    PubMed  PubMed Central  Google Scholar 

  51. Mutreja, Y., Combs, B. & Gamblin, T. C. FTDP-17 mutations alter the aggregation and microtubule stabilization propensity of tau in an isoform-specific fashion. Biochemistry 58, 742–754 (2019).

    CAS  PubMed  Google Scholar 

  52. Niblock, M. & Gallo, J.-M. Tau alternative splicing in familial and sporadic tauopathies. Biochem. Soc. Trans. 40, 677–680 (2012).

    CAS  PubMed  Google Scholar 

  53. Goedert, M., Spillantini, M. G., Jakes, R., Rutherford, D. & Crowther, R. A. Multiple isoforms of human microtubule-associated protein tau: sequences and localization in neurofibrillary tangles of Alzheimer’s disease. Neuron 3, 519–526 (1989).

    CAS  PubMed  Google Scholar 

  54. Gustke, N., Trinczek, B., Biernat, J., Mandelkow, E. M. & Mandelkow, E. Domains of tau protein and interactions with microtubules. Biochemistry 33, 9511–9522 (1994).

    CAS  PubMed  Google Scholar 

  55. Goode, B. L., Chau, M., Denis, P. E. & Feinstein, S. C. Structural and functional differences between 3-repeat and 4-repeat tau isoforms. Implications for normal tau function and the onset of neurodegenerative disease. J. Biol. Chem. 275, 38182–38189 (2000).

    CAS  PubMed  Google Scholar 

  56. Goedert, M., Spillantini, M. G., Potier, M. C., Ulrich, J. & Crowther, R. A. Cloning and sequencing of the cDNA encoding an isoform of microtubule-associated protein tau containing four tandem repeats: differential expression of tau protein mRNAs in human brain. EMBO J. 8, 393–399 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Spillantini, M. G. & Goedert, M. Tau pathology and neurodegeneration. Lancet Neurol. 12, 609–622 (2013).

    CAS  PubMed  Google Scholar 

  58. Gu, J. et al. Rbfox3/NeuN regulates alternative splicing of tau exon 10. J. Alzheimer’s Dis. 66, 1695–1704 (2018).

    CAS  Google Scholar 

  59. Qian, W. & Liu, F. Regulation of alternative splicing of tau exon 10. Neurosci. Bull. 30, 367–377 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Goedert, M. & Jakes, R. Expression of separate isoforms of human tau protein: correlation with the tau pattern in brain and effects on tubulin polymerization. EMBO J. 9, 4225–4230 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Rösler, T. W. et al. Four-repeat tauopathies. Prog. Neurobiol. 180, 101644 (2019).

    PubMed  Google Scholar 

  62. Stanford, P. M. et al. Mutations in the tau gene that cause an increase in three repeat tau and frontotemporal dementia. Brain 126, 814–826 (2003).

    PubMed  Google Scholar 

  63. Lacovich, V. et al. Tau isoforms imbalance impairs the axonal transport of the amyloid precursor protein in human neurons. J. Neurosci. 37, 58–69 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Qian, W. et al. Regulation of the alternative splicing of tau exon 10 by SC35 and Dyrk1A. Nucleic Acids Res. 39, 6161–6171 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Gu, J. et al. Cyclic AMP-dependent protein kinase regulates 9G8-mediated alternative splicing of tau exon 10. FEBS Lett. 586, 2239–2244 (2012).

    CAS  PubMed  Google Scholar 

  66. Hernández, F. et al. Glycogen synthase kinase-3 plays a crucial role in tau exon 10 splicing and intranuclear distribution of SC35: implications for Alzheimer’s disease. J. Biol. Chem. 279, 3801–3806 (2004).

    PubMed  Google Scholar 

  67. Yu, Q., Guo, J. & Zhou, J. A minimal length between tau exon 10 and 11 is required for correct splicing of exon 10. J. Neurochem. 90, 164–172 (2004).

    CAS  PubMed  Google Scholar 

  68. Kondo, S. et al. Tra2β, SF2/ASF and SRp30c modulate the function of an exonic splicing enhancer in exon 10 of tau pre-mRNA. Genes Cell 9, 121–130 (2004).

    CAS  Google Scholar 

  69. Wang, J. et al. Tau exon 10, whose missplicing causes frontotemporal dementia, is regulated by an intricate interplay of cis elements and trans factors. J. Neurochem. 88, 1078–1090 (2004).

    CAS  PubMed  Google Scholar 

  70. Wu, J. Y., Kar, A., Kuo, D., Yu, B. & Havlioglu, N. SRp54 (SFRS11), a regulator for tau exon 10 alternative splicing identified by an expression cloning strategy. Mol. Cell Biol. 26, 6739–6747 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Jiang, Z. et al. Mutations in tau gene exon 10 associated with FTDP-17 alter the activity of an exonic splicing enhancer to interact with Tra2β. J. Biol. Chem. 278, 18997–19007 (2003).

    CAS  PubMed  Google Scholar 

  72. Gao, L., Wang, J., Wang, Y. & Andreadis, A. SR protein 9G8 modulates splicing of tau exon 10 via its proximal downstream intron, a clustering region for frontotemporal dementia mutations. Mol. Cell Neurosci. 34, 48–58 (2007).

    CAS  PubMed  Google Scholar 

  73. D’Souza, I. & Schellenberg, G. D. Arginine/serine-rich protein interaction domain-dependent modulation of a tau exon 10 splicing enhancer: altered interactions and mechanisms for functionally antagonistic FTDP-17 mutations Δ280K AND N279K. J. Biol. Chem. 281, 2460–2469 (2006).

    PubMed  Google Scholar 

  74. Ke, Y. et al. Tau-mediated nuclear depletion and cytoplasmic accumulation of SFPQ in Alzheimer’s and Pick’s disease. PLoS ONE 7, e35678 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Lu, J., Shu, R. & Zhu, Y. Dysregulation and dislocation of SFPQ disturbed DNA organization in Alzheimer’s disease and frontotemporal dementia. J. Alzheimers Dis. 61, 1311–1321 (2018).

