Variations of secretome profiles according to conditioned medium preparation: The example of human mesenchymal stem cell‐derived adipocytes

One challenging point in analyzing cellular secretome collected as conditioned medium is cross‐contamination by cell culture media components, especially bovine serum proteins. A common approach for serum removal is to wash the cells, an alternative is to grow cells using serum‐free conditions. Given that the sample processing may influence the phenotype of cells and thus the secretome, it is important to establish the optimal protocol for each cell type. In this study, we compared two methods for preparing conditioned medium from human adipocytes derived from mesenchymal stem cells. Cells were either washed twice with PBS or cultured the last four days of differentiation in serum‐free adipogenic medium. Gene expression of the cells was evaluated by using real‐time PCR and 1D LC‐MS/MS was used to compare secreted proteins present in the culture supernatants. Surprisingly, results showed significant differences in gene expression patterns of the cells and in protein content of the conditioned media and suggested that PBS washes induced severe modifications of the phenotype of cells and thus changes in protein secretion profiles. These data emphasize the significant variations in protein species related to cell manipulations and underline the importance of procedure optimization prior to any proteomic investigation.     

Widespread presence of bovine proteins in human cell lines

HPLC‐MS/MS analysis of various human cell lines shows the presence of a major amount of bovine protein contaminants. These likely originate from fetal bovine serum (FBS), typically used in cell cultures. If evaluated against a human protein database, on average 10% of the identified human proteins will be misleading (bovine proteins, but indicated as if they were human). Bovine contaminants therefore may cause major bias in proteomic studies of cell cultures, if not considered explicitly.     

Identification of mammalian cell lines using MALDI-TOF and LC-ESI-MS/MS mass spectrometry

Direct mass spectrometric analysis of complex biological samples is becoming an increasingly useful technique in the field of proteomics. Matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS) is a rapid and sensitive analytical tool well suited for obtaining molecular weights of peptides and proteins from complex samples. Here, a fast and simple approach to cellular protein profiling is described in which mammalian cells are lysed directly in the MALDI matrix 2,5-dihydroxybenzoic acid (DHB) and mass analyzed using MALDI-time of flight (TOF). Using the unique MALDI mass spectral "fingerprint" generated in these analyses, it is possible to differentiate among several different mammalian cell lines. A number of techniques, including MALDI-post source decay (PSD), MALDI tandem time-of-flight (TOF-TOF), MALDI-Fourier transform ion cyclotron resonance (FTICR), and nanoflow liquid chromatography followed by electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) were employed to attempt to identify the proteins represented in the MALDI spectra. Performing a tryptic digestion of the supernatant of the cells lysed in DHB with subsequent LC-ESI-MS/MS analysis was by far the most successful method to identify proteins.     

Evaluation of matrix effects in analysis of estrogen using liquid chromatography–tandem mass spectrometry

Matrix effects of different biological samples, including phosphate‐buffered saline–bovine serum albumin (PBS‐BSA), gelded horse serum, mouse serum, and mouse brain, were investigated for the determination of 17α‐ and β‐estradiol using derivatization with dansyl chloride prior to LC‐MS/MS. Matrix effects were evaluated based on the slopes of regression lines plotted from results obtained in biological matrices versus pure standard solutions. Such plots indicate the enhancement or suppression of signal based on the presence of a particular biological fluid for a particular method. The matrix effects from PBS‐BSA were similar to those of mouse serum. In contrast, analyses performed from horse serum and mouse brain yielded significant ion suppression, especially for 17β‐estradiol. Precipitation during derivatization was observed when pre‐concentrated samples were processed with ethyl acetate as an extraction solvent. This was overcome with the use of methyl tert‐butyl ether; however, matrix effects from this preparation were still present, evidenced by signal suppression and poor linearity in the standard curve. This work affirms that caution should be taken in the transfer of methods for use with different biological matrices, especially in the case where surrogate matrices are necessary for calibration purposes.     

