A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain
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Abstract
BACKGROUND: Alzheimer's disease (AD) is the most common form of dementia. This neurodegenerative disorder is associated with neuronal death and gliosis heavily impacting the cerebral cortex. AD has a substantial but heterogeneous genetic component, presenting both Mendelian and complex genetic architectures. Using bulk RNA-seq from the parietal lobes and deconvolution methods, we previously reported that brains exhibiting different AD genetic architecture exhibit different cellular proportions. Here, we sought to directly investigate AD brain changes in cell proportion and gene expression using single-cell resolution. METHODS: We generated unsorted single-nuclei RNA sequencing data from brain tissue. We leveraged the tissue donated from a carrier of a Mendelian genetic mutation, PSEN1 p.A79V, and two family members who suffer from sporadic AD, but do not carry any autosomal mutations. We evaluated alternative alignment approaches to maximize the titer of reads, genes, and cells with high quality. In addition, we employed distinct clustering strategies to determine the best approach to identify cell clusters that reveal neuronal and glial cell types and avoid artifacts such as sample and batch effects. We propose an approach to cluster cells that reduces biases and enable further analyses. RESULTS: We identified distinct types of neurons, both excitatory and inhibitory, and glial cells, including astrocytes, oligodendrocytes, and microglia, among others. In particular, we identified a reduced proportion of excitatory neurons in the Mendelian mutation carrier, but a similar distribution of inhibitory neurons. Furthermore, we investigated whether single-nuclei RNA-seq from the human brains recapitulate the expression profile of disease-associated microglia (DAM) discovered in mouse models. We also determined that when analyzing human single-nuclei data, it is critical to control for biases introduced by donor-specific expression profiles. CONCLUSION: We propose a collection of best practices to generate a highly detailed molecular cell atlas of highly informative frozen tissue stored in brain banks. Importantly, we have developed a new web application to make this unique single-nuclei molecular atlas publicly available.
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snRNA-seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer's disease.
“snRNA-seq analyses of human brain samples have failed to detect a consistent microglial activation signature in Alzheimer’s disease.”
From Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans (2020) · cites this paper as Del-Aguila et al., 2019
The Results section (page unavailable) says the study did not sequence enough microglial cells to replicate the previously reported disease-associated microglia (DAM) marker findings. But it found five markers consistently associated with microglia across all three samples. The claim overgeneralizes this limited finding to a failure to detect any consistent microglial activation signature in human Alzheimer’s disease samples. (LLM, conf=0.84)
Experimental — accuracy not yet measuredItm2b interacts with Trem2, influencing Trem2 processing and expression levels.
“Moreover, Itm2b (also known as Bri2) has been shown to interact with Trem2, influencing Trem2 processing and expression levels [Del-Aguila et al., 2019; Yin et al., 2024].”
From Cell signaling pathways discovery from multi-modal data (2025) · cites this paper as Del-Aguila et al., 2019
The Results section on disease-associated microglia discusses TREM2’s role in microglial activation, but does not address an interaction with ITM2B/Bri2. Searches for ITM2B, Bri2, and TREM2 processing or expression found no passage supporting the claimed interaction. (LLM, conf=0.75)
Experimental — accuracy not yet measuredBrain single-nucleus RNA-seq data were annotated using a marker gene list curated previously.
“We employed a list of marker genes that we had previously curated64 to annotate brain single-nucleus RNA-seq data.”
From Meningeal lymphatics affect microglia responses and anti-Aβ immunotherapy (2021) · cites this paper as [64]
CD33 is a microglia-specific gene.
“CD33 is a microglia-specific gene36 and likely affects microglia activity and innate immune response.”
From Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders (2021) · cites this paper as [36]
A small sample size in a single cell genomics study does affect statistical power, but does not preclude the possibility of drawing meaningful inferences of cell type gene expression in the human brain.
“A small sample size in a single cell genomics study does affect statistical power, but does not preclude the possibility of drawing meaningful inferences of cell type gene expression in the human brain (9,41) .”
From Single cell transcriptome profiling of the human alcohol-dependent brain (2020) · cites this paper as [9]
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- Authors
- Del-Aguila, J. L., Li, Z., Dube, U., Mihindukulasuriya, K. A., Budde, J. P., Fernandez, M. V., Ibanez, L., Bradley, J., Wang, F., Bergmann, K., Davenport, R., Morris, J. C., Holtzman, D. M., Perrin, R. J., Benitez, B. A., Dougherty, J., Cruchaga, C., & Harari, O.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Cruchaga, Carlos
- Harari, Oscar
- ORCID
- Venue
- Alzheimer's Research & Therapy
- Published
- 2019-08-09
- Volume
- 11
- Issue
- 1
- Pages
- 71-71
- ISSN
- 1758-9193 (ISSN-L)
- PMC
- PMC6689177
- OpenAlex
- W2966903908
- Cited by
- 183
- References
- 39
- Citations by year
- 2026: 11 · 2025: 21 · 2024: 19 · 2023: 33 · 2022: 30 · 2021: 38 · 2020: 28 · 2019: 3
- FWCI
- 8.15
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Alzheimer s Research & Therapy (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- NIH (R01AG057777)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Neuroscience › Neurology › Neuroinflammation and Neurodegeneration Mechanisms
- Keywords
- Alzheimer's disease, single-nucleus RNA sequencing, sporadic Alzheimer's disease, cell type composition, excitatory neurons, inhibitory neurons, astrocytes, oligodendrocytes, microglia, disease-associated microglia, cell clustering, parietal lobe, brain banks
- MeSH terms
- Aged, 80 and over, Alzheimer Disease, Atlases as Topic, Female, Humans, Male, Mutation, Neurons, Parietal Lobe, Gene Expression, Sequence Analysis, RNA, Microglia, Presenilin-1
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