    CAS  PubMed  Google Scholar 

  76. Younas, N. et al. SFPQ and tau: critical factors contributing to rapid progression of Alzheimer’s disease. Acta Neuropathol. 140, 317–339 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Ray, P. et al. PSF suppresses tau exon 10 inclusion by interacting with a stem-loop structure downstream of exon 10. J. Mol. Neurosci. 45, 453–466 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Xing, S. et al. Identification of HnRNPC as a novel tau exon 10 splicing factor using RNA antisense purification mass spectrometry. RNA Biol. 19, 104–116 (2022).

    CAS  PubMed  Google Scholar 

  79. Benilova, I., Karran, E. & De Strooper, B. The toxic Aβ oligomer and Alzheimer’s disease: an emperor in need of clothes. Nat. Neurosci. 15, 349–357 (2012).

    CAS  PubMed  Google Scholar 

  80. Qiu, T., Liu, Q., Chen, Y.-X., Zhao, Y.-F. & Li, Y.-M. Aβ42 and Aβ40: similarities and differences. J. Pept. Sci. 21, 522–529 (2015).

    CAS  PubMed  Google Scholar 

  81. Chang, C.-C. et al. Synergistic interactions between Alzheimer’s Aβ40 and Aβ42 on the surface of primary neurons revealed by single molecule microscopy. PLoS ONE 8, e82139 (2013).

    PubMed  PubMed Central  Google Scholar 

  82. Mullan, M. et al. A pathogenic mutation for probable Alzheimer’s disease in the APP gene at the N-terminus of β-amyloid. Nat. Genet. 1, 345–347 (1992).

    CAS  PubMed  Google Scholar 

  83. Finckh, U. et al. Novel mutations and repeated findings of mutations in familial Alzheimer disease. Neurogenetics 6, 85–89 (2005).

    CAS  PubMed  Google Scholar 

  84. Gan, C.-L., Zhang, T. & Lee, T. H. The genetics of Alzheimer’s disease in the Chinese population. Int. J. Mol. Sci. 21, 2381 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Karch, C. M. & Goate, A. M. Alzheimer’s disease risk genes and mechanisms of disease pathogenesis. Biol. Psychiatry 77, 43–51 (2015).

    CAS  PubMed  Google Scholar 

  86. Neve, R. L., Finch, E. A. & Dawes, L. R. Expression of the Alzheimer amyloid precursor gene transcripts in the human brain. Neuron 1, 669–677 (1988).

    CAS  PubMed  Google Scholar 

  87. Tanzi, R. E. et al. Protease inhibitor domain encoded by an amyloid protein precursor mRNA associated with Alzheimer’s disease. Nature 331, 528–530 (1988).

    CAS  PubMed  Google Scholar 

  88. Wang, X. et al. Modifications and trafficking of APP in the pathogenesis of Alzheimer’s disease. Front. Mol. Neurosci. 10, 294 (2017).

    PubMed  PubMed Central  Google Scholar 

  89. Golde, T. E., Estus, S., Usiak, M., Younkin, L. H. & Younkin, S. G. Expression of β amyloid protein precursor mRNAs: recognition of a novel alternatively spliced form and quantitation in Alzheimer’s disease using PCR. Neuron 4, 253–267 (1990).

    CAS  PubMed  Google Scholar 

  90. Matsui, T. et al. Expression of APP pathway mRNAs and proteins in Alzheimer’s disease. Brain Res. 1161, 116–123 (2007).

    CAS  PubMed  Google Scholar 

  91. Barrachina, M. et al. Amyloid-β deposition in the cerebral cortex in dementia with Lewy bodies is accompanied by a relative increase in AβPP mRNA isoforms containing the Kunitz protease inhibitor. Neurochem. Int. 46, 253–260 (2005).

    CAS  PubMed  Google Scholar 

  92. Zhan, S. S., Sandbrink, R., Beyreuther, K. & Schmitt, H. P. APP with Kunitz type protease inhibitor domain (KPI) correlates with neuritic plaque density but not with cortical synaptophysin immunoreactivity in Alzheimer’s disease and non-demented aged subjects: a multifactorial analysis. Clin. Neuropathol. 14, 142–149 (1995).

    CAS  PubMed  Google Scholar 

  93. Johnson, S. A., McNeill, T., Cordell, B. & Finch, C. E. Relation of neuronal APP-751/APP-695 mRNA ratio and neuritic plaque density in Alzheimer’s disease. Science 248, 854–857 (1990).

    CAS  PubMed  Google Scholar 

  94. Moir, R. D. et al. Relative increase in Alzheimer’s disease of soluble forms of cerebral Aβ amyloid protein precursor containing the Kunitz protease inhibitory domain. J. Biol. Chem. 273, 5013–5019 (1998).

    CAS  PubMed  Google Scholar 

  95. Han, S. et al. Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus. BMC Med. Genomics 12, 13 (2019).

    PubMed  PubMed Central  Google Scholar 

  96. Tanaka, S., Nakamura, S. & Ueda, K. [Expression of amyloid beta-protein gene in Alzheimer’s disease]. Rinsho Byori 38, 489–493 (1990).

    CAS  PubMed  Google Scholar 

  97. Ho, L., Fukuchi, K. & Younkin, S. G. The alternatively spliced Kunitz protease inhibitor domain alters amyloid β protein precursor processing and amyloid β protein production in cultured cells. J. Biol. Chem. 271, 30929–30934 (1996).

    CAS  PubMed  Google Scholar 

  98. Belyaev, N. D. et al. The transcriptionally active amyloid precursor protein (APP) intracellular domain is preferentially produced from the 695 isoform of APP in a β-secretase-dependent pathway. J. Biol. Chem. 285, 41443–41454 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Khalifa, N. B. et al. Contribution of Kunitz protease inhibitor and transmembrane domains to amyloid precursor protein homodimerization. Neurodegener. Dis. 10, 92–95 (2012).

    PubMed  Google Scholar 

  100. Eggert, S. et al. Dimerization leads to changes in APP (amyloid precursor protein) trafficking mediated by LRP1 and SorLA. Cell. Mol. Life Sci. 75, 301–322 (2018).

    CAS  PubMed  Google Scholar 

  101. Chua, L.-M., Lim, M.-L. & Wong, B.-S. The Kunitz-protease inhibitor domain in amyloid precursor protein reduces cellular mitochondrial enzymes expression and function. Biochem. Biophys. Res. Commun. 437, 642–647 (2013).

