Comparison of the amyloid plaque proteome in Down syndrome, early‐onset Alzheimer's disease, and late‐onset Alzheimer's disease
Open accessAbstract
Abstract Background Down syndrome (DS) is strongly associated with Alzheimer’s disease (AD), attributable to APP overexpression. DS exhibits Amyloid-β (Aβ) and Tau pathology similar to early-onset AD (EOAD) and late-onset AD (LOAD). The study aimed to evaluate the Aβ plaque proteome of DS, EOAD and LOAD.Methods Using unbiased localized proteomics, we analyzed amyloid plaques and adjacent plaque-devoid tissue (‘non-plaque’) from post-mortem paraffin-embedded tissues in four cohorts (n = 20/group): DS (59.8 ± 4.99 y/o), EOAD (63 ± 4.07 y/o), LOAD (82.1 ± 6.37 y/o) and controls (66.4 ± 13.04). We assessed functional associations using Gene Ontology (GO) enrichment and protein interaction networks.Results We identified differentially abundant Aβ plaque proteins vs. non-plaques (FDR < 5%, fold-change > 1.5) in DS (n = 132), EOAD (n = 192) and in LOAD (n = 128); there were 43 plaque-associated proteins shared between all groups. Positive correlations (p < 0.0001) were observed between plaque-associated proteins in DS and EOAD (R2 = 0.77), DS and LOAD (R2 = 0.73), and EOAD vs. LOAD (R2 = 0.67). Top Biological process (BP) GO terms (p < 0.0001) included lysosomal transport for DS, immune system regulation for EOAD, and lysosome organization for LOAD. Protein networks revealed a plaque enriched signature across all cohorts involving APP metabolism, immune response, and lysosomal functions. In DS, EOAD and LOAD non-plaque vs. control tissue, we identified 263, 269, and 301 differentially abundant proteins, including 65 altered non-plaque proteins across all cohorts. Differentially abundant non-plaque proteins in DS showed a significant (p < 0.0001) but weaker positive correlation with EOAD (R2 = 0.59) and LOAD (R2 = 0.33) compared to the stronger correlation between EOAD and LOAD (R2 = 0.79). The top BP GO term for all groups was chromatin remodeling (DS p = 0.0013, EOAD p = 5.79x10− 9, and LOAD p = 1.69x10− 10). Additional GO terms for DS included extracellular matrix (p = 0.0068), while EOAD and LOAD were associated with protein-DNA complexes and gene expression regulation (p < 0.0001).Conclusions We found strong similarities among the Aβ plaque proteomes in individuals with DS, EOAD and LOAD, and a robust association between the plaque proteomes and lysosomal and immune-related pathways. Further, non-plaque proteomes highlighted altered pathways related to chromatin structure and extracellular matrix (ECM), the latter particularly associated with DS. We identified novel Aβ plaque proteins, which may serve as biomarkers or therapeutic targets.
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Proteomic PPI networks in CA1, CA2, and subiculum showed increased abundance of proteins involved in glial activation, neutrophil degranulation, leukocyte adhesion, complement C1q complexes, and RAC-NOX2-mediated inflammatory signaling supporting proteomics findings in DS-AD and other subtypes of AD.
“Moreover, proteomic PPI networks in CA1, CA2, and subiculum showed increased abundance of proteins involved in glial activation, neutrophil degranulation, leukocyte adhesion, complement C1q complexes, and RAC–NOX2–mediated inflammatory signaling supporting proteomics findings in DS‐AD and other subtypes of AD. 51 , 63”
From Disruption of hippocampal upstream regulators of mTOR and insulin pathways in Down syndrome with Alzheimer's disease neuropathology: Preliminary observations (2026) · cites this paper as [51]
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Experimental — accuracy not yet measuredRaised abundance of CBR1 and PFKL in the brain of individuals with DSAD has recently been reported.
“Raised abundance of CBR1 (carbonyl reductase 1) and PFKL (6-phosphofructokinase) in the brain of individuals with DSAD has recently been reported [43].”
From Apolipoprotein E abundance is elevated in the brains of individuals with Down syndrome–Alzheimer’s disease (2025) · cites this paper as [43]
The Results section, under “Protein-coding genes present in Hsa21,” reports significant enrichment of CBR1 in Down syndrome non-plaque brain tissue. Our copy does not report raised PFKL abundance; searches for PFKL and 6-phosphofructokinase found no supporting passage. No page number is available in the indexed copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredIn a recent proteomic report comparing the plaque and non-plaque-associated proteome of DSAD, EOAD, and LOAD cases, an 8-fold enrichment of APOE was observed in DSAD, and a 5.9-fold enrichment of APOE in EOAD was observed.
“In a recent proteomic report comparing the plaque and non-plaque-associated proteome of DSAD, EOAD, and LOAD cases, an 8-fold enrichment of APOE was observed in DSAD, and a 5.9-fold enrichment of APOE in EOAD was observed [43].”
From Apolipoprotein E abundance is elevated in the brains of individuals with Down syndrome–Alzheimer’s disease (2025) · cites this paper as [43]
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Self-citationMultiomics and proteomic insights into Alzheimer’s disease biology in Down syndrome
Martá-Ariza, M., & Wisniewski, T. R. (2026) · Expert Review of Neurotherapeutics · doi:10.1080/14737175.2026.2695187
Self-citationDeepPlaque: a scalable multimodal platform for Aβ pathology and cell analysis in Alzheimer’s disease
Wong, H. Y., Jin, C., Yuen, S. L., Yang, X., Gill, S. S., Xu, J., Lai, K. P. E., Fu, W., Gao, W., Wang, X., et al. (2026) · EMBO Molecular Medicine · doi:10.1038/s44321-026-00488-4
Thierry, M., Leitner, D., Balcomb, K., Kavanagh, T., Tang, L., Kanshin, E., William, C. M., Oakley, D., Hyman, B. T., Ueberheide, B. M., et al. (2026) · Acta Neuropathologica · doi:10.1007/s00401-026-03064-9
Self-citation
- Authors
- Martá-Ariza, M., Leitner, D. F., Kanshin, E., Suazo, J., Giusti Pedrosa, A., Thierry, M., Lee, E. B., Devinsky, O., Drummond, E., Fortea, J., Lleó, A., Ueberheide, B., & Wisniewski, T.
- Affiliations
- Universitat Autònoma de Barcelona (ES)
- NYU Langone Health (US)
- New York University (US)
- University of Pennsylvania (US)
- The University of Sydney (AU)
- ORCID
- Venue
- Acta Neuropathologica
- Published
- 2025-01-18
- Volume
- 149
- Issue
- 1
- Pages
- 9-9
- ISSN
- 0001-6322 (ISSN-L)
- 1432-0533
- PMC
- PMC11742868
- OpenAlex
- W4406561587
- Cited by
- 15
- References
- 149
- Citations by year
- 2026: 7 · 2025: 8
- FWCI
- 9.65
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Acta Neuropathologica (publishedVersion, cc-by-nc-nd)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Dipòsit Digital de Documents de la UAB (Universitat Autònoma de Barcelona) (submittedVersion, cc-by-nc-nd)
- PubMed Central (submittedVersion, cc-by)
- Funders
- National Institutes of Health (P01AG060882, P30AG072979)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Keywords
- Down syndrome, Alzheimer's disease, amyloid plaques, amyloid-beta, early-onset Alzheimer's disease, late-onset Alzheimer's disease, APP overexpression, lysosomal trafficking, immune response, chromatin remodeling, protein networks, APP metabolism, tau pathology, biomarkers, differential protein abundance, postmortem brain
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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