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GSE277082

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Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]

Organism: Homo sapiens
Platform: GPL24676
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing Other
Submitted: Sep 12 2024
Last Updated: Feb 18 2025
Status: Public on Feb 18 2025
Contact: Kevin,,Rhine (University of Arizona)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1160343

Summary

Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging markers. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins – like the dementia and ALS-associated protein TDP-43 – mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components typically are recruited to stress granules, but aged neurons suffer from chronic stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity, and the failure to respond to new stress events. Together our data demonstrates that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

Overall Design

Riboseq of isogenic transdifferentiated and iPSC-derived neurons; bulk RNA was isolated from untreated cells whereas RNA for ribosomal footprinting (to calculate translation efficiency) was derived from cells treated with cycloheximide, which locks RNA on ribosomes

Analysis (2 steps)

View Data Processing
Processing steps for GSE277082
  1. Riboseq data was analyzed as described previously; see Tirosh et al.
  2. 2015 doi:10.1371/journal.ppat.1005288

Supplementary Files (2)

GSE277082_nk_aging_effect_fp.csv.gz Download
GSE277082_nk_aging_effect_mrna.csv.gz Download
GEO Samples (8)

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— rp_NGN_rep1_S19_L001_R1_001.fastq.gz OTHER 804.3 MB link
— rp_NGN_rep2_S20_L001_R1_001.fastq.gz OTHER 705.2 MB link
— rp_NK_rep1_S21_L001_R1_001.fastq.gz OTHER 940.7 MB link
— rp_NK_rep2_S22_L001_R1_001.fastq.gz OTHER 735.8 MB link
— rnaseq_NGN_rep1_S27_L001_R1_001.fastq.gz RNA-Seq 317.0 MB link
— rnaseq_NGN_rep2_S28_L001_R1_001.fastq.gz RNA-Seq 536.7 MB link
— rnaseq_NK_rep1_S29_L001_R1_001.fastq.gz RNA-Seq 529.8 MB link
— rnaseq_NK_rep2_S30_L001_R1_001.fastq.gz RNA-Seq 2.6 GB link