PXD067152-1

PXD067152 is an original dataset announced via ProteomeXchange.

Title	Comparative proteomic analysis of skin wound healing responses to biomaterial treatments identifies key pathways which govern differential regenerative outcomes Comparative proteomic analysis of skin wound healing responses to biomaterial treatments identifies key pathways which govern differential regenerative outcomes
Description	The wound healing cascade is characterized by the steady progression of distinct stages. Though biomaterials are used clinically to enhance wound closure rate and quality of healed tissue, their mechanisms of action are less understood. Here we use proteomic analysis to characterize changes in the wound healing response across three biomaterial treatments: a clinically used collagen hydrogel, and two synthetic biomaterials that are characterized by an increased regenerative response either through decreased fibrosis or through an activation of adaptive immunity. We identified close to 5,000 proteins shared across the biomaterial treatment groups, sampled at timepoints representing the inflammation, proliferation, and resolution phases of wound healing. The collagen hydrogel maintains an enrichment of immune-related pathways throughout the healing process. The fibrosis-suppressing material enriches gene ontology (GO) terms related to increased epidermis development pathways, collagen synthesis, and collagen fibril organization. In contrast, the adaptive immunity-activating biomaterial shows an early enrichment of GO terms related to broad immunity and inflammation. Later, this same material promotes keratinization, muscle and lipid oxidation GO pathways. Taken together, this work determines the key temporal pathways (immunity, keratinization, muscle system process, and ECM organization) mediated by three biomaterials, which result in varying healed tissue structure.
HostingRepository	PRIDE
AnnounceDate	2025-09-15
AnnouncementXML	Submission_2025-09-14_23:07:26.974.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD067152
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alejandra Suarez-Arnedo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-09 09:42:54	ID requested
⏵ 1	2025-09-14 23:07:27	announced

10.6019/PXD067152;

Suarez-Arnedo A, Caston ELP, Liu Y, Bai H, Muddiman DC, Segura T, Comparative proteomic analysis of skin wound healing responses to biomaterial treatments identifies key pathways which govern differential regenerative outcomes. Biomaterials, 326():123667(2025) [pubmed]

10.1016/j.biomaterials.2025.123667;

submitter keyword: proteomics, regeneration, wound healing, Gene ontology, chirality, MAP scaffold

David Muddiman
contact affiliation	Biological Imaging Laboratory for Disease and Exposure Research (BILDER), Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
contact email	dcmuddim@ncsu.edu
lab head
Alejandra Suarez-Arnedo
contact affiliation	PhD student
contact email	alejandra.suarez.arnedo@duke.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD067152
     1. Label: PRIDE project
     2. Name: Comparative proteomic analysis of skin wound healing responses to biomaterial treatments identifies key pathways which govern differential regenerative outcomes Comparative proteomic analysis of skin wound healing responses to biomaterial treatments identifies key pathways which govern differential regenerative outcomes