    CAS  PubMed  Google Scholar 

  102. Wamsley, B. et al. Rbfox1 mediates cell-type-specific splicing in cortical interneurons. Neuron 100, 846–859.e7 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Alam, S., Suzuki, H. & Tsukahara, T. Alternative splicing regulation of APP exon 7 by RBFox proteins. Neurochem. Int. 78, 7–17 (2014).

    CAS  PubMed  Google Scholar 

  104. Alkallas, R., Fish, L., Goodarzi, H. & Najafabadi, H. S. Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease. Nat. Commun. 8, 909 (2017).

    PubMed  PubMed Central  Google Scholar 

  105. Vuong, J. K. et al. PTBP1 and PTBP2 serve both specific and redundant functions in neuronal pre-mRNA splicing. Cell Rep. 17, 2766–2775 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Makeyev, E. V., Zhang, J., Carrasco, M. A. & Maniatis, T. The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27, 435–448 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Smith, P., Al Hashimi, A., Girard, J., Delay, C. & Hébert, S. S. In vivo regulation of amyloid precursor protein neuronal splicing by microRNAs. J. Neurochem. 116, 240–247 (2011).

    CAS  PubMed  Google Scholar 

  108. Han, D., Dong, X., Zheng, D. & Nao, J. MiR-124 and the underlying therapeutic promise of neurodegenerative disorders. Front. Pharmacol. 10, 01555 (2020).

    Google Scholar 

  109. Ehehalt, R. et al. Splice variants of the b-site APP-cleaving enzyme BACE1 in human brain and pancreas. Biochem. Biophys. Res. Commun. 293, 240–247 (2002).

    Google Scholar 

  110. Holsinger, R. M. D., Goense, N., Bohorquez, J. & Strappe, P. Splice variants of the Alzheimer’s disease beta-secretase, BACE1. Neurogenetics 14, 1–9 (2013).

    CAS  PubMed  Google Scholar 

  111. Mowrer, K. R. & Wolfe, M. S. Promotion of BACE1 mRNA alternative splicing reduces amyloid β-peptide production. J. Biol. Chem. 283, 18694–18701 (2008).

    CAS  PubMed  Google Scholar 

  112. Tanahashi, H. & Tabira, T. Three novel alternatively spliced isoforms of the human beta-site amyloid precursor protein cleaving enzyme (BACE) and their effect on amyloid beta-peptide production. Neurosci. Lett. 307, 9–12 (2001).

    CAS  PubMed  Google Scholar 

  113. Kolisnyk, B. et al. Cholinergic surveillance over hippocampal RNA metabolism and Alzheimer’s-like pathology. Cereb. Cortex 27, 3553–3567 (2017).

    PubMed  Google Scholar 

  114. Berson, A. et al. Cholinergic-associated loss of hnRNP-A/B in Alzheimer’s disease impairs cortical splicing and cognitive function in mice. EMBO Mol. Med. 4, 730–742 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Kolisnyk, B. et al. Cholinergic regulation of hnRNPA2/B1 translation by M1 muscarinic receptors. J. Neurosci. 36, 6287–6296 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Hampel, H. et al. The β-secretase BACE1 in Alzheimer’s disease. Biol. Psychiatry 89, 745–756 (2021).

    CAS  PubMed  Google Scholar 

  117. Selkoe, D. J. & Hardy, J. The amyloid hypothesis of Alzheimer’s disease at 25 years. EMBO Mol. Med. 8, 595–608 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Arber, C. et al. Familial Alzheimer’s disease patient-derived neurons reveal distinct mutation-specific effects on amyloid beta. Mol. Psychiatry 25, 2919–2931 (2020).

    PubMed  Google Scholar 

  119. Sun, L., Zhou, R., Yang, G. & Shi, Y. Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase. Proc. Natl Acad. Sci. USA 114, E476–E485 (2017).

    CAS  PubMed  Google Scholar 

  120. Schellenberg, G. D. et al. Genetic linkage evidence for a familial Alzheimer’s disease locus on chromosome 14. Science 258, 668–671 (1992).

    CAS  PubMed  Google Scholar 

  121. De Jonghe, C. et al. Aberrant splicing in the presenilin-1 intron 4 mutation causes presenile Alzheimer’s disease by increased Aβ42 secretion. Hum. Mol. Genet. 8, 1529–1540 (1999).

    PubMed  Google Scholar 

  122. Aguilar, L. R. et al. Genetic origin of a large family with a novel PSEN1 mutation (ILE416THR). Alzheimers Dement. 15, 709–719 (2019).

    PubMed Central  Google Scholar 

  123. Kwok, J. B. J. et al. Presenilin-1 mutation L271V results in altered exon 8 splicing and Alzheimer’s disease with non-cored plaques and no neuritic dystrophy. J. Biol. Chem. 278, 6748–6754 (2003).

    CAS  PubMed  Google Scholar 

  124. Rogaev, E. I. et al. Analysis of the 5′ sequence, genomic structure, and alternative splicing of the presenilin-1 gene (PSEN1) associated with early onset Alzheimer disease. Genomics 40, 415–424 (1997).

    CAS  PubMed  Google Scholar 

  125. Scheper, W., Zwart, R. & Baas, F. Alternative splicing in the N-terminus of Alzheimer’s presenilin 1. Neurogenetics 5, 223–227 (2004).

    CAS  PubMed  Google Scholar 

  126. Braggin, J. E. et al. Alternative splicing in a presenilin 2 variant associated with Alzheimer disease. Ann. Clin. Transl. Neurol. 6, 762–777 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. Bu, G. Apolipoprotein E and its receptors in Alzheimer’s disease: pathways, pathogenesis and therapy. Nat. Rev. Neurosci. 10, 333–344 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Liu, C.-C., Kanekiyo, T., Xu, H. & Bu, G. Apolipoprotein E and Alzheimer disease: risk, mechanisms, and therapy. Nat. Rev. Neurol. 9, 106–118 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Tang, M.-X. et al. The APOE-4 allele and the risk of Alzheimer disease among African Americans, Whites, and Hispanics. J. Am. Med. Assoc. 279, 751–755 (1998).

