Human dermal fibroblast-derived secretory proteins for regulating nerve restoration: A bioinformatic approach

Skin Res Technol. 2024 Jun;30(6):e13810. doi: 10.1111/srt.13810.

Abstract

Background: Human dermal fibroblasts secrete diverse proteins that regulate wound repair and tissue regeneration.

Methods: In this study, dermal fibroblast-conditioned medium (DFCM) proteins potentially regulating nerve restoration were bioinformatically selected among the 337 protein lists identified by quantitative liquid chromatography-tandem mass spectrometry. Using these proteins, protein-protein interaction network analysis was conducted. In addition, the roles of DFCM proteins were reviewed according to their protein classifications.

Results: Gene Ontology protein classification categorized these 57 DFCM proteins into various classes, including protein-binding activity modulator (N = 11), cytoskeletal protein (N = 8), extracellular matrix protein (N = 6), metabolite interconversion enzyme (N = 5), chaperone (N = 4), scaffold/adapter protein (N = 4), calcium-binding protein (N = 3), cell adhesion molecule (N = 2), intercellular signal molecule (N = 2), protein modifying enzyme (N = 2), transfer/carrier protein (N = 2), membrane traffic protein (N = 1), translational protein (N = 1), and unclassified proteins (N = 6). Further protein-protein interaction network analysis of 57 proteins revealed significant interactions among the proteins that varied according to the settings of confidence score.

Conclusions: Our bioinformatic analysis demonstrated that DFCM contains many secretory proteins that form significant protein-protein interaction networks crucial for regulating nerve restoration. These findings underscore DFCM proteins' critical roles in various nerve restoration stages during the wound repair process.

Keywords: bioinformatics; dermal fibroblast‐conditioned media; human dermal fibroblast; nerve restoration; neurogenesis; proteomic analysis; secretory protein.

MeSH terms

  • Cells, Cultured
  • Computational Biology*
  • Culture Media, Conditioned
  • Dermis / cytology
  • Dermis / metabolism
  • Fibroblasts* / metabolism
  • Humans
  • Nerve Regeneration* / physiology
  • Protein Interaction Maps* / physiology
  • Tandem Mass Spectrometry
  • Wound Healing / physiology

Substances

  • Culture Media, Conditioned