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Protective effects of two different chaperones demonstrated in a mouse model of sporadic AD

GSE288054 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2025/01/29 Platform GPL13112

At a glance

RNA-seq (gene expression) · mouse · 20 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 20 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Previously, using various animal models of AD, we demonstrated the protective effect of intranasal administration of chaperones of such different structure as HSP70 and YB-1 at the level of animal’s behavior and functional state and morphology of different brain regions. We also described transcriptional changes in the brain of mice after bulbectomy (OBX mice) representing a model of sporadic AD with elements of major depression.

Read the full summary ↓

Herein, we investigated the effects of recombinant HSP70 and YB1 sub-chronic administration on transcription in the hippocampus and cortex of the OBX mice. Both chaperones introduction caused significant changes in the transcription of the studied brain regions, partially reverting it to a pattern of the control sham operated mice. More than 60% of genes with altered transcription levels due to bulbectomy exhibited complete restoration of their normal expression levels after both chaperones treatment. Importantly, the number of genes with altered expression after chaperones treatment was twice as high in the hippocampus as in the cortex. The administration of the chaperones led to complete or partial normalization of the expression of many genes related to the metabolism of beta-amyloid and tau protein in the brain of OBX mice. Thus, both proteins reduced the expression of genes such as Kmt2d, Apba, Casp9, Sorl1, Ywhag, Ywhaz and others, that increased expression as a result of bulbectomy and in parallel compensatory increased the expression of such genes as Prepl, Pfdn2, Fbxl16, Nsf etc. Both chaperones normalized the expression of many genes involved in rRNA processing and ribosome biogenesis, as well as genes involved in the processes of neurotransmitter transport and secretion, cognition, apoptosis, ferroptosis and mitochondrial regulation. Thus, both chaperones normalized the expression of 47 genes involved in mitochondria function, including the expression of the Pet117 gene, responsible for the rate of oxygen consumption by mitochondria and the expression of Mgst1 gene which affects the protection of mitochondria from oxidative stress. Importantly, administration of YB-1 and Hsp70 normalized the expression of a number of genes involved in the formation of the cytoskeleton. A significant compensatory effect of both chaperones was demonstrated in all six cell types studied in the brain of OBX mice with the most pronounced effect observed in the astrocytes. Notably, besides genes specific for AD, administration of both proteins normalized the expression of a few genes specific for major depression altered in OBX mice and several genes implicated in the development of other neurodegenerative diseases.

This dataset

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Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE288054_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1215950 and SRA study SRP559984. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 20 more — browse all 20 samples with per-sample file links →

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