    CAS  Google Scholar 

  130. Farrer, L. A. et al. Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease: a meta-analysis. J. Am. Med. Assoc. 278, 1349–1356 (1997).

    CAS  Google Scholar 

  131. Qian, J. et al. APOE-related risk of mild cognitive impairment and dementia for prevention trials: an analysis of four cohorts. PLoS Med. 14, e1002254 (2017).

    PubMed  PubMed Central  Google Scholar 

  132. Twine, N. A., Janitz, K., Wilkins, M. R. & Janitz, M. Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer’s disease. PLoS ONE 6, e16266 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  133. Mills, J. D. et al. The alternative splicing of the apolipoprotein E gene is unperturbed in the brains of Alzheimer’s disease patients. Mol. Biol. Rep. 41, 6365–6376 (2014).

    CAS  PubMed  Google Scholar 

  134. Xu, Q. et al. Intron-3 retention/splicing controls neuronal expression of apolipoprotein E in the CNS. J. Neurosci. 28, 1452–1459 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  135. Gallo, C. M., Ho, A. & Beffert, U. ApoER2: functional tuning through splicing. Front. Mol. Neurosci. 13, 144 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Zhang, Y. et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J. Neurosci. 34, 11929–11947 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. Gallo, C. M., Labadorf, A. T., Ho, A. & Beffert, U. Single molecule, long-read Apoer2 sequencing identifies conserved and species-specific splicing patterns. Genomics 114, 110318 (2022).

    CAS  PubMed  Google Scholar 

  138. Beffert, U. et al. Modulation of synaptic plasticity and memory by Reelin involves differential splicing of the lipoprotein receptor Apoer2. Neuron 47, 567–579 (2005). This study shows that the ApoER2 alternative exon is necessary for Reelin-induced tyrosine phosphorylation of NMDA receptor subunits and hence has an important role in modulating synaptic transmission and memory processes.

    CAS  PubMed  Google Scholar 

  139. Hinrich, A. J. et al. Therapeutic correction of ApoER2 splicing in Alzheimer’s disease mice using antisense oligonucleotides. EMBO Mol. Med. 8, 328–345 (2016). This study targets the dysregulated splice isoforms of the Apoe receptor ApoER2 by using an ASO to promote an alternative splicing event that rescued synaptic function and alleviate cognitive defects in mice without altering total beta-amyloid levels.

    CAS  PubMed  PubMed Central  Google Scholar 

  140. Beffert, U. et al. ApoE receptor 2 controls neuronal survival in the adult brain. Curr. Biol. 16, 2446–2452 (2006).

    CAS  PubMed  Google Scholar 

  141. Samii, A., Nutt, J. G. & Ransom, B. R. Parkinson’s disease. Lancet 363, 1783–1793 (2004).

    CAS  PubMed  Google Scholar 

  142. Spillantini, M. G. et al. α-Synuclein in Lewy bodies. Nature 388, 839–840 (1997).

    CAS  PubMed  Google Scholar 

  143. Burré, J. The synaptic function of α-synuclein. J. Parkinsons Dis. 5, 699–713 (2015).

    PubMed  PubMed Central  Google Scholar 

  144. Poewe, W. et al. Parkinson disease. Nat. Rev. Dis. Prim. 3, 17013 (2017).

    PubMed  Google Scholar 

  145. Lunati, A., Lesage, S. & Brice, A. The genetic landscape of Parkinson’s disease. Rev. Neurol. 174, 628–643 (2018).

    CAS  PubMed  Google Scholar 

  146. Polymeropoulos, M. H. et al. Mutation in the α-synuclein gene identified in families with Parkinson’s disease. Science 276, 2045–2047 (1997).

    CAS  PubMed  Google Scholar 

  147. Singleton, A. B. et al. α-Synuclein locus triplication causes Parkinson’s disease. Science 302, 841 (2003).

    CAS  PubMed  Google Scholar 

  148. Gómez-Benito, M. et al. Modeling Parkinson’s disease with the α-synuclein protein. Front. Pharmacol. 11, 356 (2020).

    PubMed  PubMed Central  Google Scholar 

  149. Beyer, K. & Ariza, A. α-Synuclein posttranslational modification and alternative splicing as a trigger for neurodegeneration. Mol. Neurobiol. 47, 509–524 (2013).

    CAS  PubMed  Google Scholar 

  150. Tseng, E. et al. The landscape of SNCA transcripts across synucleinopathies: new insights from long reads sequencing analysis. Front. Genet. 10, 584 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  151. Campion, D. et al. The NACP/synuclein gene: chromosomal assignment and screening for alterations in Alzheimer disease. Genomics 26, 254–257 (1995).

    CAS  PubMed  Google Scholar 

  152. Beyer, K. et al. Identification and characterization of a new alpha-synuclein isoform and its role in Lewy body diseases. Neurogenetics 9, 15–23 (2008).

    PubMed  Google Scholar 

  153. Beyer, K. et al. Differential expression of α-synuclein, parkin, and synphilin-1 isoforms in Lewy body disease. Neurogenetics 9, 163–172 (2008).

    CAS  PubMed  Google Scholar 

  154. Beyer, K. et al. Differential expression of α-synuclein isoforms in dementia with Lewy bodies. Neuropathol. Appl. Neurobiol. 30, 601–607 (2004).

    CAS  PubMed  Google Scholar 

  155. McLean, J. R., Hallett, P. J., Cooper, O., Stanley, M. & Isacson, O. Transcript expression levels of full-length α-synuclein and its three alternatively spliced variants in Parkinson’s disease brain regions and in a transgenic mouse model of α-synuclein overexpression. Mol. Cell Neurosci. 49, 230–239 (2012).

    CAS  PubMed  Google Scholar 

  156. Cardo, L. F. et al. α-Synuclein transcript isoforms in three different brain regions from Parkinson’s disease and healthy subjects in relation to the SNCA rs356165/rs11931074 polymorphisms. Neurosci. Lett. 562, 45–49 (2014).

    CAS  PubMed  Google Scholar 

  157. Beyer, K. et al. Low α-synuclein 126 mRNA levels in dementia with Lewy bodies and Alzheimer disease. NeuroReport 17, 1327–1330 (2006).

