ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function
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PROVIDER: PRJNA805280 | ENA |
REPOSITORIES: ENA
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Project description:ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function [RNA-seq]
| PRJNA805277 | ENA
Project description:ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function [RIP-seq]
| PRJNA805281 | ENA
Project description:Understanding the pathogenic mechanisms of disease mutations is critical to advancing treatments. ALS-associated mutations in the gene encoding the microtubule motor KIF5A result in skipping of exon 27 (KIF5AΔExon27) and the encoding of a protein with a novel 39-amino acid residue C-terminal sequence. Here, we report that expression of ALS-linked mutant KIF5A results in dysregulated motor activity, cellular mislocalization, altered axonal transport, and decreased neuronal survival. Single-molecule analysis revealed that the altered C-terminus of mutant KIF5A results in a constitutively active state. Further, mutant KIF5A possesses novel protein and RNA interactions and its expression results in altered gene expression/splicing. Taken together, our data support the hypothesis that causative ALS mutations result in a toxic gain of function in the intracellular motor KIF5A that disrupts intracellular trafficking and neuronal homeostasis.
2022-06-09 | PXD031012 | Pride
Project description:Purpose: The goal of this study is to identify and compare the mRNA interactomes of WT and ALS-related mutant (d27) KIF5A Methods: RNA samples were extracted and sequenced on an Illumina NovaSeq6000 instrument at the Yale Center for Genome Analysis. The sample sequence quality control check was performed using FastQc. The STAR aligner program was used for read mapping with reference file and HTSeq was used to count the reads for each transcript in strand specific mode. The Differential expression analysis was performed using the DESeq2 package to compare the gene expression profiles between wild type and mutant was performed using the Wald test to generate p-values and Log2 fold changes. The STAR aligned RNA Sequence sample bam files were used to detect differential alternative splicing events with the Multivariate Analysis of Transcript Splicing (MATS) method. Pathway analysis was performed with Metascape Results: With the RNA RIP Sequence pipeline, we analyzed the RNA Sequence from SKNAS cells expressing WT KIF5A and cells epxressing the KIF5a ALS delta27 mutant. We identified 1,184 transcripts that displayed enriched binding to KIF5AΔExon27 and 303 that showed decreased binding to KIF5A ΔExon27. Pathway analysis revealed several categories related to ALS pathogenesis. KIF5AΔExon27 enriched pathways included NGF-stimulated transcription, which is related to neurite outgrowth. Pathways that were underrepresented in KIF5A ΔExon27 samples compared to KIF5AWT included interactions between L1 and Ankyrins, synapse assembly, and potassium channels. The results demonstrate that mutations in KIF5A can result in altered interaction with proteins and RNA associated with ALS-related pathways. Conclusions: Our analysis demonstates that ALS-related mutant KIF5A (d27) has altered RNA interactions compared to the WT protein.
2022-02-17 | GSE196538 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-02-17 | GSE196539 | GEO
Project description:Purpose: The goal of this study was to identify gene expression changes in iMNs containing a patient KIF5a mutation compared to an isogenic control. Further, splicing changes were evaluated in the mutant vs WT sample. Methods: RNA samples were extracted and sequenced on an Illumina NovaSeq6000 instrument at the Yale Center for Genome Analysis. The sample sequence quality control check was performed using FastQc. The STAR aligner program was used for read mapping with reference file and HTSeq was used to count the reads for each transcript in strand specific mode. The Differential expression analysis was performed using the DESeq2 package to compare the gene expression profiles between wild type and mutant was performed using the Wald test to generate p-values and Log2 fold changes. The STAR aligned RNA Sequence sample bam files were used to detect differential alternative splicing events with the Multivariate Analysis of Transcript Splicing (MATS) method. Pathway analysis was performed with Metascape Results: With the RNA Sequence pipeline, we analyzed the RNA Sequence from wild-type parental line (Iso Control) and the heterozygous mutant line (KIF5AR1007K). The RNA Sequence analysis of the iMNs revealed 57 genes displaying altered expression. Using the method, Multivariate Analysis of Transcript Splicing (MATS), we identified 1,919 transcripts with altered splicing compared to the isogenic control iMNs. Of these, 1,000 exons showed decreased skipping, while 919 showed increased skipping in KIF5AR1007K lines. Pathway analysis of each of these groups suggests that this group of altered genes, as a whole, represents cytoskeletal and transport defects in the cell, both of which are hallmarks of neurodegenerative disease.
