Alzheimer's disease (AD) is characterized by cortical atrophy, glutamatergic neuron loss, and cognitive decline. However, large-scale quantitative assessments of cellular changes during AD pathology remain scarce.
Objective
This study aims to integrate single-nuclei sequencing data from the Seattle Alzheimer's Disease Cortical Atlas (SEA-AD) with spatial transcriptomics to quantify cellular changes in the prefrontal cortex and temporal gyrus, regions vulnerable to AD neuropathological changes (ADNC).
Methods
We mapped differentially expressed genes (DEGs) and analyzed their interactions with pathological factors such as APOE expression and Lewy bodies. Cellular proportions were assessed, focusing on neurons, glial cells, and immune cells.
Results
RORB-expressing L4-like neurons, though vulnerable to ADNC, exhibited stable cell numbers throughout disease progression. In contrast, astrocytes displayed increased reactivity, with upregulated cytokine signaling and oxidative stress responses, suggesting a role in neuroinflammation. A reduction in synaptic maintenance pathways indicated a decline in astrocytic support functions. Microglia showed heightened immune surveillance and phagocytic activity, indicating their role in maintaining cortical homeostasis.
Conclusions
The study underscores the critical roles of glial cells, particularly astrocytes and microglia, in AD progression. These findings contribute to a better understanding of cellular dynamics and may inform therapeutic strategies targeting glial cell function in AD.
ScheltensPDe StrooperBKivipeltoM, et al.Alzheimer's disease. Lancet2021; 397: 1577–1590.
2.
KhanSBarveKHKumarMS. Recent advancements in pathogenesis, diagnostics and treatment of Alzheimer's disease. Curr Neuropharmacol2020; 18: 1106–1125.
3.
DuboisBFeldmanHHJacovaC, et al.Advancing research diagnostic criteria for Alzheimer's disease: the IWG-2 criteria. Lancet Neurol2014; 13: 614–629.
4.
MontineTJPhelpsCHBeachTG, et al.National Institute on Aging-Alzheimer's Association guidelines for the neuropathologic assessment of Alzheimer's disease: a practical approach. Acta Neuropathol2012; 123: 1–11.
5.
HymanBTPhelpsCHBeachTG, et al.National Institute on Aging-Alzheimer's Association guidelines for the neuropathologic assessment of Alzheimer's disease. Alzheimers Dement2012; 8: 1–13.
6.
JackCRJr.AndrewsJSBeachTG, et al.Revised criteria for diagnosis and staging of Alzheimer's disease: alzheimer's Association Workgroup. Alzheimers Dement2024; 20: 5143–5169.
Graff-RadfordJYongKXXApostolovaLG, et al.New insights into atypical Alzheimer's disease in the era of biomarkers. Lancet Neurol2021; 20: 222–234.
9.
Trejo-LopezJAYachnisATProkopS. Neuropathology of Alzheimer's disease. Neurotherapeutics2022; 19: 173–185.
10.
MuralidarSAmbiSVSekaranS, et al.Role of tau protein in Alzheimer's disease: the prime pathological player. Int J Biol Macromol2020; 163: 1599–1617.
11.
BatemanRJXiongCBenzingerTL, et al.Clinical and biomarker changes in dominantly inherited Alzheimer's disease. N Engl J Med2012; 367: 795–804.
12.
VillemagneVLBurnhamSBourgeatP, et al.Amyloid β deposition, neurodegeneration, and cognitive decline in sporadic Alzheimer's disease: a prospective cohort study. Lancet Neurol2013; 12: 357–367.
13.
VillemagneVLPikeKEChételatG, et al.Longitudinal assessment of Aβ and cognition in aging and Alzheimer disease. Ann Neurol2011; 69: 181–192.
14.
JovicDLiangXZengH, et al.Single-cell RNA sequencing technologies and applications: a brief overview. Clin Transl Med2022; 12: e694.
15.
TianLChenFMacoskoEZ. The expanding vistas of spatial transcriptomics. Nat Biotechnol2023; 41: 773–782.
16.
RaoABarkleyDFrançaGS, et al.Exploring tissue architecture using spatial transcriptomics. Nature2021; 596: 211–220.
17.
BressanDBattistoniGHannonGJ. The dawn of spatial omics. Science2023; 381: eabq4964.
18.
FangRXiaCCloseJL, et al.Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science2022; 377: 56–62.
19.
ChenALiaoSChengM, et al.Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell2022; 185: 1777–1792.e1721.
20.
ChenASunYLeiY, et al.Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex. Cell2023; 186: 3726–3743.e3724.
21.
TasicBYaoZGraybuckLT, et al.Shared and distinct transcriptomic cell types across neocortical areas. Nature2018; 563: 72–78.
22.
MathysHDavila-VelderrainJPengZ, et al.Single-cell transcriptomic analysis of Alzheimer's disease. Nature2019; 570: 332–337.
23.
Serrano-PozoALiHLiZ, et al.Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer's disease. Nat Neurosci2024; 27: 2384–2400.
24.
MaynardKRCollado-TorresLWeberLM, et al.Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci2021; 24: 425–436.
25.
GabittoMITravagliniKJRachleffVM, et al.Integrated multimodal cell atlas of Alzheimer's disease. Nat Neurosci2024; 27: 2366–2383.
26.
ChenW-TLuACraessaertsK, et al.Spatial transcriptomics and in situ sequencing to study Alzheimer's disease. Cell2020; 182: 976–991.e919.
27.
