Proteome analysis, bioinformatic prediction and experimental evidence revealed immune response down-regulation function for serum-starved human fibroblasts

Negar Jafari; Reza Gheitasi; Hamid Reza Khorasani; Monireh Golpour; Maryam Mehri; Kosar Nayeri; Roghayeh Pourbagher; Mobina Mostafazadeh; Behnam Kalali; Amrollah Mostafazadeh

doi:10.1016/j.heliyon.2023.e19238

Proteome analysis, bioinformatic prediction and experimental evidence revealed immune response down-regulation function for serum-starved human fibroblasts

Heliyon. 2023 Aug 22;9(9):e19238. doi: 10.1016/j.heliyon.2023.e19238. eCollection 2023 Sep.

Authors

Negar Jafari^{1

2}, Reza Gheitasi³, Hamid Reza Khorasani^{4

5}, Monireh Golpour⁶, Maryam Mehri^{1

2}, Kosar Nayeri^{1

2}, Roghayeh Pourbagher^{1

2}, Mobina Mostafazadeh⁷, Behnam Kalali⁸, Amrollah Mostafazadeh²

Affiliations

¹ Student Research Committee, Babol University of Medical Sciences, Babol, Iran.
² Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
³ Institutes for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.
⁴ Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Babol, Iran.
⁵ Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran.
⁶ Department of Immunology, Molecular and Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
⁷ Faculty of Sciences, Islamic Azad University of Sari, Sari, Iran.
⁸ Department of Medicine II, Klinikum Grosshadern, LMU University, 81377, Munich, Germany.

Abstract

Emerging evidence indicates that fibroblasts play pivotal roles in immunoregulation by producing various proteins under health and disease states. In the present study, for the first time, we compared the proteomes of serum-starved human skin fibroblasts and peripheral blood mononuclear cells (PBMCs) using Nano-LC-ESI-tandem mass spectrometry. This analysis contributes to a better understanding of the underlying molecular mechanisms of chronic inflammation and cancer, which are intrinsically accompanied by growth factor deficiency.The proteomes of starved fibroblasts and PBMCs consisted of 307 and 294 proteins, respectively, which are involved in lymphocyte migration, complement activation, inflammation, acute phase response, and immune regulation. Starved fibroblasts predominantly produced extracellular matrix-related proteins such as collagen/collagenase, while PBMCs produced focal adhesion-related proteins like beta-parvin and vinculin which are involved in lymphocyte migration. PBMCs produced a more diverse set of inflammatory molecules like heat shock proteins, while fibroblasts produced human leukocytes antigen-G and -E that are known as main immunomodulatory molecules. Fifty-four proteins were commonly found in both proteomes, including serum albumin, amyloid-beta, heat shock cognate 71 kDa, and complement C3. GeneMANIA bioinformatic tool predicted 418 functions for PBMCs, including reactive oxygen species metabolic processes and 241 functions for starved fibroblasts such as antigen processing and presentation including non-classical MHC -Ib pathway, and negative regulation of the immune response. Protein-protein interactions network analysis indicated the immunosuppressive function for starved fibroblasts-derived human leucocytes antigen-G and -E. Moreover, in an in vitro model of allogeneic transplantation, the immunosuppressive activity of starved fibroblasts was experimentally documented.

Conclusion: Under serum starvation-induced metabolic stress, both PBMCs and fibroblasts produced molecules like heat shock proteins and amyloid-beta, which can have pathogenic roles in auto-inflammatory diseases such as rheumatoid arthritis, type 1 diabetes mellitus, systemic lupus erythematosus, aging, and cancer. However, starved fibroblasts showed immunosuppressive activity in an in vitro model of allogeneic transplantation, suggesting their potential to modify such adverse reactions by down-regulating the immune system.

Keywords: Bioinformatics; Cell culture; Fibroblasts; PBMCs; Proteome; Serum; Starvation.