Inhibition of the autophagic protein ULK1 attenuates axonal degeneration in vitro and in vivo and modulates differential splicing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA509593 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8313100_1.fastq.gz | Fastqsanger.gz | |||
| SRR8313100_2.fastq.gz | Fastqsanger.gz | |||
| SRR8313095_1.fastq.gz | Fastqsanger.gz | |||
| SRR8313095_2.fastq.gz | Fastqsanger.gz | |||
| SRR8313096_1.fastq.gz | Fastqsanger.gz |
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Project description:Several traumatic and neurodegenerative disorders of the CNS show axonal degeneration as a key and early pathological feature. Following a focal axonal lesion, an extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, activation of autophagic proteins including Unc-51 like autophagy activating kinase 1 (ULK1) has been demonstrated, but its role is incompletely understood. Here, we overexpressed a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons in vitro and in the spinal cord (SC) and optic nerve (ON) in vivo. We found a significant inhibitory effect on autophagy in vitro and in vivo. While no effect on cell survival could be observed, ULK1.DN attenuated AAD after axotomy in microfluidic chambers in vitro. Models of SC injury and ON crush in vivo confirmed an attenuation of axonal degeneration by ULK1.DN. In a translational approach, we employed the selective ULK1 inhibitor SBI-0206965 (SBI) and found an attenuation of AAD after ON crush in vivo mediated by a reduction of autophagy by SBI. Quantitative proteomic profiling after ULK1.DN overexpression in vitro revealed a regulation of proteins associated with translation and splicing. A differential exon expression analysis identified the genes kinesin family member 1B (Kif1b), DNA damage inducible transcript 3 (Ddit3) and WD repeat domain 6 (Wdr6) as targets of ULK1.DN and potential mediators of its degeneration-attenuating effect. These findings reveal ULK1 as an important mediator of axonal degeneration and elucidate its function in splicing, defining it as a putative therapeutic target.
2020-09-23 | GSE123687 | GEO
Project description:Several traumatic and neurodegenerative disorders of the CNS show axonal degeneration as a key and early pathological feature. Following a focal axonal lesion, an extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, activation of autophagic proteins, including Unc-51 like autophagy activating kinase 1 (ULK1), has been shown but its role is incompletely understood. Here, we overexpressed a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons in vitro and in the spinal cord (SC) and optic nerve (ON) in vivo. We found a significant inhibitory effect on autophagy in vitro and in vivo. While no effect on cell survival could be observed, ULK1.DN attenuated AAD after axotomy in microfluidic chambers in vitro. Models of SC injury and ON crush in vivo confirmed an attenuation of axonal degeneration by ULK1.DN. In a translational approach, we employed the selective ULK1 inhibitor SBI-0206965 (SBI) and found an attenuation of AAD after ON crush in vivo mediated by a reduction of autophagy by SBI. Quantitative proteomic profiling after ULK1.DN overexpression in vitro revealed a regulation of proteins associated with translation and splicing. A differential exon expression analysis then identified the genes kinesin family member 1B (Kif1b), DNA damage inducible transcript 3 (Ddit3) and WD repeat domain 6 (Wdr6) as targets of ULK1.DN and potential mediators of its degeneration-attenuating effect. These findings reveal ULK1 as an important mediator of axonal degeneration and elucidate its function in splicing, defining it as a putative therapeutic target.
2020-04-30 | PXD011862 | Pride
Project description:Axonal degeneration is a key and early pathological feature in traumatic and neurodegenerative disorders of the CNS. Following a focal lesion to axons, extended axonal disintegration by acute axonal degeneration (AAD) occurs within several hours. During AAD, the accumulation of autophagic proteins including Unc-51 like autophagy activating kinase 1 (ULK1) has been demonstrated, but its role is incompletely understood. Here, we study the effect of ULK1 inhibition in different models of lesion-induced axonal degeneration in vitro and in vivo. Overexpression of a dominant negative of ULK1 (ULK1.DN) in primary rat cortical neurons attenuates axotomy-induced AAD in vitro. Both ULK1.DN and the ULK1 inhibitor SBI-0206965 protect against AAD after rat optic nerve crush in vivo. ULK1.DN additionally attenuates long-term axonal degeneration after rat spinal cord injury in vivo. Mechanistically, ULK1.DN decreases autophagy and leads to an mTOR-mediated increase in translational proteins. Consistently, treatment with SBI-0206965 results in enhanced mTOR activation. ULK1.DN additionally modulates the differential splicing of the degeneration-associated genes Kif1b and Ddit3. These findings uncover ULK1 as an important mediator of axonal degeneration in vitro and in vivo, and elucidate its function in splicing, defining it as a putative therapeutic target.
| S-EPMC7493890 | biostudies-literature
Project description:Axonal degeneration is a core feature of ischemic brain injury that limits functional recovery. The pro-degenerative molecule Sarm1 is required for Wallerian axon degeneration after traumatic and chemotoxic nerve injuries, however it is unclear if a similar mechanism mediates axonal degradation after ischemic injury. Here we show that loss of Sarm1 in male mice tested results in profound attenuation of axonal degeneration after focal ischemia to the subcortical white matter. Moreover, absence of Sarm1 significantly promotes the survival of neurons distal but connected to the infarct after ischemic injuries to the subcortical white matter as well as to the cortex. To further understand the mechanism of Sarm1-/- mediated neuronal protection, we performed differential gene expression analysis of male wildtype and Sarm1-/- stroke-injured neurons and found that that loss of Sarm1 activates a pro-regenerative molecular program that promotes new axon and synapse formation after white matter ischemia. Using a functional genomics approach to recapitulate such a molecular program in Sarm1-/- neurons, we identify molecular compounds sufficient to enhance cortical neurite outgrowth in vitro, and all of which elicit a conserved epigenetic signature promoting axonogenesis. These results indicate that Sarm1 concurrently promotes axonal degeneration and inhibits a regenerative program encoded at the level of the epigenome that can be modulated pharmacologically. Our findings thus reveal a novel role for Sarm1 as a crucial regulator of both axonal degeneration and axonal remodeling after ischemic stroke.
