GSE196538
ALS-Associated KIF5A Mutations Abolish Autoinhibition Resulting in a Toxic Gain of Function [RIP-seq]
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 KIF5A?Exon27 and 303 that showed decreased binding to KIF5A ?Exon27. Pathway analysis revealed several categories related to ALS pathogenesis. KIF5A?Exon27 enriched pathways included NGF-stimulated transcription, which is related to neurite outgrowth. Pathways that were underrepresented in KIF5A ?Exon27 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. Overall design: mRNA interactomes for WT and Mutant (d27) KIF5A