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

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.

Analyzing secretory proteins in human dermal fibroblast-conditioned medium for angiogenesis: A bioinformatic approach.

BACKGROUND: The conditioned medium from human dermal fibroblasts (dermal fibroblast-conditioned medium; DFCM) contains a diverse array of secretory proteins, including growth factors and wound repair-promoting proteins. Angiogenesis, a crucial process that facilitates the infiltration of inflammatory cells during wound repair, is induced by a hypoxic environment and inflammatory cytokines. METHODS: In this study, we conducted a comprehensive bioinformatic analysis of 337 proteins identified through proteomics analysis of DFCM. We specifically focused on 64 DFCM proteins with potential involvement in angiogenesis. These proteins were further classified based on their characteristics, and we conducted a detailed analysis of their protein-protein interactions. RESULTS: Gene Ontology protein classification categorized these 64 DFCM proteins into various classes, including metabolite interconversion enzymes (N = 11), protein modifying enzymes (N = 10), protein-binding activity modulators (N = 9), cell adhesion molecules (N = 6), extracellular matrix proteins (N = 6), transfer/carrier proteins (N = 3), calcium-binding proteins (N = 2), chaperones (N = 2), cytoskeletal proteins (N = 2), RNA metabolism proteins (N = 1), intercellular signal molecules (N = 1), transporters (N = 1), scaffold/adaptor proteins (N = 1), and unclassified proteins (N = 9). Furthermore, our protein-protein interaction network analysis of DFCM proteins revealed two distinct networks: one with medium confidence level interaction scores, consisting of 60 proteins with significant connections, and another at a high confidence level, comprising 52 proteins with significant interactions. CONCLUSIONS: Our bioinformatic analysis highlights the presence of a multitude of secretory proteins in DFCM that form significant protein-protein interaction networks crucial for regulating angiogenesis. These findings underscore the critical roles played by DFCM proteins in various stages of angiogenesis during the wound repair process.

Proteomic Identification and Quantification of Secretory Proteins in Human Dermal Fibroblast-Conditioned Medium for Wound Repair and Hair Regeneration.

Background: Human dermal fibroblasts secrete numerous growth factors and proteins that have been suggested to promote wound repair and hair regeneration. Methods: Human dermal fibroblast-conditioned medium (DFCM) was prepared, and proteomic analysis was performed. Secretory proteins in DFCM were identified using 1-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis, in-gel trypsin protein digestion, and quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS). Identified proteins were analyzed using bioinformatic methods for the classification and evaluation of protein-protein interactions. Results: Using LC-MS/MS, 337 proteins were identified in DFCM. Among them, 160 proteins were associated with wound repair, and 57 proteins were associated with hair regeneration. Protein-protein interaction network analysis of 160 DFCM proteins for wound repair at the highest confidence score (0.9) revealed that 110 proteins were grouped into seven distinctive interaction networks. Additionally, protein-protein interaction network analysis of 57 proteins for hair regeneration at the highest confidence score revealed that 29 proteins were grouped into five distinctive interaction networks. The identified DFCM proteins were associated with several pathways for wound repair and hair regeneration, including epidermal growth factor receptor, fibroblast growth factor, integrin, Wnt, cadherin, and transforming growth factor-ß signaling pathways. Conclusion: DFCM contains numerous secretory proteins that comprise groups of protein-protein interaction networks that regulate wound repair and hair regeneration.

Effects of Human Fibroblast-Derived Multi-Peptide Factors on the Proliferation and Migration of Nitrogen Plasma-Treated Human Dermal Fibroblasts.

Background: Human fibroblast-derived multi-peptide factors (MPFs) promote wound repair by playing crucial roles in cell recruitment, adhesion, attachment, migration, and proliferation. Methods: Cultured human dermal fibroblasts (HDFs) were directly treated with non-contact low- and high-energy nitrogen plasma and further cultured in various conditioned media. Cell proliferation and wound-healing properties were evaluated. Results: In Opti-modified Eagle's medium + GlutaMAX culture, reduced HDF viability was observed 24 h after 2-J/pulse plasma treatment and 12 and 24 h after 3-J/pulse treatment. Meanwhile, in dermal fibroblast-conditioned medium (DFCM) containing MPF culture, reduced HDF viability was observed only 24 h after 3-J/pulse treatment. Under DFCM-MPF culture, the wound area percentage was significantly decreased after 12 and 24 h in untreated HDFs; at 9, 12, and 24 h after 1-J/pulse plasma treatment; at 3, 6, 9, 12, and 24 h after 2-J/pulse plasma treatment; and at 9, 12, and 24 h after 3-J/pulse plasma treatment. Greater migration of HDFs with or without plasma treatment was found in DFCM-MPFs than in other conditioned media. Conclusion: Low-energy nitrogen plasma treatment promotes HDF proliferation and wound repair. DFCM-MPFs enhanced cell proliferation and improved the wound healing properties of HDFs treated with low- and high-energy plasma.