Evidence map›Paper›PMID 37587197›Full record

ArticleNature communications2023

Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature.

Eloise Berson, Anjali Sreenivas, Thanaphong Phongpreecha, Amalia Perna, Fiorella C Grandi, Lei Xue, Neal G Ravindra, Neelufar Payrovnaziri, Samson Mataraso, Yeasul Kim and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

  1. Cellular Senescence of Patient-derived Fibroblasts Reveals the Mid-old Stage as a Critical Window for Transcriptomic Signatures Linked to Alzheimer's Disease Biomarkers and Classification.Clinical psychopharmacology and neuroscience : the official scientific journal of the Korean College of Neuropsychopharmacology · 2026
    Article
  2. Epigenomic profile of GBA1 in Parkinson's disease.Parkinsonism & related disorders · 2025
    Article
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  11. LD-informed deep learning for Alzheimer's gene loci detection using WGS data.medRxiv : the preprint server for health sciences · 2024
    Article
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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

19 authors.

Eloise BersonDepartment of Pathology, Stanford University, Stanford, CA, USA. eloiseb@stanford.edu.ORCID http://orcid.org/0000-0003-1046-125X
Anjali SreenivasDepartment of Pathology, Stanford University, Stanford, CA, USA.
Thanaphong PhongpreechaDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-9245-6686
Amalia PernaDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5569-8512
Fiorella C GrandiGladstone Institute of Neurological Disease, San Francisco, CA, USA.
Lei XueDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.
Neal G RavindraDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5558-3758
Neelufar PayrovnaziriDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.
Samson MatarasoDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-3146-2243
Yeasul KimDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.
Camilo EspinosaDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1630-1564
Alan L ChangDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1716-0134
Martin BeckerDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-4296-3481
Kathleen S MontineDepartment of Pathology, Stanford University, Stanford, CA, USA.
Edward J FoxDepartment of Pathology, Stanford University, Stanford, CA, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-9459-4393
M Ryan CorcesGladstone Institute of Neurological Disease, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7465-7652
Nima AghaeepourDepartment of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-6117-8764
Thomas J MontineDepartment of Pathology, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-1346-2728

Funding

Project 4: Novel reagent development to enable molecular characterizationU19AG065156 · NIA · UNIVERSITY OF WASHINGTON · PI TIAN, LU · 2020 to 2024
$15.9M
Multi-omic functional assessment of novel AD variants using high-throughput and single-cell technologiesU01AG072573 · NIA · STANFORD UNIVERSITY · PI KUNDAJE, ANSHUL, MONTGOMERY, STEPHEN · 2021 to 2025
$8.3M
Molecular Phenotyping in Alzheimer's DiseaseRF1AG053959 · NIA · STANFORD UNIVERSITY · PI LARSON, ERIC B, MACCOSS, MICHAEL · 2016 to 2017
$4.1M
Machine Learning for Integrative Modeling of the Immune System in Clinical SettingsR35GM138353 · NIGMS · STANFORD UNIVERSITY · PI AGHAEEPOUR, NIMA · 2020 to 2024
$2.2M
Neuropathology of synapses in AD and ADRDRF1AG077443 · NIA · STANFORD UNIVERSITY · PI AGHAEEPOUR, NIMA, MONTINE, THOMAS J · 2023 to 2023
$2.2M
Neuropathology of synapses in AD and ADRDR01AG077443 · NIA · STANFORD UNIVERSITY · PI Nima Aghaeepour, Thomas J Montine · 2026 to 2026
$707k
NIA NIH HHS R01 AG077443NIA NIH HHS RF1 AG053959NIA NIH HHS RF1 AG077443NIA NIH HHS U01 AG072573NIA NIH HHS U19 AG065156NIGMS NIH HHS R35 GM138353
6 · The paper itself

Abstract

Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) accurately depicts the chromatin regulatory state and altered mechanisms guiding gene expression in disease. However, bulk sequencing entangles information from different cell types and obscures cellular heterogeneity. To address this, we developed Cellformer, a deep learning method that deconvolutes bulk ATAC-seq into cell type-specific expression across the whole genome. Cellformer enables cost-effective cell type-specific open chromatin profiling in large cohorts. Applied to 191 bulk samples from 3 brain regions, Cellformer identifies cell type-specific gene regulatory mechanisms involved in resilience to Alzheimer's disease, an uncommon group of cognitively healthy individuals that harbor a high pathological load of Alzheimer's disease. Cell type-resolved chromatin profiling unveils cell type-specific pathways and nominates potential epigenetic mediators underlying resilience that may illuminate therapeutic opportunities to limit the cognitive impact of the disease. Cellformer is freely available to facilitate future investigations using high-throughput bulk ATAC-seq data.

Indexed as

Alzheimer DiseaseBiological AssayCell CycleChromatinEpigenesis, GeneticHumansChromatin

Identifiers

PMID37587197
PMCPMC10432546

What OpenQuestion holds

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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 OpenQuestion graph.