Secreted proteome of the murine multipotent hematopoietic progenitor cell line DKmix

Administration of the multipotent hematopoietic progenitor cell (HPC) line DKmix improved cardiac function after myocardial infarction and accelerated dermal wound healing due to paracrine mechanisms. The aim of this study was to analyse the secreted proteins of DKmix cells in order to identify the responsible paracrine factors and assess their relevance to the wide spectrum of therapeutic effects. A mass spectrometry (MS)‐based approach was used to identify secreted proteins of DKmix cells. Serum free culture supernatants of DKmix‐conditioned medium were collected and the proteins present were separated, digested by trypsin and the resulting peptides were then analyzed by matrix‐assisted laser desorption/ionization tandem time‐of‐flight (MALDI‐TOF/TOF) MS. Overall 95 different proteins were identified. Among them, secretory proteins galectin‐3 and gelsolin were identified. These proteins are known to stimulate cell migration and influence wound healing and cardiac remodelling. The remaining proteins originate from intracellular compartments like cytoplasm (69%), nucleus (12%), mitochondria (4%), and cytoplasmic membrane (3%) indicating permeable or leaky DKmix cells in the conditioned medium. Additionally, a sandwich immunoassay was used to detect and quantify cytokines and chemokines. Interleukin‐6 (IL‐6), interleukin‐13 (IL‐13), monocyte‐chemoattractant protein‐1 (MCP‐1), monocyte‐chemoattractant protein‐3 (MCP‐3), monocyte‐chemoattractant protein‐1α (MIP‐1α) and monocyte‐chemoattractant protein‐1β (MIP‐1β) were detected in low concentrations. This study identified a subset of proteins present in the DKmix‐conditioned medium that act as paracrine modulators of tissue repair. Moreover, it suggests that DKmix‐derived conditioned medium might have therapeutic potency by promoting tissue regeneration. Copyright © 2010 John Wiley & Sons, Ltd.     

Reproducible method to enrich membrane proteins with high purity and high yield for an LC‐MS/MS approach in quantitative membrane proteomics

The proportionately low abundance of membrane proteins hampers their proteomic analysis, especially for a quantitative LC‐MS/MS approach. To overcome this limitation, a method was developed that consists of one cell disruption step in a hypotonic reagent using liquid nitrogen, one isolation step using a low speed centrifugation, and three wash steps using high speed centrifugation. Pellets contained plasma, nuclear, and mitochondrial membranes, including their integral, peripheral, and anchored membrane proteins. The reproducibility of this method was verified by protein assay of four separate experiments with a CV of 7.7%, and by comparative LC‐MS/MS label‐free quantification of individual proteins between two experiments with 99% of the quantified proteins having a CV ≤30%. Western blot and LC‐MS/MS results of markers for cytoplasm, nucleus, mitochondria, and their membranes indicated that the enriched membrane fraction was highly pure by the absence of, or presence of trace amounts of, nonmembrane marker proteins. The average yield of membrane proteins was 237 μg/10 million HT29‐MTX cells. LC‐MS/MS analysis of the membrane‐enriched sample resulted in the identification of 2597 protein groups. In summary, the developed method is reproducible, produces a highly pure membrane fraction, and generates a high yield of membrane proteins.     

Orthogonal organic and aqueous‐based washes of tissue sections to enhance protein sensitivity by MALDI imaging mass spectrometry

Imaging mass spectrometry (IMS) is an emergent and innovative approach for measuring the composition, abundance and regioselectivity of molecules within an investigated area of fixed dimension. Although providing unprecedented molecular information compared with conventional MS techniques, enhancement of protein signature by IMS is still necessary and challenging. This paper demonstrates the combination of conventional organic washes with an optimized aqueous‐based buffer for tissue section preparation before matrix‐assisted laser desorption/ionization (MALDI) IMS of proteins. Based on a 500 mM ammonium formate in water–acetonitrile (9:1; v/v, 0.1% trifluororacetic acid, 0.1% Triton) solution, this buffer wash has shown to significantly enhance protein signature by profiling and IMS (~fourfold) when used after organic washes (70% EtOH followed by 90% EtOH), improving the quality and number of ion images obtained from mouse kidney and a 14‐day mouse fetus whole‐body tissue sections, while maintaining a similar reproducibility with conventional tissue rinsing. Even if some protein losses were observed, the data mining has demonstrated that it was primarily low abundant signals and that the number of new peaks found is greater with the described procedure. The proposed buffer has thus demonstrated to be of high efficiency for tissue section preparation providing novel and complementary information for direct on‐tissue MALDI analysis compared with solely conventional organic rinsing. Copyright © 2013 John Wiley & Sons, Ltd.     

