Label‐free quantitative proteomic analysis of human periodontal ligament stem cells by high‐resolution mass spectrometry

Abstract

Background and Objectives Proteome analysis of periodontal ligament stem cells (PDLSCs) could be used to study the function of PDL tissue. We used a label‐free quantitative proteomic technique to investigate differentially expressed proteins (DEPs) in human PDLSCs (hPDLSCs) compared to human bone marrow mesenchymal stem cells (hBMSCs) and identify proteins specific to hPDLSCs. Material and Methods hPDLSCs (n = 3) and hBMSCs (n = 3) were cultured and harvested for protein extraction and trypsin digestion. The proteomes of both cell types were analyzed by nano‐liquid chromatography/tandem mass spectrometry. DEPs in hPDLSCs compared to hBMSCs were detected by label‐free quantification and evaluated through signal transduction pathway and gene ontology (GO) analysis. Results In total, 690 and 771 proteins were identified from hPDLSCs and hBMSCs, of which 561 proteins were in common and 124 DEPs were found between hPDLSCs and hBMSCs. Fifty‐eight proteins were expressed at significantly higher levels in hPDLSCs, whereas 66 proteins were expressed at lower levels compared to hBMSCs. The more highly expressed proteins were associated with translation and initiating protein synthesis, and lower expressed proteins were related to cell aging and metabolic processes. Proteins unique to hPDLSCs and hBMSCs were associated with translation and metabolic processes, respectively. Conclusion Our results demonstrate evidence of distinct differences in protein expression between hPDLSCs and hBMSCs by using label‐free quantitative proteomic analysis which was the first attempt in this field. DEPs included previously reported hPDLSC marker proteins and novel marker candidates, such as microtubule‐associated protein, CTP synthase 1 and stathmin, which could be the markers for developing periodontal disease diagnostics and therapies.

UBA2 activates Wnt/β-catenin signaling pathway during protection of R28 retinal precursor cells from hypoxia by extracellular vesicles derived from placental mesenchymal stem cells

“…To investigate the exosome mechanism during the recovery process in CoCl 2 -damaged R28 cells, we gathered clues on the functions of exosomes, using proteomics, and tried to prove the pathway through functional studies. The identified protein markers validated the accuracy of the proteomic analysis [48]. This analysis confirmed that exosomes derived from hPMSCs had a number of characterized proteins involved in protein-containing complexes and RNA binding for molecular functions.…”

“…Additional samples are required for high-throughput analysis to obtain more accurate proteomic data. Full coverage of peptides could not be achieved for complex biologic samples such as exosomes, since the dynamic range was only suitable to detect the most abundant ionized peptides in MS. Other data-independent acquisition methods may help expand the overall detection ability for proteomes and validate the candidate marker proteins identified by relative protein quantification [48]. The establishment of a proteome map and quantitative analysis platform may provide biologists the tools to investigate unknown biological functions [48].…”

UBA2 Activates Wnt/β-catenin Signaling Pathway during Protection of R28 Retinal Precursor Cells from Hypoxia by Extracellular Vesicles derived from Placental Mesenchymal Stem Cells

“…To investigate the exosome mechanism during the recovery process in CoCl 2 -damaged R28 cells, we gathered clues on the functions of exosomes, using proteomics, and tried to prove the pathway through functional studies. The identi ed protein markers validated the accuracy of the proteomic analysis [41]. This analysis confirmed that exosomes derived from hPMSCs had a number of characterized proteins involved in protein-containing complexes and RNA binding for molecular functions.…”

“…Additional samples are required for high-throughput analysis to obtain more accurate proteomic data. Full coverage of peptides could not be achieved for complex biologic samples such as exosomes, since the dynamic range was only suitable to detect the most abundant ionized peptides in MS. Other data-independent acquisition methods may help expand the overall detection ability for proteomes and validate the candidate marker proteins identi ed by relative protein quanti cation [41]. Establishment of a proteome map and quantitative analysis platform may provide biologists the tools to investigate unknown biological functions [41].…”

Aggregation‐induced integrated stress response rejuvenates culture‐expanded human mesenchymal stem cells

“…In this study, 1,016, 790, and 1,104 proteins in bMSCs, ASCs, and fibroblasts were identified, respectively, which suggest that the extraction and labelfree proteomics analysis in our study are more sensitive. Label-free analysis of bone marrow-sourced stem cells has also been utilized previously to study the function of tissues (Han, Hong, & Park, 2019) and in the characterization of cellular responses to chondrogenic treatment regimens (Oswald, Brown, Bulinski, & Hung, 2011). In particular, our PCA results illustrate a significant separation of 2D…”