PXD054819

PXD054819 is an original dataset announced via ProteomeXchange.

Title	Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity
Description	Many diseases, such as obesity, have systemic effects that impact multiple organ systems throughout the body. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here, we developed a suite of deep learning-based image analysis algorithms (MouseMapper) and integrated it with tissue clearing and light sheet microscopy to enable a comprehensive quantitative analysis of diseases impacting diverse systems across the mouse body. This technological approach enables quantitative analysis of cellular and structural changes across the entire mouse body at unprecedented resolution and scale, including tracking nerves over several centimeters in whole animal bodies. To demonstrate its power, we applied MouseMapper to study nervous and immune systems in chow and high-fat diet (HFD)-induced obese mice. We uncovered widespread changes in both immune cell distribution and nerve structures, including alterations in the trigeminal nerve characterized by reduced nerve endings in obese mice. These structural abnormalities were associated with functional deficits of whiskers that they innervate and proteomic changes in their ganglion, primarily affecting pathways related to axon growth, and the complement system. Additionally, we revealed whole-body inflammation, which showed heterogeneity across different tissues in obese mice. Our study demonstrates MouseMapper's capability to discover and quantify pathological alterations at the whole-body level, offering a powerful new approach for investigating the systemic impacts of various diseases.
HostingRepository	PRIDE
AnnounceDate	2026-05-06
AnnouncementXML	Submission_2026-05-06_08:45:41.251.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ali Erturk
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-12 10:24:44	ID requested
⏵ 1	2026-05-06 08:45:42	announced

Dataset with its publication pending

submitter keyword: Obesity, Tissue clearing, Trigeminal ganglion, Imaging, High-fat diet

Prof. Ali Erturk
contact affiliation	Helmholtz Munich
contact email	ali.erturk@helmholtz-munich.de
lab head
Ali Erturk
contact affiliation	Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Munich
contact email	ali.erturk@helmholtz-munich.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD054819

PRIDE project URI

• PRIDE
  1. PXD054819
     1. Label: PRIDE project
     2. Name: Deep Learning and 3D Imaging Reveal Whole-Body Alterations in Obesity