RNA splicing is a fundamental post-transcriptional process that removes introns from precursor messenger RNA (pre-mRNA) and joins exons to produce mature mRNA transcripts. This process is mediated by the spliceosome, a large ribonucleoprotein complex. Emerging evidence demonstrates that dysregulated RNA splicing plays a critical role in neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD)[1][2].
Alternative splicing, wherein a single gene can generate multiple mRNA isoforms, is particularly important for neuronal function. The nervous system has the highest rate of alternative splicing in the human body, and disruption of this process contributes to neurodegeneration through multiple mechanisms including altered protein isoform expression, toxic gain-of-function from aberrant splicing products, and loss of essential neuronal splice variants[3].
The human spliceosome consists of two distinct complexes:
Major spliceosome (U2-dependent): Processes ~99.5% of pre-mRNA introns. Core components include:
Minor spliceosome (U12-dependent): Processes ~0.5% of introns with distinct consensus sequences. Mutations in minor spliceosome components cause severe neurological disorders including microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)[4].
Key splicing regulators include:
Tau protein, encoded by the MAPT gene, is central to AD pathogenesis. Alternative splicing of MAPT exon 10 produces isoforms with 3 repeats (3R) or 4 repeats (4R) of the microtubule-binding domain. The 3R:4R ratio is tightly regulated in normal brain (1:1), and dysregulation toward 4R-tau predominance is a hallmark of several tauopathies including progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS)[5].
Splicing factors regulating tau exon 10:
Alternative splicing of APP (amyloid precursor protein) generates isoforms with varying amyloid-beta (Aβ) production potential. The APP-770 isoform contains the Kunitz protease inhibitor (KPI) domain, which enhances Aβ production. Increased KPI-containing APP isoforms have been observed in AD brain[6].
BACE1 (β-secretase) alternative splicing also influences amyloidogenesis. A BACE1 isoform lacking the prodomain shows altered subcellular localization and may contribute to pathogenic Aβ production in AD.
SNCA (alpha-synuclein) gene undergoes complex alternative splicing producing multiple isoforms (SNCA-126, SNCA-140, and smaller isoforms). Exon 3 inclusion/exclusion produces isoforms with or without the NAC (non-Aβ component) region implicated in aggregation. Altered SNCA splicing patterns have been reported in PD brain, with some studies showing increased inclusion of exon 5 in PD[7].
LRRK2 (leucine-rich repeat kinase 2) mutations are a common cause of familial PD. Alternative splicing of LRRK2 produces multiple isoforms with differential kinase activity. Studies have identified PD-associated splicing variants that affect LRRK2 subcellular localization and pathogenic signaling.
PRKN (parkin) and PINK1 (PTEN-induced kinase 1) are critical genes in mitochondrial quality control. Alternative splicing of these genes produces isoforms with different functional properties. Splicing variants in both genes have been associated with earlier onset of PD[8].
ALS and FTD share a common pathological feature: cytoplasmic aggregates of TDP-43 (TAR DNA-binding protein 43, encoded by TARDBP). Normally a nuclear protein, TDP-43 regulates RNA splicing of numerous neuronal transcripts. In ALS/FTD, TDP-43 mislocalization to the cytoplasm leads to:
The most common genetic cause of familial ALS and FTD is a GGGGCC hexanucleotide repeat expansion in the C9orf72 gene. This expansion causes disease through three mechanisms:
These mechanisms lead to widespread splicing dysregulation, including altered splicing of UNC13A, a critical determinant of ALS prognosis[10].
FUS (fused in sarcoma) is another RNA-binding protein mutated in familial ALS. FUS and TDP-43 cooperate in splicing regulation, and disease-causing mutations in either protein disrupt this partnership, leading to coordinated splicing abnormalities.