HaoYHaoSAndersen-NissenE, et al.Integrated analysis of multimodal single-cell data. Cell2021; 184: 3573–3587.e3529.
28.
YuGWangLGHanY, et al.Clusterprofiler: an R package for comparing biological themes among gene clusters. Omics2012; 16: 284–287.
29.
WickhamH. Data analysis. In: WickhamH (eds) Ggplot2: elegant graphics for data analysis. Cham: Springer International Publishing, 2016, pp.189–201.
30.
QuadrosRMMiuraHHarmsDW, et al.Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins. Genome Biol2017; 18: 92.
31.
ConwayJRLexAGehlenborgN. Upsetr: an R package for the visualization of intersecting sets and their properties. Bioinformatics2017; 33: 2938–2940.
32.
LiuLZhangYNiuG, et al.Brainbase: a curated knowledgebase for brain diseases. Nucleic Acids Res2022; 50: D1131–d1138.
33.
DobinADavisCASchlesingerF, et al.STAR: ultrafast universal RNA-Seq aligner. Bioinformatics2013; 29: 15–21.
WeiSLuoMWangP, et al.Charting the spatial transcriptome of the human cerebral cortex at single-cell resolution. bioRxiv2024. https://doi.org/10.1101/2024.01.31.576150 .
36.
JorstadNLCloseJJohansenN, et al.Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science2023; 382: eadf6812.
37.
SilettiKHodgeRMossi AlbiachA, et al.Transcriptomic diversity of cell types across the adult human brain. Science2023; 382: eadd7046.
38.
SofroniewMVVintersHV. Astrocytes: biology and pathology. Acta Neuropathol2010; 119: 7–35.
39.
HenekaMTCarsonMJEl KhouryJ, et al.Neuroinflammation in Alzheimer's disease. Lancet Neurol2015; 14: 388–405.
40.
TostoGReitzC. Genome-wide association studies in Alzheimer's disease: a review. Curr Neurol Neurosci Rep2013; 13: 381.
41.
SmithMAHarrisPLSayreLM, et al.Iron accumulation in Alzheimer disease is a source of redox-generated free radicals. Proc Natl Acad Sci U S A1997; 94: 9866–9868.
42.
Serrano-PozoAFroschMPMasliahE, et al.Neuropathological alterations in Alzheimer disease. Cold Spring Harb Perspect Med2011; 1: a006189.
43.
YouLHYanCZZhengBJ, et al.Astrocyte hepcidin is a key factor in LPS-induced neuronal apoptosis. Cell Death Dis2017; 8: e2676.
44.
PicardMJusterRPMcEwenBS. Mitochondrial allostatic load puts the ‘gluc’ back in glucocorticoids. Nat Rev Endocrinol2014; 10: 303–310.
45.
YouLYuPPDongT, et al.Astrocyte-derived hepcidin controls iron traffic at the blood-brain-barrier via regulating ferroportin 1 of microvascular endothelial cells. Cell Death Dis2022; 13: 667.
46.
ZhangNYuXXieJ, et al.New insights into the role of ferritin in iron homeostasis and neurodegenerative diseases. Mol Neurobiol2021; 58: 2812–2823.
47.
BezerraGADobrovetskyESeitovaA, et al.Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels. Sci Rep2015; 5: 8769.
48.
LiHLQuYJLuYC, et al.DPP10 Is an inactivation modulatory protein of Kv4.3 and Kv1.4. Am J Physiol Cell Physiol2006; 291: C966–C976.
49.
MorrisonJHHofPR. Chapter 37 selective vulnerability of corticocortical and hippocampal circuits in aging and Alzheimer's disease. Prog Brain Res2002; 136: 467–486.
50.
ArendtTBrücknerMKMorawskiM, et al.Early neurone loss in Alzheimer's disease: cortical or subcortical?Acta Neuropathol Commun2015; 3: 10.
51.
MattsonMPMagnusT. Ageing and neuronal vulnerability. Nat Rev Neurosci2006; 7: 278–294.
52.
StranahanAMMattsonMP. Selective vulnerability of neurons in layer II of the entorhinal cortex during aging and Alzheimer’s disease. Neural Plasticity2010; 2010: 108190.
53.
LengKLiEEserR, et al.Molecular characterization of selectively vulnerable neurons in Alzheimer's disease. Nat Neurosci2021; 24: 276–287.
54.
GazestaniVKamathTNadafNM, et al.Early Alzheimer’s disease pathology in human cortex involves transient cell states. Cell2023; 186: 4438–4453.e4423.
55.
HofPRNimchinskyEACelioMR, et al.Calretinin-immunoreactive neocortical interneurons are unaffected in Alzheimer's disease. Neurosci Lett1993; 152: 145–149.
56.
IwamotoNEmsonPC. Demonstration of neurofibrillary tangles in parvalbumin-immunoreactive interneurones in the cerebral cortex of Alzheimer-type dementia brain. Neurosci Lett1991; 128: 81–84.
57.
FuHRodriguezGAHermanM, et al.Tau pathology induces excitatory neuron loss, grid cell dysfunction, and spatial memory deficits reminiscent of early Alzheimer;s disease. Neuron2017; 93: 533–541.e535.
58.
FischerJAyersT. Single nucleus RNA-Sequencing: how it's done, applications and limitations. Emerg Top Life Sci2021; 5: 687–690.
59.
SunFLiHSunD, et al.Single-cell omics: experimental workflow, data analyses and applications. Sci China Life Sci2025; 68: 5–102.
60.
BaysoyABaiZSatijaR, et al.The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol2023; 24: 695–713.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