    CAS  PubMed  Google Scholar 

  158. Brudek, T. et al. Altered α-synuclein, parkin, and synphilin isoform levels in multiple system atrophy brains. J. Neurochem. 136, 172–185 (2016).

    CAS  PubMed  Google Scholar 

  159. Soll, L. G. et al. α-Synuclein-112 impairs synaptic vesicle recycling consistent with its enhanced membrane binding properties. Front. Cell Dev. Biol. 8, 405 (2020).

    PubMed  PubMed Central  Google Scholar 

  160. McCarthy, J. J. et al. The effect of SNCA 3′ region on the levels of SNCA-112 splicing variant. Neurogenetics 12, 59–64 (2011).

    CAS  PubMed  Google Scholar 

  161. Manda, K. M., Yedlapudi, D., Korukonda, S., Bojja, S. & Kalivendi, S. V. The chaperone-like activity of α-synuclein attenuates aggregation of its alternatively spliced isoform, 112-synuclein in vitro: plausible cross-talk between isoforms in protein aggregation. PLoS ONE 9, e98657 (2014).

    PubMed  PubMed Central  Google Scholar 

  162. Oueslati, A. Implication of alpha-synuclein phosphorylation at S129 in synucleinopathies: what have we learned in the last decade? J. Parkinsons Dis. 6, 39–51 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  163. Gámez-Valero, A. & Beyer, K. Alternative splicing of α- and β-synuclein genes plays differential roles in synucleinopathies. Genes 9, 63 (2018).

    PubMed  PubMed Central  Google Scholar 

  164. Bungeroth, M. et al. Differential aggregation properties of α-synuclein isoforms. Neurobiol. Aging 35, 1913–1919 (2014).

    CAS  PubMed  Google Scholar 

  165. Tan, S. H. et al. Emerging pathways to neurodegeneration: dissecting the critical molecular mechanisms in Alzheimer’s disease, Parkinson’s disease. Biomed. Pharmacother. 111, 765–777 (2019).

    CAS  PubMed  Google Scholar 

  166. Kalivendi, S. V., Yedlapudi, D., Hillard, C. J. & Kalyanaraman, B. Oxidants induce alternative splicing of alpha-synuclein: implications for Parkinson’s disease. Free Radic. Biol. Med. 48, 377–383 (2010).

    CAS  PubMed  Google Scholar 

  167. Barrie, E. S. et al. Alpha-synuclein mRNA isoform formation and translation affected by polymorphism in the human SNCA 3′ UTR. Mol. Genet. Genom. Med. 6, 565–574 (2018).

    CAS  Google Scholar 

  168. Shehadeh, L. A. et al. SRRM2, a potential blood biomarker revealing high alternative splicing in Parkinson’s disease. PLoS ONE 5, e9104 (2010).

    PubMed  PubMed Central  Google Scholar 

  169. Molochnikov, L. et al. A molecular signature in blood identifies early Parkinson’s disease. Mol. Neurodegener. 7, 26 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  170. Cooper-Knock, J. et al. Gene expression profiling in human neurodegenerative disease. Nat. Rev. Neurol. 8, 518–530 (2012).

    CAS  PubMed  Google Scholar 

  171. Knopman, D. S. & Roberts, R. O. Estimating the number of persons with frontotemporal lobar degeneration in the US population. J. Mol. Neurosci. 45, 330–335 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  172. Finger, E. C. Frontotemporal dementias. Continuum 22, 464–489 (2016).

    PubMed  PubMed Central  Google Scholar 

  173. Lulé, D. E. et al. Story of the ALS–FTD continuum retold: rather two distinct entities. J. Neurol. Neurosurg. Psychiatry 90, 586–589 (2019).

    PubMed  Google Scholar 

  174. Abramzon, Y. A., Fratta, P., Traynor, B. J. & Chia, R. The overlapping genetics of amyotrophic lateral sclerosis and frontotemporal dementia. Front. Neurosci. 14, 42 (2020).

    PubMed  PubMed Central  Google Scholar 

  175. Butti, Z. & Patten, S. A. RNA dysregulation in amyotrophic lateral sclerosis. Front. Genet. 9, 712 (2019).

    PubMed  PubMed Central  Google Scholar 

  176. Lynch, T. et al. Clinical characteristics of a family with chromosome 17‐linked disinhibition–dementia–Parkinsonism–amyotrophy complex. Neurology 44, 1878–1878 (1994).

    CAS  PubMed  Google Scholar 

  177. Wilhelmsen, K. C., Lynch, T., Pavlou, E., Higgins, M. & Nygaard, T. G. Localization of disinhibition–dementia–parkinsonism–amyotrophy complex to 17q21-22. Am. J. Hum. Genet. 55, 1159–1165 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  178. Sima, Aa. F. et al. The neuropathology of chromosome 17-linked dementia. Ann. Neurol. 39, 734–743 (1996).

    CAS  PubMed  Google Scholar 

  179. DeJesus-Hernandez, M. et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245–256 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  180. Renton, A. E. et al. A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72, 257–268 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  181. Majounie, E. et al. Frequency of the C9orf72 hexanucleotide repeat expansion in patients with amyotrophic lateral sclerosis and frontotemporal dementia: a cross-sectional study. Lancet Neurol. 11, 323–330 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  182. Gendron, T. F. & Petrucelli, L. Disease mechanisms of C9ORF72 repeat expansions. Cold Spring Harb. Perspect. Med. 8, a024224 (2018).

    PubMed  PubMed Central  Google Scholar 

  183. Lee, Y.-B. et al. Hexanucleotide repeats in ALS/FTD form length-dependent RNA foci, sequester RNA binding proteins, and are neurotoxic. Cell Rep. 5, 1178–1186 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  184. Conlon, E. G. et al. The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains. eLife 5, e17820 (2016).

    PubMed  PubMed Central  Google Scholar 

  185. Kwon, I. et al. Poly-dipeptides encoded by the C9orf72 repeats bind nucleoli, impede RNA biogenesis, and kill cells. Science 345, 1139–1145 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  186. Yin, S. et al. Evidence that C9ORF72 dipeptide repeat proteins associate with U2 snRNP to cause mis-splicing in ALS/FTD patients. Cell Rep. 19, 2244–2256 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  187. Neumann, M. et al. Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314, 130–133 (2006).

