Early, sex-dependent and progressive proteomic imbalance in the amygdala during Alzheimer´s disease continuum.

Overview

1. Clinical Neuro proteomics Unit Proteomics Platform Sex & Gender in Health Research Area, Navarrabiomed Hospitalario, Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Navarra Institute for Health Research,Pamplona, Spain
2. Department of Pathology and Experimental Therapeutics, UB, IDIBELL, CIBERNED-ISCIII,Barcelona, Spain

Abstract

Background: The amygdala is involved in the emotional expression, memory processing and managing stimulatory input. Although amygdala atrophy is early evidenced in Alzheimer’s Disease (AD), the molecular mechanisms disrupted in initial neuropathological stages are still unknown. In the present study, we investigated the proteomic impairment of the amygdaloid region from AD-Braak stage I-II and III-IV subjects to better understand the neuropathological processes occurred early in this area and to identify potential targets that may face AD from the beginning of the disease.

Methods: Label-free quantitative proteomics was applied using an Orbitrap Exploris 480 mass-spectrometer in 24 postmortem amygdala specimens derived from non-demented (n = 3F/5M), AD-Braak stage I-II (n = 4F/4M) and AD-Braak stage III-IV (n = 4F/4M). Data analysis was performed using MaxQuant and Perseus software (two-way Student T-test; p < 0.05). Metascape and Ingenuity Pathway Analysis softwares were considered for biological interpretation. Connectivity map platform was used for drug repurposing analyses. Transcriptomic/proteomic data of other brain regions were obtained from AlzData, Neuropro, and Agora repositories.

Results: Amygdaloid proteome of AD-Braak stage I-II and III-IV subjects compared to controls revealed a progressive proteomic impairment with a minimal overlap across Braak stages. Some of the amygdaloid DEPs were known interactors of human Aβ plaques, APP, or Tau proteins or were previously identified at transcriptional or translational level in other brain regions affected by AD. Interestingly, amygdaloid proteome was more severely affected in women than in men with a particular protein expression profile associated to each AD stage. Comparing our sex-dependent differential proteome datasets with transcriptomic data of different brain regions, we identified potential sex-specific proteins related to cognitive decline and neurodegeneration. Finally, data-driven drug repositioning using amygdaloid omics profiles unveiled that most of the small molecule candidates were neuropathological stage and/or sex-specific.

Conclusions: Early and sex-specific amygdaloid proteome dysregulation in AD highlights the consideration of a deliberate stratification by sex in future research and clinical trials to develop effective therapeutic strategies in AD for both sexes.

Plain english summary: The amygdala is a brain region involved in the expression of emotions, memory processing and managing incoming stimulus. Atrophy of this area is evidenced at the first stages of Alzheimer’s Disease (AD), pointing out a potential involvement of amygdala in the pathology of this disease. However, the molecular changes occurred early in this area are not fully understood. To this end, we interrogated the proteome of amygdala postmortem samples came from subjects of early AD stages. By applying data and functional analyses, we observed a stage-dependent and progressive proteomic impairment in this area. We detected proteins differentially expressed that were already known to interact with well-stablished neuropathological proteins or were altered in other brain areas. Importantly, data stratification by sex revealed that protein expression changes of amygdala were more abundant in women than men across AD progression. After comparing our results with published data in different brain regions affected by AD, we identified sex-specific proteins that could be used as biomarkers of cognitive decline and neurodegeneration. Finally, a drug repositioning-based approach proposed candidates with the potential to reverse amygdaloid malignant AD signature more effectively in one sex than in other or just in one sex. These observations highlight the consideration to include sex differences in future research to develop more precise and effective treatments in AD.

Supplementary Information: The online version contains supplementary material available at 10.1186/s13293-026-00930-9.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

Datasets cited

• figshare:33099795, at figshare; found in DataCite

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium ( http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [57] with the dataset identifier PXD069452. According to recent recommendations [58], sex annotation has been included in raw files to facilitate further analysis.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 5 keywords, 11 MeSH terms, 2 funders, 59 references.

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This paper

Romero-Murillo, S., Lachén-Montes, M., Cartas-Cejudo, P., Anaya-Cubero, E., de Miguel, M., Extramiana, L., Ferrer, I., Fernández-Irigoyen, J., & Santamaría, E. (2026). Early, sex-dependent and progressive proteomic imbalance in the amygdala during Alzheimer´s disease continuum. Biology of sex differences, 17(1), 139. https://doi.org/10.1186/s13293-026-00930-9

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