GEO series
Chronic Aducanumab-mediated clearance of amyloid plaques decreases microglial activation and induces a unique microglial phenotype associated with antigen presentation
GSE288801
Mus musculus (mouse)
RNA-seq (gene expression)
30 samples
Submitted 2025/08/20
Platform GPL34328
At a glance
RNA-seq (gene expression) · mouse · 30 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
- 30 samples: 5 conditions, mostly with about 6 replicates eachGroups 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
- Early intervention anti-Aβ immunotherapy attenuates microglial activation without inducing exhaustion at residual plaquesMolecular neurodegeneration · 2025
Summary (written by the submitters)
Anti-amyloid β-peptide (Aβ) immune therapy was developed as treatment for Alzheimer’s disease (AD) to reduce and prevent amyloid plaque pathology. This approach has proven successful in phase 3 clinical trials of Aducanumab, Lecanemab and Donanemab. These antibodies induce robust amyloid plaque clearance, slow memory decline, and have beneficial effects on daily living activities.
Read the full summary ↓
The therapeutic effects correlate with the efficacy of plaque removal. Treatment is associated with adverse side-effects, such as oedema and haemorrhages (ARIA-E and -H), which are potentially linked to the induced immune response. To improve therapeutic safety, it is therefore imperative to understand the effects of anti-Aβ antibody treatment on immune cell function. We investigated the effects of long-term chronic Aducanumab treatment on amyloid plaque pathology and microglial response in the APP-SAA triple knock-in mouse model. Mice were treated weekly with Aducanumab from 4-8 months of age. Long-term treatment with Aducanumab results in a robust and dose-dependent removal of amyloid plaque pathology. Analysis of the CSF proteome indicates a reduction of markers for neurodegeneration including tau and α-synuclein. Consistent with a reduction of glucose uptake, the therapeutic effects were accompanied by reduced microglial activation. RNAseq confirmed a dose-dependent decrease in the disease-associated microglia (DAM) transcriptional signature of microglia, which is supported by a parallel decrease of Trem2 protein. However, genes associated with antigen-presentation were still increased after treatment. IHC confirms that Aducanumab treatment increases microglial clustering, as well as MHC-II expression around plaques and ELISA confirmed increased cytokine levels. These findings demonstrate that long-term chronic Aducanumab-mediated removal of Aβ leads to a dose dependent decrease in microglial activation and neurodegeneration, but induces a unique antibody treatment-related microglial phenotype associated with antigen presentation, which may be related to plaques still present after the 4 months treatment period.
Published in
de Weerd L, Hummel S, Müller SA et al.
· Molecular neurodegeneration 2025
· PMID 40830489
· doi:10.1186/s13024-025-00878-1
This dataset
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.
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 GSE288801_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1219494 and SRA study SRP561692. Searching any of these in the dataset finder brings you back here.
Study design
5 conditions, mostly with about 6 replicates each
Aducanumab, 1 mg/kg, ×6
Aducanumab, 10 mg/kg, ×6
Untreated, ×6
Aducanumab, 3 mg/kg, ×6
Isotype control, 10 mg/kg, ×6
Supports a between-group comparison across 30 samples.
How we read this: 5 replicated groups read from 30 sample titles; they account for 30 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
- GSM8775705 Aducanumab, 1 mg/kg, replicate 4 Aducanumab, 1 mg/kg,
- GSM8775706 Aducanumab, 1 mg/kg, replicate 1 Aducanumab, 1 mg/kg,
- GSM8775707 Aducanumab, 1 mg/kg, replicate 2 Aducanumab, 1 mg/kg,
- GSM8775708 Aducanumab, 1 mg/kg, replicate 3 Aducanumab, 1 mg/kg,
- GSM8775709 Aducanumab, 10 mg/kg, replicate 4 Aducanumab, 10 mg/kg,
- GSM8775710 Untreated, replicate 3 Untreated,
- GSM8775711 Untreated, replicate 4 Untreated,
- GSM8775712 Untreated, replicate 1 Untreated,
- GSM8775713 Aducanumab, 1 mg/kg, replicate 5 Aducanumab, 1 mg/kg,
- GSM8775714 Aducanumab, 1 mg/kg, replicate 6 Aducanumab, 1 mg/kg,
- GSM8775715 Aducanumab, 10 mg/kg, replicate 3 Aducanumab, 10 mg/kg,
- GSM8775716 Aducanumab, 10 mg/kg, replicate 6 Aducanumab, 10 mg/kg,
- GSM8775717 Aducanumab, 10 mg/kg, replicate 1 Aducanumab, 10 mg/kg,
- GSM8775718 Aducanumab, 10 mg/kg, replicate 2 Aducanumab, 10 mg/kg,
- GSM8775719 Aducanumab, 10 mg/kg, replicate 5 Aducanumab, 10 mg/kg,
- GSM8775720 Aducanumab, 3 mg/kg, replicate 4 Aducanumab, 3 mg/kg,
- GSM8775721 Aducanumab, 3 mg/kg, replicate 3 Aducanumab, 3 mg/kg,
- GSM8775722 Aducanumab, 3 mg/kg, replicate 6 Aducanumab, 3 mg/kg,
- GSM8775723 Aducanumab, 3 mg/kg, replicate 1 Aducanumab, 3 mg/kg,
- GSM8775724 Aducanumab, 3 mg/kg, replicate 2 Aducanumab, 3 mg/kg,
- GSM8775725 Aducanumab, 3 mg/kg, replicate 5 Aducanumab, 3 mg/kg,
- GSM8775726 Untreated, replicate 5 Untreated,
- GSM8775727 Untreated, replicate 2 Untreated,
- GSM8775728 Untreated, replicate 6 Untreated,
- GSM8775729 Isotype control, 10 mg/kg, replicate 5 Isotype control, 10 mg/…
- GSM8775730 Isotype control, 10 mg/kg, replicate 6 Isotype control, 10 mg/…
- GSM8775731 Isotype control, 10 mg/kg, replicate 1 Isotype control, 10 mg/…
- GSM8775732 Isotype control, 10 mg/kg, replicate 2 Isotype control, 10 mg/…
- GSM8775733 Isotype control, 10 mg/kg, replicate 3 Isotype control, 10 mg/…
- GSM8775734 Isotype control, 10 mg/kg, replicate 4 Isotype control, 10 mg/…
Datasets on a similar topic
- GSE275510 Deciphering Motor Dysfunction and Microglial Activation in mThy1-α-Synuclein Mice: A Comprehensive Study of Behavioral, Gene Experssion, and Methylation Changes [RNA-Seq] 20 samples shares microglial, activation
- GSE327618 Targeting microglial phosphatidylethanolamine synthesis pathway promotes GABARAP-associated phagocytosis and A clearance in Alzheimer's disease 9 samples shares microglial, clearance
- GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares activation
- GSE331176 Phagosome-mediated activation of STING by purine and pyrimidine-based bacterial cyclic dinucleotides 380 samples shares activation
- GSE254229 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits in mice 141 samples shares microglial
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares activation
- GSE327428 GPR34 regulation of disease-associated microglial states in mice 96 samples shares microglial
- GSE297515 Piezo1-dependent activation of stromal cells ignites muscle inflammation in exercise and injury and is associated with inflammaging 90 samples shares activation
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.