    CAS  PubMed  Google Scholar 

  188. Arai, T. et al. TDP-43 is a component of ubiquitin-positive tau-negative inclusions in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Biochem. Biophys. Res. Commun. 351, 602–611 (2006).

    CAS  PubMed  Google Scholar 

  189. Cairns, N. J. et al. TDP-43 in familial and sporadic frontotemporal lobar degeneration with ubiquitin inclusions. Am. J. Pathol. 171, 227–240 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  190. Perrone, B. et al. Alternative splicing of ALS genes: misregulation and potential therapies. Cell Mol. Neurobiol. 40, 1–14 (2020).

    PubMed  Google Scholar 

  191. Ling, J. P., Pletnikova, O., Troncoso, J. C. & Wong, P. C. TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD. Science 349, 650–655 (2015). This study demonstrates that the loss of TDP-43 induces cryptic exon splicing in ALS–FTD patient tissue with TDP-43 pathology.

    CAS  PubMed  PubMed Central  Google Scholar 

  192. Deshaies, J.-E. et al. TDP-43 regulates the alternative splicing of hnRNP A1 to yield an aggregation-prone variant in amyotrophic lateral sclerosis. Brain 141, 1320–1333 (2018).

    PubMed  PubMed Central  Google Scholar 

  193. Melamed, Z. et al. Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration. Nat. Neurosci. 22, 180–190 (2019). Together with Klim et al. (2019), this study was among the first to establish a functional connection between the loss of TDP-43 splicing function and the occurrence of cryptic splicing events in stathmin-2 that promoted disease pathology in both sporadic and familial ALS.

    CAS  PubMed  PubMed Central  Google Scholar 

  194. Klim, J. R. et al. ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. Nat. Neurosci. 22, 167–179 (2019). Together with Melamed et al. (2019), this study was among the first to establish a functional connection between the loss of TDP-43 splicing function and the occurrence of cryptic splicing events in stathmin-2 that promoted disease pathology in both sporadic and familial ALS.

    CAS  PubMed  PubMed Central  Google Scholar 

  195. Brown, A.-L. et al. TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A. Nature 603, 131–137 (2022). Together with Ma et al. (2022), this study links TDP-43 depletion with dysregulated splicing of UNC13a, a key neuronal protein that is functionally impaired in patients with FTD with TDP-43 proteinopathy.

    CAS  PubMed  PubMed Central  Google Scholar 

  196. Ma, X. R. et al. TDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A. Nature 603, 124–130 (2022). Together with Brown et al. (2022), this study links TDP-43 depletion with dysregulated splicing of UNC13a, a key neuronal protein that is functionally impaired in patients with FTD with TDP-43 proteinopathy.

    CAS  PubMed  PubMed Central  Google Scholar 

  197. Ishigaki, S. & Sobue, G. Importance of functional loss of FUS in FTLD/ALS. Front. Mol. Biosci. 5, 44 (2018).

    PubMed  PubMed Central  Google Scholar 

  198. Humphrey, J. et al. FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention. Nucleic Acids Res. 48, 6889–6905 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  199. Kim, G., Gautier, O., Tassoni-Tsuchida, E., Ma, X. R. & Gitler, A. D. ALS genetics: gains, losses, and implications for future therapies. Neuron 108, 822–842 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  200. Korobeynikov, V. A., Lyashchenko, A. K., Blanco-Redondo, B., Jafar-Nejad, P. & Shneider, N. A. Antisense oligonucleotide silencing of FUS expression as a therapeutic approach in amyotrophic lateral sclerosis. Nat. Med. 28, 104–116 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  201. Paulson, H. in Handbook of Clinical Neurology, Vol. 147 (eds Geschwind, D. H., Paulson, H. L. & Klein, C.) Ch. 9, 105–123 (Elsevier, 2018).

  202. Zhang, N. & Ashizawa, T. RNA toxicity and foci formation in microsatellite expansion diseases. Curr. Opin. Genet. Dev. 44, 17–29 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  203. Du, H. et al. Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy. Nat. Struct. Mol. Biol. 17, 187–193 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  204. Turner, C. & Hilton-Jones, D. Myotonic dystrophy: diagnosis, management and new therapies. Curr. Opin. Neurol. 27, 599 (2014).

    PubMed  Google Scholar 

  205. Goodwin, M. et al. MBNL sequestration by toxic RNAs and RNA mis-processing in the myotonic dystrophy brain. Cell Rep. 12, 1159–1168 (2015). This study shows that MBNL2 proteins are directly sequestered by microsatellite expansion RNAs in the myotonic dystrophy brain, resulting in disruption of the normal MBNL2 function in regulating alternative splicing.

    CAS  PubMed  PubMed Central  Google Scholar 

  206. Charlet-B, N. et al. Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing. Mol. Cell 10, 45–53 (2002).

    CAS  PubMed  Google Scholar 

  207. Kanadia, R. N. et al. A muscleblind knockout model for myotonic dystrophy. Science 302, 1978–1980 (2003).

    CAS  PubMed  Google Scholar 

  208. Berg, J., Jiang, H., Thornton, C. A. & Cannon, S. C. Truncated ClC-1 mRNA in myotonic dystrophy exerts a dominant-negative effect on the Cl current. Neurology 63, 2371–2375 (2004).

    CAS  PubMed  Google Scholar 

  209. Ashizawa, T., Öz, G. & Paulson, H. L. Spinocerebellar ataxias: prospects and challenges for therapy development. Nat. Rev. Neurol. 14, 590–605 (2018).

    PubMed  PubMed Central  Google Scholar 

  210. Hale, M. A., Johnson, N. E. & Berglund, J. A. Repeat-associated RNA structure and aberrant splicing. Biochim. Biophys. Acta Gene Regul. Mech. 1862, 194405 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  211. Li, D., McIntosh, C. S., Mastaglia, F. L., Wilton, S. D. & Aung-Htut, M. T. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl. Neurodegener. 10, 16 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  212. Tabrizi, S. J., Flower, M. D., Ross, C. A. & Wild, E. J. Huntington disease: new insights into molecular pathogenesis and therapeutic opportunities. Nat. Rev. Neurol. 16, 529–546 (2020).

