Evidence map›Paper›PMID 41000710›Full record

ArticlebioRxiv : the preprint server for biology2025

Integrative Spatial Omics for Systems-Level Mapping of Pathological Niches.

Angela R S Kruse, Roy Lardenoije, Lukasz G Migas, Claire F Scott, Cody Marshall, Morad C Malek, Adel Eskaros, Thai Pham, Kristie Aamodt, Madeline Colley and 7 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

17 authors.

Angela R S KruseMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0000-0001-8776-2769
Roy LardenoijeDepartment of Intelligent Systems, Delft University of Technology, Delft, Netherlands.ORCID 0000-0002-9026-7870
Lukasz G MigasDelft Center for Systems and Control, Delft University of Technology, Delft, Netherlands.ORCID 0000-0002-1884-6405
Claire F ScottMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0000-0002-8467-3370
Cody MarshallMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0009-0005-9639-0537
Morad C MalekMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0000-0002-6796-1899
Adel EskarosDepartment of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.ORCID 0000-0001-9028-338X
Thai PhamMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.
Kristie AamodtDivision of Pediatric Endocrinology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
Madeline ColleyMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0000-0002-9515-3493
Lissa Ventura-AntunesDepartment of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.ORCID 0000-0001-5508-0990
Melissa A FarrowMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0000-0002-1602-2082
Raf Van de PlasDelft Center for Systems and Control, Delft University of Technology, Delft, Netherlands.ORCID 0000-0002-2232-7130
Joana GoncalvesDepartment of Intelligent Systems, Delft University of Technology, Delft, Netherlands.
Matthew SchragDepartment of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.ORCID 0000-0001-7048-0503
Alvin C PowersDepartment of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.ORCID 0000-0003-1941-5786
Jeffrey M SpragginsMass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA.ORCID 0000-0001-9198-5498

Funding

Human Pancreas Analysis Program for Type 1 Diabetes - HPAP-T1DU01DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI MARK A. ATKINSON, KLAUS H KAESTNER · 2021 to 2026
$46.8M
Vanderbilt Diabetes Research CenterP30DK020593 · NIDDK · VANDERBILT UNIVERSITY MEDICAL CENTER · PI ALVIN C POWERS · 2012 to 2026
$29.3M
Flexible Hybrid Cloud Infrastructure for Seamless Integration and Use of Human Biomolecular Data and Reference Maps [1 of 5]OT2OD033759 · OD · CARNEGIE-MELLON UNIVERSITY · PI BLOOD, PHILIP D., SILVERSTEIN, JONATHAN C. · 2022 to 2025
$20.4M
Penn integrated Human Pancreas procurement and Analysis ProgramUC4DK112217 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BETTS, MICHAEL R, FELDMAN, MICHAEL D · 2016 to 2020
$17.8M
Diabetes-Docs: Physician-Scientist Career Development Program (DiabDocs)K12DK133995 · NIDDK · STANFORD UNIVERSITY · PI LINDA A DIMEGLIO, David Matthew Maahs · 2022 to 2026
$16.0M
Human Pancreas Analysis Program-T2DU01DK123716 · NIDDK · VANDERBILT UNIVERSITY MEDICAL CENTER · PI ATKINSON, MARK A., BOTTINO, RITA · 2019 to 2024
$6.6M
Discovery of Pancreatic Signatures in Type 2 Diabetes MellitusR24DK106755 · NIDDK · VANDERBILT UNIVERSITY MEDICAL CENTER · PI CAI, LONG, CAPRIOLI, RICHARD M · 2015 to 2019
$6.2M
Pancreas Organ Specific ProjectU54EY032442 · NEI · VANDERBILT UNIVERSITY · PI CAPRIOLI, RICHARD M · 2020 to 2024
$5.7M
Integrated Training in Engineering and DiabetesT32DK101003 · NIDDK · VANDERBILT UNIVERSITY · PI Jamey D. Young · 2014 to 2026
$3.9M
Elucidating Molecular Drivers of Aging and Alzheimer's Disease via Multimodal Imaging Mass SpectrometryR01AG078803 · NIA · VANDERBILT UNIVERSITY · PI Rena A. S. Robinson, Matthew Schrag · 2022 to 2026
$3.5M
Vanderbilt Interdisciplinary Training Program in Alzheimer's DiseaseT32AG058524 · NIA · VANDERBILT UNIVERSITY · PI ANGELA L. JEFFERSON · 2018 to 2026
$3.5M
BLRD VA I01 BX000666NEI NIH HHS U54 EY032442NIA NIH HHS R01 AG078803NIA NIH HHS T32 AG058524NIDDK NIH HHS K12 DK133995NIDDK NIH HHS P30 DK020593NIDDK NIH HHS R24 DK106755NIDDK NIH HHS T32 DK101003NIDDK NIH HHS U01 DK112217NIDDK NIH HHS U01 DK123716NIDDK NIH HHS UC4 DK112217NIH HHS OT2 OD033759
6 · The paper itself

Abstract

Spatial 'omics technologies are a powerful tool for mapping the relationship between cellular organization and molecular distributions in healthy and diseased tissue microenvironments. Here, we describe a novel multimodal pipeline that represents experimental and computational advances for spatiomolecular analysis of tissue samples across molecular classes. This adaptable method integrates matrix-assisted laser desorption/ionization imaging mass spectrometry spatial lipidomics, spatial transcriptomics, protein imaging via multiplexed immunofluorescence microscopy, and histopathological staining to uncover spatiomolecular profiles associated with unique cellular niches and pathological features. We demonstrate the power of this approach using two different complex human disease systems: Alzheimer's disease in human brain tissue and type 2 diabetes mellitus in the human pancreas. This work establishes and demonstrates a generalizable framework for multimodal spatial integration, enabling precise mapping of molecular mechanisms that underlie complex tissue pathologies.

Indexed as

AmyloidImaging Mass SpectrometryMALDIMultimodalMultiplexed immunofluorescence microscopySpatial transcriptomics

Identifiers

PMID41000710
PMCPMC12458195

What OpenQuestion holds

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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 OpenQuestion graph.