PXD072778-1

PXD072778 is an original dataset announced via ProteomeXchange.

Title	Efferocytosis triggered proteomic reprogramming of macrophages reveals CD97 as a novel apoptotic receptor.
Description	Within the human body, billions of cells undergo apoptosis daily, and it is important that these cells are efficiently removed without causing an inflammatory response. This is mainly carried out by innate immune cells, such as macrophages, in a process referred to as efferocytosis. During efferocytosis, apoptotic cells attract macrophages via 'find-me' signals exposed on their cell surface and trigger phagocytosis via 'eat-me' signals. Following uptake and digestion, macrophages undergo extensive reprogramming towards a pro-resolving phenotype that promotes tissue repair. To date, no study has investigated these reprogramming events on the proteome level, and so in order to differentiate between the proteomes of the macrophage and apoptotic cell, we employed stable isotope labeling by amino acids in cell culture (SILAC). We show that using this approach, we can successfully dissect the mixed proteomes and successfully map the reprogramming events in macrophages following efferocytosis. Specifically, we show that these cells adopt a unique pro-resolving phenotype underpinned by an increase in efferocytic and anti-inflammatory markers. Notably, we also show that the secretome of efferocytic macrophages can alter the phenotype of naive macrophages, shifting them towards an efferocytosis-like phenotype. These results have important implications for clinical aspects of efferocytosis, specifically in cases where we can map macrophage reprogramming in disease states.
HostingRepository	PRIDE
AnnounceDate	2026-09-09
AnnouncementXML	Submission_2026-09-09_00:15:57.454.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthias Trost
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	6x(13)C labeled residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-07 15:33:08	ID requested
⏵ 1	2026-09-09 00:15:57	announced

Dataset with its publication pending

submitter keyword: DIA,Macrophages, Efferocytosis, LC-MS/MS

Matthias Trost
contact affiliation	Laboratory for Biomedical Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
contact email	matthias.trost@newcastle.ac.uk
lab head
Matthias Trost
contact affiliation	Newcastle University
contact email	matthias.trost@ncl.ac.uk
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/2026/09/PXD072778

PRIDE project URI

• PRIDE
  1. PXD072778
     1. Label: PRIDE project
     2. Name: Efferocytosis triggered proteomic reprogramming of macrophages reveals CD97 as a novel apoptotic receptor.