    PubMed  Google Scholar 

  213. Elorza, A. et al. Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors. Brain 144, 2009–2023 (2021).

    PubMed  PubMed Central  Google Scholar 

  214. Schilling, J. et al. Deregulated splicing is a major mechanism of RNA-induced toxicity in Huntington’s disease. J. Mol. Biol. 431, 1869–1877 (2019).

    CAS  PubMed  Google Scholar 

  215. Sathasivam, K. et al. Aberrant splicing of HTT generates the pathogenic exon 1 protein in Huntington disease. Proc. Natl Acad. Sci. USA 110, 2366–2370 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  216. Franich, N. R. et al. Phenotype onset in Huntington’s disease knock-in mice is correlated with the incomplete splicing of the mutant huntingtin gene. J. Neurosci. Res. 97, 1590–1605 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  217. Neueder, A. et al. The pathogenic exon 1 HTT protein is produced by incomplete splicing in Huntington’s disease patients. Sci. Rep. 7, 1307 (2017).

    PubMed  PubMed Central  Google Scholar 

  218. Mason, M. A. et al. Silencing Srsf6 does not modulate incomplete splicing of the huntingtin gene in Huntington’s disease models. Sci. Rep. 10, 14057 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  219. Gu, X. et al. Uninterrupted CAG repeat drives striatum-selective transcriptionopathy and nuclear pathogenesis in human Huntingtin BAC mice. Neuron 110, 1173–1192.e7 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  220. Levin, A. A. Treating disease at the RNA level with oligonucleotides. N. Engl. J. Med. 380, 57–70 (2019).

    PubMed  Google Scholar 

  221. Zamecnik, P. C. & Stephenson, M. L. Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. Proc. Natl Acad. Sci. USA 75, 280–284 (1978).

    CAS  PubMed  PubMed Central  Google Scholar 

  222. Stephenson, M. L. & Zamecnik, P. C. Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. Proc. Natl Acad. Sci. USA 75, 285–288 (1978).

    CAS  PubMed  PubMed Central  Google Scholar 

  223. Mendell, J. R. et al. Longitudinal effect of eteplirsen versus historical control on ambulation in Duchenne muscular dystrophy. Ann. Neurol. 79, 257–271 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  224. Verma, A. Recent advances in antisense oligonucleotide therapy in genetic neuromuscular diseases. Ann. Indian Acad. Neurol. 21, 3–8 (2018).

    PubMed  PubMed Central  Google Scholar 

  225. Alfano, L. N. et al. Long-term treatment with eteplirsen in nonambulatory patients with Duchenne muscular dystrophy. Medicine 98, e15858 (2019).

    PubMed  PubMed Central  Google Scholar 

  226. Pascual-Morena, C. et al. Restorative treatments of dystrophin expression in Duchenne muscular dystrophy: a systematic review. Ann. Clin. Transl. Neurol. 7, 1738–1752 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  227. Finkel, R. S. et al. Nusinersen versus Sham control in infantile-onset spinal muscular atrophy. N. Engl. J. Med. 377, 1723–1732 (2017). This study reported the clinical efficacy and safety of a splice-switching ASO for spinal muscular atrophy in infants, supporting the modulation of targeted pre-mRNA splicing as a therapeutic approach for treating genetic disorders.

    CAS  PubMed  Google Scholar 

  228. Kim, J. et al. Patient-customized oligonucleotide therapy for a rare genetic disease. N. Engl. J. Med. 381, 1644–1652 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  229. Hua, Y. et al. Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev. 24, 1634–1644 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  230. Goodkey, K., Aslesh, T., Maruyama, R. & Yokota, T. in Exon Skipping and Inclusion Therapies: Methods and Protocols (eds Yokota, T. & Maruyama, R.) 69–76 (Springer, 2018).

  231. Ottesen, E. W. ISS-N1 makes the first FDA-approved drug for spinal muscular atrophy. Transl. Neurosci. 8, 1–6 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  232. Suñé-Pou, M. et al. Targeting splicing in the treatment of human disease. Genes 8, 87 (2017).

    PubMed  PubMed Central  Google Scholar 

  233. Schoch, K. M. et al. Increased 4R-tau induces pathological changes in a human-tau mouse model. Neuron 90, 941–947 (2016). This study shows that increasing 4R-tau expression, without altering the total tau level, leads to tau pathology and abnormal behaviour in a mouse model, providing direct evidence supporting the role of splicing deregulation in tauopathy.

    CAS  PubMed  PubMed Central  Google Scholar 

  234. Chang, J. L. et al. Targeting amyloid-β precursor protein, APP, splicing with antisense oligonucleotides reduces toxic amyloid-β production. Mol. Ther. 26, 1539–1551 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  235. Ring, S. et al. The secreted β-amyloid precursor protein ectodomain APPsα is sufficient to rescue the anatomical, behavioral, and electrophysiological abnormalities of APP-deficient mice. J. Neurosci. 27, 7817–7826 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  236. Chauhan, N. B. & Siegel, G. J. Antisense inhibition at the β-secretase-site of β-amyloid precursor protein reduces cerebral amyloid and acetyl cholinesterase activity in Tg2576. Neuroscience 146, 143–151 (2007).

    CAS  PubMed  Google Scholar 

  237. Daoutsali, E. et al. Antisense oligonucleotide-induced amyloid precursor protein splicing modulation as a therapeutic approach for Dutch-type cerebral amyloid angiopathy. Nucleic Acid Ther. 31, 351–363 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  238. Zheng, H. et al. β-amyloid precursor protein-deficient mice show reactive gliosis and decreased locomotor activity. Cell 81, 525–531 (1995).

    CAS  PubMed  Google Scholar 

  239. Dawson, G. R. et al. Age-related cognitive deficits, impaired long-term potentiation and reduction in synaptic marker density in mice lacking the β-amyloid precursor protein. Neuroscience 90, 1–13 (1999).

    CAS  PubMed  Google Scholar 

  240. Müller, U. et al. Behavioral and anatomical deficits in mice homozygous for a modified beta-amyloid precursor protein gene. Cell 79, 755–765 (1994).