Antisense oligonucleotides (ASOs) can directly correct pathological splicing:
Several drug classes can modulate splicing:
Viral delivery of wild-type splicing factors:
| Factor | Gene | Function | Disease Association |
|---|---|---|---|
| TDP-43 | TARDBP | RNA binding, splicing regulation | ALS, FTD |
| FUS | FUS | RNA binding, splicing regulation | ALS |
| TAF15 | TAF15 | RNA binding, transcription/splicing | ALS |
| hnRNPA1 | HNRNPA1 | Splicing repression | ALS, Inclusion body myopathy |
| hnRNPA2B1 | HNRNPA2B1 | Splicing regulation | ALS, CBD |
| SRRM4 | SRRM4 | Neural-specific splicing | ALS, PD |
| RBFOX1 | RBFOX1 | Neuronal splicing regulation | Epilepsy, ASD |
Splicing signatures in cerebrospinal fluid (CSF) and blood represent promising biomarkers:
Patient-derived induced pluripotent stem cells (iPSCs) enable study of neuronal splicing:
Recent advances have clarified RNA splicing defects in neurodegeneration:
C9orf72 repeat expansion and splicing: Studies reveal that GGGGCC repeats in C9orf72 cause aberrant splicing of multiple genes through toxic dipeptide repeat proteins, with antisense oligonucleotides showing promise in clinical trials[11].
Spliceosome dysfunction in ALS/FTD: Research demonstrates that mutations in splicing factors (TDP-43, FUS, U2AF2) disrupt spliceosome assembly and cause widespread splicing changes in ALS and frontotemporal dementia[12].
Alternative splicing of tau: Recent work identifies specific tau splice variants (3R vs 4R tau) regulated by splicing factors, with implications for Alzheimer's disease and other tauopathies[13].
RNA-binding protein aggregates: Studies show that TDP-43 and FUS form stress granules and liquid-liquid phase separations that sequester mRNA splicing factors, disrupting neural function[14].
Therapeutic splice-modulating oligonucleotides: Antisense oligonucleotides targeting specific splice events (e.g., SOD1, C9orf72) have advanced to clinical trials for ALS[15].
Cooper TA, Wan L, Dreyfuss G. RNA and disease. Cell. 2014. ↩︎
Belzil VV, Rouleur G, Lagier-Tourenne C. RNA-binding proteins in neurodegenerative diseases. Adv Neurobiol. 2018. ↩︎
Raj B, Blencowe BJ. 'Alternative splicing in the mammalian nervous system: more insights then ever'. Trends Neurosci. 2015. ↩︎
He H, Liyanarachchi S, Akagi K, et al. Mutations in the U12 spliceosome gene MPN1 cause progressive neurodegeneration. Proc Natl Acad Sci U S A. 2019. ↩︎
Qian W, Liu F. Regulation of alternative splicing of tau exon 10. J Neurosci Res. 2014. ↩︎
Belyaev ND, Kellett KA, Beckett C, et al. The transcriptionally active amyloid precursor protein (APP) gene is differentially expressed in APP-transgenic models. J Neurosci Res. 2010. ↩︎
Beyer K, Humbert J, Ferrer A, et al. Alpha-synuclein variability in Parkinson's disease. J Neurosci Res. 2009. ↩︎
Sironi L, Cova M, Troglio L, et al. Alternative splicing of PRKN and PINK1 in Parkinson's disease. Parkinsonism Relat Disord. 2012. ↩︎
Lee EB, Lee VM, Trojanowski JQ. 'Gain-of-function mechanisms in ALS/FTD: not just a matter of proteins'. Trends Neurosci. 2012. ↩︎
Liu EY, Russ J, Wu K, et al. C9orf72 hypermethylation reduces cryptic splicing in ALS/FTD. bioRxiv. 2020. ↩︎
Zhang et al. C9orf72 splicing and antisense therapy. Nature Neuroscience. 2025. 2025. ↩︎
Lagier-Tourenne et al. Spliceosome dysfunction in ALS/FTD. Neuron. 2024. 2024. ↩︎
Himmrich et al. Alternative splicing of tau. Brain. 2025. 2025. ↩︎
Ramaswami et al. RNA-binding protein aggregates. Cell. 2024. 2024. ↩︎
Miller et al. Antisense oligonucleotides for ALS. Nature Medicine. 2025. 2025. ↩︎