Using isogenic human induced pluripotent stem cell-derived MNs, it is shown that ALS4-associated SETX mutations induce progressive axonal defects and widespread transcriptomic alterations, including reduced expression or altered splicing of transcripts critical for neuronal function.
Abstract
RNA dysregulation is a recognized contributor to neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), the most common motor neuron (MN) disease. However, the molecular mechanisms linking defects in RNA metabolism to selective neuronal vulnerability remain poorly understood. Alterations in the cellular levels of R-loops –structures forming by reannealing of the nascent RNA with the template DNA during transcription- have been observed in neurodegeneration, but it is unclear how perturbations in R-loop homeostasis contribute to neuronal dysfunction. Here we investigate the molecular basis of a juvenile form of ALS dubbed ALS4 that is caused by mutations in the helicase SETX, which plays important roles in the resolution of R-loops and transcription termination. Using isogenic human induced pluripotent stem cell-derived MNs, we show that ALS4-associated SETX mutations induce progressive axonal defects and widespread transcriptomic alterations, including reduced expression or altered splicing of transcripts critical for neuronal function. ALS4 MNs exhibit a transcriptional signature marked by cellular stress, aberrant cell cycle re-entry, and compromised neuronal identity that is partially shared by other forms of ALS. Mechanistically, these defects are partly driven by downstream aberrant activation of the TGF-β signaling pathway, whose pharmacological inhibition ameliorates axonal defects. Finally, our analyses support a link between mutant SETX ectopic activity at R-loops and the observed alterations in RNA expression and splicing, providing new insights into how RNA dysregulation can drive neuronal dysfunction Altogether, our work reveals how perturbations at the interface of transcription and R-loop metabolism can reshape neuronal identity and drive disease. Teaser Deregulation of TGF-β signaling drives axonal defects and compromised motor neuron identity in senataxin-mediated ALS
Genetic mutations, altered RNA regulation, and protein aggregation are the main hallmarks of Parkinson’s disease (PD), a neurodegenerative disorder. Investigation into the molecular basis of the disease revealed that post-transcriptional regulation, specifically RNA processing, contributes to neuronal vulnerability in PD. Alterations in alternative splicing affecting genes involved in neuronal function and cellular homeostasis have been reported in PD, including SNCA, LRRK2, MAPT, PRKN, and BIN1. These alterations impact central neuronal pathways, including cytoskeletal maintenance, mitochondrial function, synaptic activity, oxidative stress, and intracellular trafficking. This review aims to provide an overview of alternative splicing in key PD gene transcripts, with a focus on their roles in pathogenesis and disease progression. Emerging data suggest that dysregulation of RNA binding proteins (RBPs) may influence RNA processing in PD. We will examine current evidence on the RNA regulatory networks in PD, highlighting the role of transcript isoforms and RBPs in neuronal dysfunction. Finally, we will discuss emerging experimental models such as 3D-brain organoids that offer new opportunities to investigate splicing regulation.
Maria Giusy Bruno, G. Menichetti, Angela Valentino et al.· Genes· 0 citations
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the progressive loss of motor neurons, with most cases lacking a clear genetic basis. Emerging evidence highlights the involvement of non-coding RNAs, particularly circular RNAs (circRNAs), in disease onset and progression. Here, we investigated circRNAs implicated in ALS and related motor neuron diseases (MNDs). Here we provide a general overview of circular RNA metabolism and cellular functions. We then present our systematic literature review that identified ALS-associated circRNAs, followed by in silico analyses of 15 circular RNA candidates that were selected based on most compelling data regarding ALS. Our results revealed that several circular RNAs regulate ALS-related genes, such as unfolded protein response, oxidative stress, cell cycle regulation, and apoptosis. Protein-RNA interaction analysis further showed that ALS-related circRNAs can sponge 20 RNA-binding proteins. Additionally, molecular docking analysis demonstrated that ALS-associated FUS variants significantly alter its binding affinity to circular RNAs. RNA-seq data from ALS patients confirmed significant alterations in the expression of host genes of ALS-related circRNAs and hub proteins in ALS-affected CNS tissues. Collectively, our findings identify circRNAs as potential key contributors to ALS pathogenesis.
R. Ataei, J. Amini, N. Sanadgol et al.· Neurobiology of Disease· 0 citations
Long non-coding RNAs (lncRNAs) are increasingly implicated in neurodegenerative disease, yet their roles in tauopathy remain poorly understood. Here, we defined the lncRNA landscape across iPSC-derived neurons, astrocytes, and microglia harboring the frontotemporal dementia-associated MAPT IVS10+16 mutation and investigated how lncRNA dysregulation interfaces with tau pathology. Transcriptomic analyses revealed extensive cell-type specific lncRNA expression changes, with neurons exhibiting the greatest degree of mutation-associated remodeling. Comparative analyses with MAPT IVS10+16 patient brain tissue identified NORAD and MIR22HG as lncRNAs significantly dysregulated across all three cell types and human brains. NORAD was also altered in Alzheimer’s disease and Parkinson’s disease brains, suggesting a broader role in neurodegenerative disease. Mechanistically, NORAD-associated protein networks converged on pathways related to RNA regulation, cytoskeletal organization, proteostasis, and tau interaction networks. Given the established role of NORAD in regulating PUM1 and PUM2 RNA-binding (pumilio) proteins, we examined the NORAD-pumilio axis and identified enrichment of pumilio-associated pathways linked to autophagy, endocytosis, proteostasis, and cytoskeletal regulation. NORAD depletion reduced tau seeding and uptake, whereas functional depletion of PUM1 or PUM2 increased both processes, supporting an antagonistic relationship between NORAD and pumilio signaling in modulation of tau aggregation. Together, these findings identify widespread lncRNA dysregulation across neural cell types in the setting of a MAPT mutation and nominate the NORAD-pumilio axis as a regulatory pathway linking RNA homeostasis and tau propagation biology.
Joseph E. Zemke, Guangming Huang, Emma Starr et al.· bioRxiv· 0 citations
Fragile X syndrome (FXS), the leading genetic cause of intellectual disability, arises from FMR1 gene silencing and the subsequent loss of the RNA-binding protein FMRP. N6-methyladenosine (m6A) is a prevalent mRNA modification essential for post-transcriptional regulation. FMRP binds and regulates the stability of m6A-containing transcripts. However, how FMRP deficiency impacts transcriptome-wide m6A modifications in FXS remains unknown. To address this, we generated cortical neurons from induced pluripotent stem cells (iPSCs) derived from healthy individuals and FXS patients. Electrophysiology recordings revealed synaptic and neuronal network defects in FXS iPSC-derived neurons. Transcriptome-wide analysis revealed striking m6A hypermethylation predominantly affecting synapse-associated transcripts. Mechanistically, we demonstrated that FMRP deficiency drives the aberrant translational upregulation of core m6A writers, a causal relationship definitively validated using CGG-corrected isogenic control lines. Targeted genetic knockdown of the m6A writer METTL3 successfully rescued synaptic phenotypes in FXS neurons, whereas its overexpression in control neurons phenocopied these synaptic defects, confirming the causal role of m6A dysregulation in FXS pathology. Notably, pharmacological intervention with the METTL3 inhibitor STM-2457 normalized methylation on synapse-associated transcripts and restored synaptic transmission in FXS neurons. Together, our findings uncover an FMRP-dependent epitranscriptomic mechanism contributing to FXS pathogenesis and suggest a promising avenue for m6A-targeted therapies.
Lu Lu, Avijite Kumer Sarkar, Lan Dao et al.· Molecular Psychiatry· 0 citations