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Increased APOE abundance in the brain in Down syndrome - Alzheimer’s disease compared with early onset-Alzheimer's disease is associated with elevated APP and C- terminal fragment abundance

GSE284141 Homo sapiens (human) Single-nucleus RNA-seq 16 samples Submitted 2025/02/27 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 16 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
16 samples: 8 × DSAD vs 4 × EOAD vs 4 × HAGroups are read from the sample names, not from the paper. Check the list below.
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.
Paper
Apolipoprotein E abundance is elevated in the brains of individuals with Down syndrome-Alzheimer's diseasebioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Trisomy of chromosome 21, the cause of Down syndrome (DS), is the most commonly occurring genetic cause of Alzheimer’s disease (AD). Here we compare the proteome of the frontal cortex of people who have Down syndrome-Alzheimer’s disease (DSAD) with demographically matched cases of early-onset AD and healthy ageing controls from the general population.
Read the full summary ↓
We find the abundance of several chromosome 21 encoded proteins are increased in DSAD compared to both comparative groups. Moreover, wider dysregulation of the proteome occurs beyond proteins encoded by chromosome 21, including an increase in the abundance of the key AD protein APOE, in people with DSAD compared to matched cases of early-onset AD. To understand the cell-types which may contribute to these changes in protein abundance we undertook a single-nuclei RNA-sequencing study on the same cases. This demonstrated that trisomy of chromosome 21 altered transcription of these proteins in a range of cell-types. Specifically, APOE expression was raised in subtypes of astrocytes, endothelial cells and pericytes. In our case series, we also found that the abundance of APOE correlates with the abundance of full-length APP and C-terminal-fragments-α but not with amyloid-β, the key constituent of AD plaque pathology. Having increased abundance of APOE may impact the development of, or response to, AD pathology in the brain of people who have DSAD, altering the disease mechanisms, with clinical implications. Overall, these data highlight that trisomy 21 alters both the transcriptome and proteome of people who have DS in the context of AD, and that these differences should be considered when selecting therapeutic strategies for this important group of individuals who are at high risk of early-onset dementia.
Published in
Apolipoprotein E abundance is elevated in the brains of individuals with Down syndrome-Alzheimer's disease
Farrell C, Buhidma Y, Mumford P et al. · bioRxiv : the preprint server for biology 2025 · PMID 40060680 · doi:10.1101/2025.02.24.639862
This dataset
Open GSE284141 in finder → Find more human RNA-seq datasets →
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 GSE284141_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1197438 and SRA study SRP551097. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40060680) ↗
Study design
8 × DSAD vs 4 × EOAD vs 4 × HA

Supports a between-group comparison across 16 samples.

How we read this: 3 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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