Evidence map›Paper›PMID 39578645›Full record

ArticleNature genetics2024

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's disease.

Emily Miyoshi, Samuel Morabito, Caden M Henningfield, Sudeshna Das, Negin Rahimzadeh, Sepideh Kiani Shabestari, Neethu Michael, Nora Emerson, Fairlie Reese, Zechuan Shi and 17 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.

0numbers the graph read from it
0cells of the map it votes in
86citing 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

86 citing papers in PubMed.

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26 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

27 authors.

Emily Miyoshi *Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.ORCID http://orcid.org/0000-0001-8151-0560
Samuel Morabito *Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-7768-4856
Caden M HenningfieldDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Sudeshna DasDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Negin RahimzadehInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Sepideh Kiani ShabestariDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Neethu MichaelDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Nora EmersonDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Fairlie ReeseCenter for Complex Biological Systems (CCBS), University of California, Irvine, Irvine, CA, USA.
Zechuan ShiDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Zhenkun CaoDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Shushrruth Sai SrinivasanInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Vanessa M ScarfoneSue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.
Miguel A ArreolaDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Jackie LuDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Sierra WrightInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Justine SilvaDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Kelsey LeavyInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Ira T LottInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Eric DoranDepartment of Pediatrics, University of California, Irvine, School of Medicine, Orange, CA, USA.
William H YongInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Saba ShahinDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Mari Perez-RosendahlInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Alzheimer’s Biomarkers Consortium–Down Syndrome (ABC–DS)
Elizabeth HeadInstitute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA.
Kim N GreenDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA.
Vivek SwarupDepartment of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. vswarup@uci.edu.ORCID http://orcid.org/0000-0003-3762-2746

Funding

University of Pittsburgh Clinical and Translational Science InstituteUL1TR001857 · NCATS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI REIS, STEVEN E · 2016 to 2025
$129.3M
National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD)U24AG021886 · NIA · INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS · PI TATIANA M. FOROUD · 2002 to 2026
$119.8M
Project 3: Biomarkers for DS Clinical TrialsU19AG068054 · NIA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI CHRISTIAN, BRADLEY T · 2020 to 2025
$103.7M
Clinical and Translational Science AwardUL1TR001873 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI REILLY, MUREDACH P · 2016 to 2025
$99.0M
WU INSTITUTE OF CLINICAL AND TRANSLATIONAL SCIENCESUL1TR002345 · NCATS · WASHINGTON UNIVERSITY · PI William G. Powderly · 2017 to 2026
$97.8M
University of Wisconsin Institute for Clinical and Translational ResearchUL1TR002373 · NCATS · UNIVERSITY OF WISCONSIN-MADISON · PI ELIZABETH S BURNSIDE, Allan R. Brasier · 2017 to 2026
$75.9M
UC Irvine MODEL-ADU54AG054349 · NIA · UNIVERSITY OF CALIFORNIA-IRVINE · PI Kim Green · 2017 to 2026
$71.9M
WASHINGTON UNIVERSITY ALZHEIMERS DISEASE RESEARCH CENTERP50AG005681 · NIA · WASHINGTON UNIVERSITY · PI MORRIS, JOHN · 1985 to 2019
$52.1M
Satellite Diagnostic and Treatment Clinic CoreP50AG008702 · NIA · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI DE JAGER, PHILIP L · 1989 to 2019
$46.3M
TREATMENT OF DEPRESSION IN ALZHEIMER'S DISEASEP50AG005133 · NIA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI SWEET, ROBERT A · 1985 to 2019
$43.0M
Research Education ComponentP30AG062421 · NIA · MASSACHUSETTS GENERAL HOSPITAL · PI Christine S Ritchie · 2019 to 2026
$36.5M
University of California Health Participation in the National COVID Cohort Collaborative (N3C)UL1TR001414 · NCATS · UNIVERSITY OF CALIFORNIA-IRVINE · PI COOPER, DAN M, VILAIN, ERIC J. · 2015 to 2023
$35.1M
NCATS NIH HHS UL1 TR001414NCATS NIH HHS UL1 TR001857NCATS NIH HHS UL1 TR001873NCATS NIH HHS UL1 TR002345NCATS NIH HHS UL1 TR002373NIA NIH HHS F31 AG076308NIA NIH HHS P30 AG062421NIA NIH HHS P30 AG062715NIA NIH HHS P30 AG066444NIA NIH HHS P30 AG066519NIA NIH HHS P50 AG005133NIA NIH HHS P50 AG005681NIA NIH HHS P50 AG008702NIA NIH HHS R01 AG071683NIA NIH HHS RF1 AG071683NIA NIH HHS T32 AG000096NIA NIH HHS U01 AG051406NIA NIH HHS U01 AG051412NIA NIH HHS U19 AG068054NIA NIH HHS U24 AG021886NIA NIH HHS U54 AG054349NICHD NIH HHS P50 HD105353NICHD NIH HHS U54 HD087011NICHD NIH HHS U54 HD090256NIDA NIH HHS U01 DA053826NIGMS NIH HHS T32 GM136624NINDS NIH HHS P01 NS084974NINDS NIH HHS R01 NS135556
6 · The paper itself

Abstract

The pathogenesis of Alzheimer's disease (AD) depends on environmental and heritable factors, with its molecular etiology still unclear. Here we present a spatial transcriptomic (ST) and single-nucleus transcriptomic survey of late-onset sporadic AD and AD in Down syndrome (DSAD). Studying DSAD provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. We identified transcriptomic changes that may underlie cortical layer-preferential pathology accumulation. Spatial co-expression network analyses revealed transient and regionally restricted disease processes, including a glial inflammatory program dysregulated in upper cortical layers and implicated in AD genetic risk and amyloid-associated processes. Cell-cell communication analysis further contextualized this gene program in dysregulated signaling networks. Finally, we generated ST data from an amyloid AD mouse model to identify cross-species amyloid-proximal transcriptomic changes with conformational context.

Indexed as

Alzheimer DiseaseDown SyndromeTranscriptomeAgedAged, 80 and overAnimalsCell CommunicationCell NucleusDisease Models, AnimalFemaleGene Expression ProfilingGene Regulatory NetworksHumansMaleMice

Identifiers

PMID39578645
PMCPMC11631771

What Socratic holds

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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.