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SRX23980588: GSM8152497: AD 4; Homo sapiens; RNA-Seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 38.8M spots, 12G bases, 3.8Gb downloads

External Id: GSM8152497_r1
Submitted by: Neuroregeneration, Netherlands Institute for Neuroscience
Study: Gene-expression profiling of individuals resilient to Alzheimer's disease reveals higher expression of genes related to metallothionein and mitochondrial processes and no changes in the unfolded protein response
show Abstracthide Abstract
Some individuals show a discrepancy between cognition and the amount of neuropathological changes characteristic for Alzheimer's disease (AD). This phenomenon has been referred to as 'resilience'. The molecular and cellular underpinnings of resilience remain poorly understood. To obtain an unbiased understanding of the molecular changes underlying resilience, we investigated global changes in gene expression in the superior frontal gyrus of a cohort of cognitively and pathologically well-defined AD patients, resilient individuals and age-matched controls (n=11-12 per group). 897 genes were significantly altered between AD and control, 1121 between resilient and control and 6 between resilient and AD. Gene set enrichment analysis (GSEA) revealed that the expression of metallothionein (MT) and of genes related to mitochondrial processes was higher in the resilient donors. Weighted gene co-expression network analysis (WGCNA) identified gene modules related to the unfolded protein response, mitochondrial processes and synaptic signaling to be differentially associated with resilience or dementia. As changes in MT, mitochondria, heat shock proteins and the unfolded protein response (UPR) were the most pronounced changes in the GSEA and/or WGCNA, immunohistochemistry was used to further validate these processes. MT was significantly increased in astrocytes in resilient individuals. A higher proportion of the mitochondrial gene MT-CO1 was detected outside the cell body versus inside the cell body in the resilient compared to the control group and there were higher levels of heat shock protein 70 (HSP70) and X-box-binding protein 1 spliced (XBP1s), two proteins related to heat shock proteins and the UPR, in the AD donors. Finally, we show evidence for putative sex-specific alterations in resilience, including gene expression differences related to autophagy in females compared to males. Taken together, these results show possible mechanisms involving MTs, mitochondrial processes and the UPR by which individuals might maintain cognition despite the presence of AD pathology. Overall design: RNA was isolated from the grey matter in the superior frontal gyrus.
Sample: AD 4
SAMN40528751 • SRS20778707 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM8152497
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was isolated with RNeasy Mini Kit RNA (Qiagen, Valencia, CA, USA) in combination with Trizol (3 ml Trizol per 100 mg tissue; Life Technologies, Grand Island, NY, USA). NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process 35 samples (GenomeScan, Leiden, The Netherlands). Briefly, rRNA was depleted from total RNA using the rRNA depletion kit (NEB #E6310). After fragmentation of the depleted rRNA, a cDNA synthesis was performed for ligation with the sequencing adapters and PCR amplification. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. At least 15 Gb, yielding ~30-40 million read pairs, was generated per sample with a quality score of ≥30.
Runs: 2 runs, 38.8M spots, 12G bases, 3.8Gb
Run# of Spots# of BasesSizePublished
SRR2837564224,844,8937.7G2.4Gb2024-04-25
SRR2837564313,982,9924.3G1.3Gb2024-04-25

ID:
32286518

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