Evidence map›Paper›PMID 39934151›Full record

ArticleNature communications2025

Human and mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome.

Jay M Yarbro, Xian Han, Abhijit Dasgupta, Ka Yang, Danting Liu, Him K Shrestha, Masihuz Zaman, Zhen Wang, Kaiwen Yu, Dong Geun Lee and 22 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
33citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

33 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  15. Decoding Alzheimer's Disease One Cell Class at a Time.Cellular and molecular neurobiology · 2026
    Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

32 authors.

Jay M Yarbro *Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Xian Han *Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Abhijit Dasgupta *Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-6302-3512
Ka Yang *Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0001-8937-7397
Danting LiuDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Him K ShresthaDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Masihuz ZamanDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Zhen WangDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Kaiwen YuCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-6050-8477
Dong Geun LeeDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
David VanderwallDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Mingming NiuDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Huan SunDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Boer XieCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
Ping-Chung ChenDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-5982-2434
Yun JiaoDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Xue ZhangDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Zhiping WuDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Surendhar R ChepyalaDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Yingxue FuCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0003-3052-4131
Yuxin LiCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
Zuo-Fei YuanCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.ORCID http://orcid.org/0000-0003-1252-6766
Xusheng WangDepartment of Neurology, University of Tennessee Health Science Center, Memphis, TN, USA.
Suresh PoudelCenter for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA.
Barbora VagnerovaDepartment of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.
Qianying HeDepartment of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.
Andrew TangDepartment of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.
Patrick T RonaldsonDepartment of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.
Rui ChangDepartment of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.ORCID http://orcid.org/0000-0001-7950-8920
Gang YuDepartment of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID http://orcid.org/0000-0003-4932-5757
Yansheng LiuDepartment of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-2626-3912
Junmin PengDepartment of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. Junmin.peng@stjude.org.ORCID http://orcid.org/0000-0003-0472-7648

Funding

Project 4 (Genetic modifiers for APOE-associated Alzheimer's disease pathogenesis)U19AG069701 · NIA · MAYO CLINIC JACKSONVILLE · PI ALISON M GOATE, DAVID M. HOLTZMAN · 2021 to 2026
$42.0M
Utilization of proteomics and lipidomics to identify modifiers of LBDU54NS110435 · NINDS · MAYO CLINIC JACKSONVILLE · PI DICKSON, DENNIS WILLIAM, MCLEAN, PAMELA J · 2019 to 2023
$14.5M
Systems Approaches to Novel Molecular Mechanism in Alzheimer's DiseaseRF1AG064909 · NIA · UT SOUTHWESTERN MEDICAL CENTER · PI PENG, JUNMIN, YU, GANG · 2019 to 2024
$6.4M
Dissecting neuron-microglia-astrocyte interaction in AD pathogenesisRF1AG068581 · NIA · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI PENG, JUNMIN, ROSSOLL, WILFRIED · 2020 to 2023
$5.4M
Multi-level Integrative Proteomics to Alzheimer's Disease PathwaysR01AG053987 · NIA · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI PENG, JUNMIN · 2016 to 2020
$2.2M
RNA splicing dysfunction in Alzheimer's diseaseR01AG047928 · NIA · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI PENG, JUNMIN · 2015 to 2019
$1.8M
Dissecting neuron-microglia-astrocyte interaction in AD pathogenesisR01AG068581 · NIA · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI PENG, JUNMIN, ROSSOLL, WILFRIED · 2024 to 2024
$1.2M
NIA NIH HHS R01 AG047928NIA NIH HHS R01 AG053987NIA NIH HHS R01 AG068581NIA NIH HHS RF1 AG064909NIA NIH HHS RF1 AG068581NIA NIH HHS U19 AG069701NINDS NIH HHS U54 NS110435
6 · The paper itself

Abstract

Murine models of Alzheimer's disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. Here we present the comprehensive, age-dependent brain proteome and phosphoproteome across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata and prioritized components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Our analysis of the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including Aβ-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identifies potential targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.

Indexed as

Alzheimer DiseaseProteomeProteomicsAmyloid beta-PeptidesAmyloid beta-Protein PrecursorAnimalsBrainDisease Models, AnimalFemaleHumansMaleMiceMice, TransgenicPlaque, Amyloidtau ProteinsTranscriptomeAmyloid beta-PeptidesAmyloid beta-Protein PrecursorProteometau Proteins

Identifiers

PMID39934151
PMCPMC11814087

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.