    PubMed  Google Scholar 

  241. Magara, F. et al. Genetic background changes the pattern of forebrain commissure defects in transgenic mice underexpressing the β-amyloid-precursor protein. Proc. Natl Acad. Sci. USA 96, 4656–4661 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  242. Klein, S. et al. Truncating mutations in APP cause a distinct neurological phenotype. Ann. Neurol. 80, 456–460 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  243. Kingwell, K. Double setback for ASO trials in Huntington disease. Nat. Rev. Drug Discov. 20, 412–413 (2021).

    CAS  PubMed  Google Scholar 

  244. Keller, C. G. et al. An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion. Nat. Commun. 13, 1150 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  245. Sreedharan, J. et al. TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis. Science 319, 1668–1672 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  246. Vance, C. et al. Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science 323, 1208–1211 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  247. Arnold, E. S. et al. ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43. Proc. Natl Acad. Sci. USA 110, E736–E745 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  248. Prudencio, M. et al. Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Nat. Neurosci. 18, 1175–1182 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  249. Dols-Icardo, O. et al. Motor cortex transcriptome reveals microglial key events in amyotrophic lateral sclerosis. Neurol. Neuroimmunol. Neuroinflamm. 7, e829 (2020).

    PubMed  PubMed Central  Google Scholar 

  250. D’Erchia, A. M. et al. Massive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS. Sci. Rep. 7, 10046 (2017).

    PubMed  PubMed Central  Google Scholar 

  251. Hasan, R. et al. Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions. Acta Neuropathol. 143, 383–401 (2022).

    CAS  PubMed  Google Scholar 

  252. Annese, A. et al. Whole transcriptome profiling of late-onset Alzheimer’s disease patients provides insights into the molecular changes involved in the disease. Sci. Rep. 8, 4282 (2018).

    PubMed  PubMed Central  Google Scholar 

  253. Wan, Y.-W. et al. Meta-analysis of the Alzheimer’s disease human brain transcriptome and functional dissection in mouse models. Cell Rep. 32, 107908 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  254. Raj, T. et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility. Nat. Genet. 50, 1584–1592 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  255. Salemi, M. et al. A transcriptome analysis of mRNAs and long non-coding RNAs in patients with Parkinson’s disease. Int. J. Mol. Sci. 23, 1535 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  256. Glaab, E. & Schneider, R. Comparative pathway and network analysis of brain transcriptome changes during adult aging and in Parkinson’s disease. Neurobiol. Dis. 74, 1–13 (2015).

    CAS  PubMed  Google Scholar 

  257. Jia, E. et al. Transcriptomic profiling of differentially expressed genes and related pathways in different brain regions in Parkinson’s disease. Neurosci. Lett. 732, 135074 (2020).

    CAS  PubMed  Google Scholar 

  258. Lin, L. et al. Transcriptome sequencing reveals aberrant alternative splicing in Huntington’s disease. Hum. Mol. Genet. 25, 3454–3466 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  259. Huang, L., Fang, L., Liu, Q., Torshizi, A. D. & Wang, K. Integrated analysis on transcriptome and behaviors defines HTT repeat-dependent network modules in Huntington’s disease. Genes Dis. 9, 479–493 (2022).

    CAS  PubMed  Google Scholar 

  260. Langfelder, P. et al. Integrated genomics and proteomics to define huntingtin CAG length-dependent networks in HD mice. Nat. Neurosci. 19, 623–633 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  261. Ingram, M. et al. Cerebellar transcriptome profiles of ATXN1 transgenic mice reveal SCA1 disease progression and protection pathways. Neuron 89, 1194–1207 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  262. Friedrich, J. et al. Antisense oligonucleotide-mediated ataxin-1 reduction prolongs survival in SCA1 mice and reveals disease-associated transcriptome profiles. JCI Insight 3, e123193 (2018).

    PubMed  PubMed Central  Google Scholar 

  263. Berger, A. et al. mRNA trans-splicing in gene therapy for genetic diseases. Wiley Interdiscip. Rev. RNA 7, 487–498 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  264. Kemaladewi, D. U. et al. Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism. Nat. Med. 23, 984–989 (2017).

    CAS  PubMed  Google Scholar 

  265. Rodriguez-Martin, T. et al. Reprogramming of tau alternative splicing by spliceosome-mediated RNA trans-splicing: implications for tauopathies. Proc. Natl Acad. Sci. USA 102, 15659–15664 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  266. Rodriguez-Martin, T. et al. Correction of tau mis-splicing caused by FTDP-17 MAPT mutations by spliceosome-mediated RNA trans- splicing. Hum. Mol. Genet. 18, 3266–3273 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  267. Wally, V., Murauer, E. M. & Bauer, J. W. Spliceosome-mediated trans-splicing: the therapeutic cut and paste. J. Investig. Dermatol. 132, 1959–1966 (2012).

    CAS  PubMed  Google Scholar 

  268. Yuan, J. et al. Genetic modulation of RNA splicing with a CRISPR-guided cytidine deaminase. Mol. Cell 72, 380–394.e7 (2018).

    CAS  PubMed  Google Scholar 

  269. Dastidar, S. et al. Efficient CRISPR/Cas9-mediated editing of trinucleotide repeat expansion in myotonic dystrophy patient-derived iPS and myogenic cells. Nucleic Acids Res. 46, 8275–8298 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  270. Montes, M., Sanford, B. L., Comiskey, D. F. & Chandler, D. S. RNA splicing and disease: animal models to therapies. Trends Genet. 35, 68–87 (2019).

    CAS  PubMed  Google Scholar 

  271. Batra, R. et al. Elimination of toxic microsatellite repeat expansion RNA by RNA-targeting Cas9. Cell 170, 899–912.e10 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work is supported by the US National Institutes of Health grants R01NS104041, R01NS125276 and R01MH116220 to S.Z.

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Nature Reviews Neuroscience thanks Tim Lynch, Felice Elefant who co-reviewed with Akanksha Bhatnagar, and Jimena Giudice who co-reviewed with Jessica Cote for their contribution to the peer review of this work.

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Glossary

Cryptic exon

Unannotated intronic sequences erroneously spliced into mRNA.

Untranslated regions

mRNA regions on each side of a coding sequence that are not translated into protein.

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Nikom, D., Zheng, S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat. Rev. Neurosci. 24, 457–473 (2023). https://doi.org/10.1038/s41583-023-00717-6

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