Exosome enrichment of human serum using multiple cycles of centrifugation

In this work, we compared the use of repeated cycles of centrifugation at conventional speeds for enrichment of exosomes from human serum compared to the use of ultracentrifugation (UC). After removal of cells and cell debris, a speed of 110 000 × g or 40 000 × g was used for the UC or centrifugation enrichment process, respectively. The enriched exosomes were analyzed using the bicinchoninic acid assay, 1D gel separation, transmission electron microscopy, Western blotting, and high‐resolution LC‐MS/MS analysis. It was found that a five‐cycle repetition of UC or centrifugation is necessary for successful removal of nonexosomal proteins in the enrichment of exosomes from human serum. More significantly, 5× centrifugation enrichment was found to provide similar or better performance than 5× UC enrichment in terms of enriched exosome protein amount, Western blot band intensity for detection of CD‐63, and numbers of identified exosome‐related proteins and cluster of differentiation (CD) proteins. A total of 478 proteins were identified in the LC‐MS/MS analyses of exosome proteins obtained from 5× UCs and 5× centrifugations including many important CD membrane proteins. The presence of previously reported exosome‐related proteins including key exosome protein markers demonstrates the utility of this method for analysis of proteins in human serum.     

“Stainomics”: Identification of mitotracker labeled proteins in mammalian cells

Organelle‐specific cell‐permeable fluorescent dyes are invaluable tools in cell biology as they reveal intracellular dynamics in living cells. Mitrotracker is a family of dyes that strongly label the mitochondrion, a key organelle associated with many crucial cellular functions. Despite the popularity of these dyes, little is known about the molecular mechanism behind their staining specificity. Here, we aimed to identify the protein targets of one member of this dye family, mitotracker red (MTR), by 2DE and MS. MTR bound to cellular proteins covalently, and its fluorescence persisted even after cell lysis, protein solubilization, denaturation, and electrophoresis. This enabled us to display MTR‐labeled proteins by 2DE. The MTR‐specific fluorescent signals on the gel revealed the spots that contained MTR‐conjugated proteins. These spots were analyzed by MS, resulting into the identification of ten proteins. We discovered that one major target is the mitochondrial protein HSP60 and that MTR staining could induce production of HSP60, predisposing cells to heat shock‐like responses. The identification of the molecular targets of biological dyes, or “stainomics,” can help correlate their intracellular staining properties with biochemical affinities. We believe this approach can be applied to a wide range of fluorescent probes.     

Direct detection of native proteins in biological matrices using extractive electrospray ionization mass spectrometry

The high-throughput and sensitive characterization of native proteins in biological samples is of increasing interest in multiple disciplines. Extractive electrospray ionization (EESI) forms ions of native proteins including lysozyme, α-chymotrypsin, myoglobin, human serum albumin, RNAse A and blood hemoglobin in extremely complex biosamples or PBS buffer solutions by softly depositing charges on the protein molecules. This method produces no significant conformational changes of the proteins in the ion formation process, and features direct detection of trace proteins present in biological matrices. The detection limit of low pmol L(-1) for lysozyme in untreated biological liquids such as human urine and tears was demonstrated using EESI mass spectrometry (MS), showing an attractive MS platform for the direct analysis of native proteins in actual biological samples.     

Bystander Effect Induced by UVC Radiation in Chinese hamster V79 cells

In past decades, researches on radiation‐induced bystander effect mainly focused on ionizing radiation such as α‐particle, β‐particle, X‐ray and γ‐ray. But few researches have been conducted on the ability of ultraviolet (UV) radiation‐induced bystander effect, and knowledge of UVC‐induced bystander effect is far limited. Here, we adopted medium transfer experiment to detect whether UVC could cause bystander effect in Chinese hamster V79 cells. We determined the cell viability, apoptosis rate, chromosome aberration and ultrastructure changes, respectively. Our results showed that: (1) the viability of UVC‐irradiated V79 cells declined significantly with the dosage of UVC; (2) similar to the irradiated cells, the main death type of bystander cells cultured in irradiation conditioned medium (ICMs) was also apoptosis; (3) soluble factors secreted by UVC‐irradiated cells could induce bystander effect in V79 cells; (4) cells treated with 4 h ICM collected from 90 mJ cm^?2 UVC‐irradiated cells displayed the strongest response. Our data revealed that UVC could cause bystander effect through the medium soluble factors excreted from irradiated cells and this bystander effect was a novel quantitative and kinetic response. These findings might provide a foundation to further explore the exact soluble bystander factors and detailed mechanism underlying UVC‐induced bystander effect.     

