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Contribution of Proteomics and Bioinformatics to The Understanding of The Platelet Secretome

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Background: Outdated allogenic platelet concentrates (PCs) from blood establishments can be used as source material for the preparation of different types of human platelet lysates (HPLs) for clinical applications in cell therapy and regenerative medicine. It is important to understand how the subs

tantial variations in the mode of preparation of HPLs can affect their protein composition and biological function in order to optimize quality and safety as well as clinical applications.Aims: To unveil the proteomes and biological functions of various HPLs to help optimize their clinical applicati

ons.Material and Methods: Outdated PCs were obtained from Taipei Blood Center. The PCs were separated into 3 sub-pools that were subjected to 3 processing methodologies to produce 7 different types of HPLs: (1) Freeze-thaw Platelet Lysate (FTPL): PC was frozen and thawed to release the platelet cont

ent into the plasma compartment; (2) Serum Converted Platelet Lysate (SCPL): PC was supplemented with calcium chloride to convert fibrinogen into fibrin; (3) Heat treated-Serum Converted Platelet Lysate (HSCPL): SCPL was heat-treated (56°C, 30 min); (4) Platelet Pellet Lysate (PPL): isolated platele

ts, depleted of plasma, were lysed by freeze/thaw; (5) Heat-treated-Platelet Pellet Lysate (HPPL): PPL was heat-treated (56°C, 30 min); (6) Micro-filtered-HPPL (HPPL0201): a 0.2-0.1 µm filtration sequence was used to remove large molecules or particles; and (7) Nanofiltered-HPPL (HPPL0201P20): HPPL0

201 was filtered through Planova 20N, a 19-nm virus removal filter. Label-free proteomic was first performed by precipitating proteins by acetone followed by trypsin digestion and LC-MS/MS analysis to obtain a global understanding of the HPL proteomes. For accurate proteome quantification, the HPLs

were depleted of 14 major plasma components using MARS (Multiple Affinity Removal Spin Cartridge Human), followed by trypsin digestion. Peptides were collected, labeled with Tandem Mass Tag (TMT) reagents and analyzed by LC-MS/MS using Orbitrap Fusion Lumos Tribrid Quadrupole-ion trap-Orbitrap mass

spectrometer. Lists of identified and quantified proteins were studied and searched against bioinformatics platforms for pathway enrichment and characterization analysis. Western blotting was then conducted to validate the quantitative results from proteomics.Results: In total, we detected 1441 prot

eins in label-free proteomics, 952 proteins in TMT-labeling experiment (1) of HPLs pairs before and after depletion and 1114 proteins in TMT-labeling experiment (2) of the seven depleted-HPLs. Most of the proteins were from cytoplasm and had catalytic activity. The identified proteomes were previous

ly identified to be associated with platelets. Most of proteins were from cytoplasm and had catalytic activity with the main biological processes involved in the hemostasis and immune system. Different processing steps impacted HPLs composition and their associated canonical pathways. The quantifica

tion achieved in proteomics was compatible with semiquantitative immunoblotting of proteins.Conclusion: Our proteomics data revealed substantial differences in those HPL preparations that may have relevant various impacts on their functionality and application in cell therapy and regenerative medic

ine. Each HPLs has a specific cohort of abundant proteins and distinct proportion of proteins that could be used to define a scientifically-based rationale for optimal clinical use.