Evidence map›Paper›PMID 39329069›Full record

ArticleGEN biotechnology2023

Influence of Alzheimer's disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex.

Sang Ho Kwon, Sowmya Parthiban, Madhavi Tippani, Heena R Divecha, Nicholas J Eagles, Jashandeep S Lobana, Stephen R Williams, Michelle Mak, Rahul A Bharadwaj, Joel E Kleinman and 6 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GEN biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing 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

12 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Review
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  11. SpotSweeper: spatially-aware quality control for spatial transcriptomics.bioRxiv : the preprint server for biology · 2024
    Article
  12. Review
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

16 authors.

Sang Ho KwonThe Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Sowmya ParthibanDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Madhavi TippaniLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Heena R DivechaLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Nicholas J EaglesLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Jashandeep S LobanaLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Stephen R Williams10x Genomics, Pleasanton, CA, USA.
Michelle Mak10x Genomics, Pleasanton, CA, USA.
Rahul A BharadwajLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Joel E KleinmanLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Thomas M HydeLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Stephanie C PageLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Stephanie C HicksDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Keri MartinowichLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Kristen R MaynardLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
Leonardo Collado-TorresLieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.

Funding

Spatial registration of gene expression in the human brainU01MH122849 · NIMH · LIEBER INSTITUTE, INC. · PI MARTINOWICH, KERI · 2020 to 2021
$1.7M
NIMH NIH HHS U01 MH122849
6 · The paper itself

Abstract

Neuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular and cellular processes that disturb homeostasis of local microenvironments. Here, we applied the 10x Genomics Visium Spatial Proteogenomics (Visium-SPG) platform, which couples spatial gene expression with immunofluorescence protein co-detection, to evaluate its ability to quantify changes in spatial gene expression with respect to amyloid-β (Aβ) and hyperphosphorylated tau (pTau) pathology in post-mortem human brain tissue from individuals with Alzheimer's disease (AD). We identified transcriptomic signatures associated with proximity to Aβ in the human inferior temporal cortex (ITC) during late-stage AD, which we further investigated at cellular resolution with combined immunofluorescence and single molecule fluorescent in situ hybridization (smFISH). The study provides a data analysis workflow for Visium-SPG, and the data represent a proof-of-principal for the power of multi-omic profiling in identifying changes in molecular dynamics that are spatially-associated with pathology in the human brain. We provide the scientific community with web-based, interactive resources to access the datasets of the spatially resolved AD-related transcriptomes at https://research.libd.org/Visium_SPG_AD/.

Indexed as

Alzheimer's diseaseamyloid-β (Aβ)neuropathologyphosphorylated tau (pTau)RNA-protein co-detectionSpatially-resolved transcriptomics

Identifiers

PMID39329069
PMCPMC11426291

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.