Comparative analysis of differentially secreted proteins in serum-free and serum-containing media by using BONCAT and pulsed SILAC

Scientific Reports
Jihye ShinCheolju Lee

Abstract

Despite the increased interest in secretomes associated with paracrine/autocrine mechanisms, the majority of mass spectrometric cell secretome studies have been performed using serum-free medium (SFM). On the other hand, serum-containing medium (SCM) is not recommended very much because the secretome obtained with SCM is easily contaminated with fetal bovine serum (FBS) proteins. In this study, through the combination of bioorthogonal non-canonical amino acid tagging (BONCAT) and pulsed-SILAC (pSILAC), we analyzed differentially secreted proteins between SFM and SCM in a cancer-derived human cell, U87MG, and a mesenchymal stem cell derived from human Wharton's jelly (hWJ-MSCs). In most cases, the bioinformatic tools predicted a protein to be truly secretory when the secretion level of the protein was more in SCM than in SFM. In the case of hWJ-MSCs, the amount of proteins secreted in SCM for 24 hours was larger than that of SFM (log2 fold change = 0.96), even considering different cell proliferation rates. hWJ-MSCs proteins secreted more in SCM included several positive markers of MSC paracrine factors implicated in angiogenesis, neurogenesis and osteogenesis, and upstream regulators of cell proliferation. Our study suggests th...Continue Reading

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Citations

May 14, 2020·International Journal of Molecular Sciences·Nuria Garrido-PérezEduardo Ruiz-Pesini
Aug 14, 2019·International Journal of Molecular Sciences·Parkyong SongJong Hyuk Yoon
Oct 8, 2020·Canadian Journal of Microbiology·Arjun SukumaranJennifer Geddes-McAlister
Nov 18, 2020·Nature Chemical Biology·Wei WeiJonathan Z Long
Oct 19, 2019·Analytical Chemistry·Suttipong SuttapitugsakulRonghu Wu
Dec 4, 2021·Journal of Proteome Research·David Vargas-Diaz, Maarten Altelaar

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Datasets Mentioned

BETA
PXD007529
50

Methods Mentioned

BETA
protein fractionation
acetylation

Software Mentioned

TMHMM
EVpedia
Ingenuity Pathway Analysis ( IPA
Proteome Discoverer
secretomeP
ProteoMiner
ProteinCenter
Proxeon
MS
BONCAT

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