Evidence map›Paper›PMID 39754192›Full record

ArticleAlzheimer's research & therapy2025

Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease.

Phoebe Valdes, Andrew B Caldwell, Qing Liu, Michael Q Fitzgerald, Srinivasan Ramachandran, Celeste M Karch, Dominantly Inherited Alzheimer Network (DIAN), Douglas R Galasko, Shauna H Yuan, Steven L Wagner and 1 more

Abstract read
In one paragraph

Article in Alzheimer's research & therapy, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–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

8 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Phoebe Valdes *Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0003-3165-7235
Andrew B Caldwell *Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0002-2850-7677
Qing LiuDepartment of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0002-8845-1417
Michael Q FitzgeraldDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0002-3693-0854
Srinivasan RamachandranDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0002-4912-0279
Celeste M KarchDepartment of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA.ORCID 0000-0002-6854-5547
Dominantly Inherited Alzheimer Network (DIAN)
Douglas R GalaskoDepartment of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0001-6195-3241
Shauna H YuanDepartment of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0003-4058-4146
Steven L WagnerDepartment of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA.ORCID 0000-0003-4674-9474
Shankar SubramaniamDepartment of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA. shankar@ucsd.edu.ORCID 0000-0002-8059-4659

Funding

VIRUS-INDUCED BRAIN PATHOLOGYP50AG005131 · NIA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GALASKO, DOUGLAS R · 1985 to 2018
$55.4M
Imaging CoreU19AG032438 · NIA · WASHINGTON UNIVERSITY · PI BATEMAN, RANDALL J · 2010 to 2025
$53.9M
UCSD Shiley-Marcos Alzheimer's Disease Research Center P30P30AG062429 · NIA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JAMES B BREWER · 2019 to 2026
$34.9M
Shear Regulation of MicroRNA Transportomes and Targetomes in Vascular HomeostasisR01HL106579 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHIEN, SHU, SHYY, JOHN YJ · 2011 to 2022
$8.3M
The Metabolomics Data Center and Workbench (MDCW)U01DK097430 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2012 to 2017
$7.4M
Biomedical Data Commons Workbench (BDCW)OT2OD030544 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2020 to 2024
$3.2M
An Integrative Omics Approach to Identify Biomarkers Related to Preeclampsia and Breast Cancer RisksR01HD084633 · NICHD · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GARMIRE, LANA X · 2016 to 2020
$3.0M
Nextgen AD Models, Endotypes, and ScreeningRF1AG084030 · NIA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MUOTRI, ALYSSON R., SUBRAMANIAM, SHANKAR · 2024 to 2024
$2.3M
Optimization of Soluble Gamma-secretase Modulators for the Treatment of AlzheimerU01NS074501 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WAGNER, STEVEN LEE · 2011 to 2015
$1.4M
Theoretical Foundations and Software Infrastructure for Biological Network DatabasesU01CA198941 · NCI · CASE WESTERN RESERVE UNIVERSITY · PI KOYUTURK, MEHMET · 2015 to 2017
$1.4M
Reconstruction and Modeling of Dynamical Molecular NetworksR01LM012595 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SUBRAMANIAM, SHANKAR · 2018 to 2021
$1.3M
Alzheimer's Association NIRG-14-322164Alzheimer's Association SG-20-690363-DIANNational Science Foundation STC CCF-0939370NCI NIH HHS U01 CA198941NHLBI NIH HHS R01 HL106579NIA NIH HHS P30 AG062429NIA NIH HHS P50 AG005131NIA NIH HHS RF1 AG084030NIA NIH HHS U19 AG032438NIA NIH HHS U19AG032438NICHD NIH HHS R01 HD084633NIDDK NIH HHS U01 DK097430NIH HHS OT2 OD030544NIH HHS P50 AGO5131 , U01 NS 074501-05, R01 LM012595 , OT2 OD030544, U01 CA198941, U01 DK097430, R01 HD084633 , R01 HL106579-07,NINDS NIH HHS U01 NS074501NLM NIH HHS R01 LM012595RRD VA I01 RX002259U.S. Department of Veterans Affairs 1I01RX002259
6 · The paper itself

Abstract

backgroundPSEN1, PSEN2, and APP mutations cause Alzheimer's disease (AD) with an early age at onset (AAO) and progressive cognitive decline. PSEN1 mutations are more common and generally have an earlier AAO; however, certain PSEN1 mutations cause a later AAO, similar to those observed in PSEN2 and APP.

methodsWe examined whether common disease endotypes exist across these mutations with a later AAO (~ 55 years) using hiPSC-derived neurons from familial Alzheimer's disease (FAD) patients harboring mutations in PSEN1

resultsWe identified common disease endotypes, such as dedifferentiation, dysregulation of synaptic signaling, repression of mitochondrial function and metabolism, and inflammation. We ascertained the master transcriptional regulators associated with these endotypes, including REST, ASCL1, and ZIC family members (activation), and NRF1 (repression).

conclusionsFAD mutations share common regulatory changes within endotypes with varying severity, resulting in reversion to a less-differentiated state. The regulatory mechanisms described offer potential targets for therapeutic interventions.

Indexed as

Alzheimer DiseaseAmyloid beta-Protein PrecursorMutationPresenilin-1Presenilin-2FemaleHumansMaleMiddle AgedMultiomicsNeuronsAmyloid beta-Protein PrecursorAPP protein, humanPresenilin-1Presenilin-2PSEN1 protein, humanPSEN2 protein, human

Identifiers

PMID39754192
PMCPMC11699654

What Socratic holds

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LicenceCC BY
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Registered trials

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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.