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GSE277082

GSE GEO
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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)

SRA Experiments (8) and Runs (8)

Total: 7181 MB
SRX26072277 SRP532400 RNA-Seq SINGLE
GSM8513850: iPSC-derived_RNA-Seq_1; Homo sapiens; RNA-Seq
Sample: SRS22641216
BioProject: PRJNA1160343
BioSample: SAMN43751959
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: iPSC-derived cortical neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652209 8571315 865702815 317.05 rnaseq_NGN_rep1_S27_L001_R1_001.fastq.gz, SRR30652209, SRR30652209.li… SRA
SRX26072278 SRP532400 RNA-Seq SINGLE
GSM8513851: iPSC-derived_RNA-Seq_2; Homo sapiens; RNA-Seq
Sample: SRS22641217
BioProject: PRJNA1160343
BioSample: SAMN43751958
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: iPSC-derived cortical neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652208 14626787 1477305487 536.66 rnaseq_NGN_rep2_S28_L001_R1_001.fastq.gz, SRR30652208, SRR30652208.li… SRA
SRX26072279 SRP532400 OTHER SINGLE
GSM8513852: iPSC-derived_footprinting_1; Homo sapiens; OTHER
Sample: SRS22641218
BioProject: PRJNA1160343
BioSample: SAMN43751957
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: iPSC-derived cortical neurons
treatment: 100 ug/mL cycloheximide
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652207 21772592 2199031792 804.29 rp_NGN_rep1_S19_L001_R1_001.fastq.gz, SRR30652207, SRR30652207.lite SRA
SRX26072280 SRP532400 OTHER SINGLE
GSM8513853: iPSC-derived_footprinting_2; Homo sapiens; OTHER
Sample: SRS22641219
BioProject: PRJNA1160343
BioSample: SAMN43751956
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: iPSC-derived cortical neurons
treatment: 100 ug/mL cycloheximidede
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652206 18927010 1911628010 705.25 rp_NGN_rep2_S20_L001_R1_001.fastq.gz, SRR30652206, SRR30652206.lite SRA
SRX26072281 SRP532400 RNA-Seq SINGLE
GSM8513854: Transdifferentiated_RNA-Seq_1; Homo sapiens; RNA-Seq
Sample: SRS22641220
BioProject: PRJNA1160343
BioSample: SAMN43751955
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: Transdifferentiated cortical neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652205 14395238 1453919038 529.78 rnaseq_NK_rep1_S29_L001_R1_001.fastq.gz, SRR30652205, SRR30652205.lite SRA
SRX26072282 SRP532400 RNA-Seq SINGLE
GSM8513855: Transdifferentiated_RNA-Seq_2; Homo sapiens; RNA-Seq
Sample: SRS22641221
BioProject: PRJNA1160343
BioSample: SAMN43751954
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: Transdifferentiated cortical neurons
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652204 73742726 7448015326 2611.52 rnaseq_NK_rep2_S30_L001_R1_001.fastq.gz, SRR30652204, SRR30652204.lite SRA
SRX26072283 SRP532400 OTHER SINGLE
GSM8513856: Transdifferentiated_footprinting_1; Homo sapiens; OTHER
Sample: SRS22641222
BioProject: PRJNA1160343
BioSample: SAMN43751953
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: Transdifferentiated cortical neurons
treatment: 100 ug/mL cycloheximide
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652203 25052479 2530300379 940.67 rp_NK_rep1_S21_L001_R1_001.fastq.gz, SRR30652203, SRR30652203.lite SRA
SRX26072284 SRP532400 OTHER SINGLE
GSM8513857: Transdifferentiated_footprinting_2; Homo sapiens; OTHER
Sample: SRS22641223
BioProject: PRJNA1160343
BioSample: SAMN43751952
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Kin17ALS1
cell line: Kin17ALS1
cell type: Transdifferentiated cortical neurons
treatment: 100 ug/mL cycloheximide
geo_loc_name: missing
collection_date: missing
Original files (1)
Kin17ALS1
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR30652202 19845818 2004427618 735.75 rp_NK_rep2_S22_L001_R1_001.fastq.gz, SRR30652202, SRR30652202.lite SRA

Linked Publications (1)

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