2025-05-01 | GSE280862 | GEO
Project description:Basal forebrain cholinergic neurons (BFCNs) extend long projections to multiple targets in the brain to regulate cognitive functions, and are compromised in numerous neurodegenerative disorders. Our previous study showed that injury to the target region of these neurons affects their viability in vivo. Moderate cortical injury in mice promoted a significant increase in proneurotrophins in the injured cortex, leading to the retrograde loss of BFCNs ipsilateral to the injury via the p75 neurotrophin receptor (p75NTR). We determined that stimulation of BFCN axon terminals with proNGF elicited retrograde degeneration of the axons leading to cell death of these neurons in vitro. Our current study investigates mechanisms of axonal p75NTR signaling, and shows that retrograde transport and local axonal protein synthesis are necessary for proNGF induced retrograde degeneration initiated at the axon terminal. Analysis of the nascent axonal proteome revealed numerous newly synthesized proteins after stimulation of axon terminals with proNGF. Pathway analysis showed that amyloid precursor protein (APP) was a key upstream regulator. Our results show a functional role for APP in promoting proNGF induced BFCN axonal degeneration and cell death.
2025-05-06 | PXD043846 | Pride
Project description:Rac1, a member of the small G protein Rho family, has been implicated in neurodegenerative diseases. However, its role in axon degeneration is not fully understood. Here we found that activation of Rac1 exacerbated axonal transport damage in an experimental glaucoma model. Inhibiting Rac1 activity by genetic or pharmacological methods alleviated the dysfunction of axonal transport and improved the integrity of microtubule by upregulating the expression of β-III tubulin and myelin basic protein. Rac1 interacted with Sirt1, a key molecule of Wallerian degeneration, which regulated the activity of PAK1, a downstream molecule of Rac1. Furthermore, Rac1 modulated Kif motors at the transcriptional level, among which Kif2a, a lysosome-location regulator, was negatively regulated by Rac1. Intravitreal injection of Kif2a siRNA reversed the improvement of Rac1 inhibition-mediated axonal transport through reducing autophagolysosomes. Our results suggest that Rac1/Kif2a accelerates the process of RGC axon degeneration by impairing the autophagic flux in glaucoma, which may be an intriguing therapy target for glaucoma.
2024-12-01 | GSE247696 | GEO
Project description:TAX1BP1 deficiency impair initiation of autophagic flow in HK-2 cells through downregulate AMPK-ULK1 pathway
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Project description:Axonal degeneration determines the clinical outcome of multiple sclerosis (MS), and is thought to result from exposure of denuded axons to immune-mediated damage. We challenge this view after finding in MS and its mouse models that myelin itself increases the risk of axons to degenerate under inflammatory conditions. We propose a model for demyelinating diseases in which for axons that remain myelinated, and thus shielded from the extracellular milieu, dependence from oligodendroglial support turns fatal in an autoimmune disease environment.
2023-05-02 | GSE222063 | GEO
Project description:We provide evidence that the Unc-51-like kinase 1 (ULK1) is phosphorylated and activated during engagement of the Type I IFN receptor. Our studies demonstrate that the function of ULK1 controls expression of key interferon stimulated genes (ISGs) that mediate important biological functions, including anti-viral and antineoplastic responses. Total RNA was isolated from untreated and IFNβ-treated Ulk1/2+/+ and Ulk1/2-/- mouse embryonic fibroblasts (MEFs). Cells were treated for 6 hours with or without mouse IFNβ (2500 IU/ml).
2014-08-26 | E-GEOD-60778 | biostudies-arrayexpress
Project description:VAMP7 is involved in autophagy and exocytosis mediating neurite growth, two yet unconnected cellular pathways. Here we show the occurrence of combined VAMP7/ATG9 secretory events. VAMP7 localized, together with LC3 and ATG9, in vesicles moving anterogradely along the axon towards growth cones. VAMP7 knockout disrupted the autophagy response to drugs and starvation. Release of extracellular vesicles triggered by autophagy was impaired in VAMP7-knockout cells and autophagy-deficient cells were impaired in VAMP7 exocytosis. Secretomics showed that VAMP7-knockout cells were impaired in unconventional secretion of cytoplasmic, exosomal and mitochondrial proteins. We further found that autophagy stimulated neurite growth in a VAMP7-dependent manner. Furthermore, neurons still grew long axons in nutrient-restricted conditions and when treated with autophagy-inducing drugs. A nanobody directed against VAMP7 inhibited the effect of nutrient restriction. We propose that VAMP7-dependent autophagic secretion contributes to a resilience mechanism to preserve axonal growth in restriction conditions, as part of brain sparing occurring in growth restriction.
2020-12-10 | PXD014231 | Pride