2022-02-17 | GSE196537 | GEO
Project description:Mutations in coding and non-coding regions of FUS cause amyotrophic lateral sclerosis (ALS). The latter mutations may exert toxicity by increasing FUS accumulation. We showhere that broad expression within the nervous system of wild type or either of two ALS-linkedmutants of human FUS produces progressive motor phenotypes accompanied bycharacteristic ALS-like pathology. FUS levels are autoregulated by a mechanism in whichwild type or ALS-linked mutants of human FUS downregulating endogenous FUS at bothmRNA and protein levels. Increasing wild type human FUS expression achieved bysaturating this autoregulatory mechanism produces a rapidly progressive neurologicalphenotype and dose-dependent lethality. Genome-wide expression analysis reveals mis-regulation of genes that are largely distinct from the alterations observed by the acute FUS reduction in the spinal cord. Among these are increased expression of lysosomal proteins,suggestive of disruption in protein homeostasis as a potential gain-of-toxic mechanism.Indeed, increased expression of wild type and ALS-linked mutations in FUS inhibitautophagy with accumulated p62/sequestosome observed in spinal cord motor neurons.Taken together, our data suggests that overriding FUS autoregulation triggers gain-of-toxicproperties in the autophagy-lysosome axis and deregulation of RNA metabolism, highlightinga disruption in protein and RNA homeostasis in FUS-mediated toxicity.
2019-01-16 | GSE125125 | GEO
Project description:Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive motor neuron loss, with additional pathophysiological involvement of non-neuronal cells such as microglia. The commonest ALS-associated genetic variant is a hexanucleotide repeat expansion (HRE) mutation in C9orf72. Here, we study its consequences for microglial function using human iPSC-derived microglia. By RNA-sequencing, we identify enrichment of pathways associated with immune cell activation and cyto-/chemokines in C9orf72 HRE mutant microglia versus healthy controls, most prominently after LPS priming. Specifically, LPS-primed C9orf72 HRE mutant microglia show consistently increased expression and release of matrix metalloproteinase-9 (MMP9). LPS-primed C9orf72 HRE mutant microglia are toxic to co-cultured healthy motor neurons, which is ameliorated by concomitant application of an MMP9 inhibitor. Finally, we identify release of dipeptidyl peptidase-4 (DPP4) as a marker for MMP9-dependent microglial dysregulation in co-culture. These results demonstrate cellular dysfunction of C9orf72 HRE mutant microglia, and a non-cell-autonomous role in driving C9orf72-ALS pathophysiology in motor neurons through MMP9 signaling.
2023-08-20 | GSE217625 | GEO
Project description:Recent genetic studies of ALS patients have identified several forms of ALS that are associated with mutations in RNA binding proteins. In animals or cultured cells, such defects broadly affect RNA metabolism. This raises the question of whether all forms of ALS have general effects on RNA metabolism. We tested this hypothesis in a mouse model of ALS that is transgenic for a human disease-causing mutation in the enzyme superoxide dismutase 1 (SOD1). We analyzed RNA from laser-captured spinal cord motor neuron cell bodies of the mutant SOD1 strain, comparing the RNA profile with that from a corresponding wild-type SOD1 transgenic strain. We prepared the samples from animals that were presymptomatic, but which manifested abnormalities at the cellular level that are seen in ALS, including aggregation of the mutant protein in motor neuron cell bodies and defective morphology of neuromuscular junctions, the connections between neuron and muscle. We observed only minor changes in the level and splicing of RNA in the SOD1 mutant animals as compared with wild-type, suggesting that mutant SOD1 produces the toxic effects of ALS by a mechanism that does not involve global RNA disturbance. RNA-Seq of laser microdissection of motor neuron bodies from two biological replicates each of SOD1 YFP (wildtype 592) and SOD1 G85R YFP (737) transgenic mice.
2012-12-04 | E-GEOD-38820 | biostudies-arrayexpress
Project description:Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease caused by loss of motor neurons. SOD1 may have a toxic role in the pathogenesis of ALS when the protein aggregates in the cytoplasm; increased accumulation of soluble nuclear SOD1 (nSOD1) represents a protective cellular reaction.
2022-01-26 | GSE183204 | GEO