Hydrophobic charge‐induction resin with 5‐aminobenzimidazol as the functional ligand: preparation,protein adsorption and immunoglobulin G purification

A new hydrophobic charge‐induction chromatography resin was prepared with 5‐aminobenzimidazol as functional ligand and polyacrylic ester beads as matrix. Adsorption isotherms and adsorption in columns were investigated using human immunoglobulin G and bovine serum albumin as model proteins, and the influence of pH and NaCl concentration was discussed. Results showed that the ligand density was 195 μmol/mL gel, and protein selectivity can be improved by controlling pH and salt addition. An optimized purification process (sample loading at pH 8.0 with 0.2 M NaCl and elution at pH 5.0) was performed to purify human immunoglobulin G from bovine serum albumin containing feedstock, which resulted in human immunoglobulin G purity of 99.7% and recovery of 94.6%. A similar process was applied for the purification of monoclonal antibody from cell culture supernatant, which showed antibody purity of 94.9% and recovery of 92.5%. The results indicated that the new resin developed had comparable performance as Protein A chromatography and would be suitable for antibody purification from complex feedstock.     

Data‐dependent electron transfer dissociation of large peptides and medium size proteins in a QTOF instrument on a liquid chromatography timescale

Liquid chromatography (LC) electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) of protein digests is demonstrated in a hybrid quadrupole‐hexapole orthogonal time‐of‐flight (OTOF) mass spectrometer. Analyte ions are selected in a mass‐analyzing quadrupole, accumulated in the hexapole linear ETD reaction cell and mutually stored with ETD reagent anions. Product ions are collected in an ion cooler and then analyzed by an OTOF mass analyzer. The hexapole structure of the ETD reaction cell allows for a broad fragment ion mass range distribution and a high ion storage capacity. Analytically useful ETD OTOF‐MS/MS spectra could be obtained at a rate of faster than 2 Hz. When used in conjunction with LC this high speed allows for several MS and MS/MS spectra to be obtained across each LC peak. An MS scan is used to select the precursor ions. With a 1 m flight tube and single reflection, resolutions of about 10 k and a mass accuracy of 5 ppm were achieved. When analyzing a 100 fmol solution of a tryptic digest of bovine serum albumin (BSA) by LC/ETD MS/MS, 27 unique peptides were identified with a summed Mascot score of 1316 using the Swiss Prot database. In addition, we explored the capability for analyzing small proteins with the present hybrid instrument. ETD MS/MS of intact ubiquitin ([M+12H]¹²⁺) leads to the identification of the protein with a Mascot score of 264. Copyright © 2009 John Wiley & Sons, Ltd.     

Mass spectrometric characterisation of proteins in rennet and in chymosin-based milk-clotting preparations

The protein composition of natural rennet and of chromatographic and crystalline chymosin preparations has been defined by on-line reverse-phase high performance liquid chromatography/electrospray ionisation mass spectrometry (RP-HPLC/ESI-MS) and by tandem mass spectrometry (MS/MS). Natural rennet was found to consist of six chymosin species, corresponding to chymosin A and B genetic variants, each of which comprised a mixture of two other forms differing at theN-terminal end, with one being three residues longer, and the other two residues shorter, than the mature chymosin. Two main tissue proteins were also identified as lysozyme (isozyme 2 plus a novel isozyme labelled 4) and bovine serum albumin. In addition to the proteins, chymosin fragments 247-323 and 288-323 were consistently present in natural rennet. Conversely, chromatographic and crystalline chymosin preparations lacked bovine serum albumin and/or lysozyme, although they contained the same six chymosin species as natural rennet. Since these tissue-specific contaminating proteins each possess specific functions in terms of stabilising enzyme solutions and protecting proteins from proteolytic enzymes, oxidising agents and bacterial proliferation, the rennet may be considered as a functional enzyme preparation that is effectively and naturally adapted to the purposes of cheesemaking. In practice, the highly complex protein composition inherent to natural rennet provided the possibility to differentiate the natural product from other bovine chymosin-based milk-clotting preparations examined in this work.     

Effect of Operating Conditions in Production of Diagnostic Salmonella Enteritidis O-Antigen-Specific Monoclonal Antibody in Different Bioreactor Systems

In this study, different cultivation systems such as roller bottles (RB), 5-L stirred-tank bioreactor (STR), and disposable bioreactors were used to cultivate hybridoma for lab-scale production of Salmonella Enteritidis O-antigen-specific monoclonal antibody (MAb). Hybridoma cell line was cultivated in either serum-containing or serum-free medium (SFM) culture conditions. In STR, MAb production scaled up to 4 L, and production capabilities of the cells were also evaluated in different featured production systems. Moreover, the growth parameters of the cells in all production systems such as glucose consumption, lactate and ammonia production, and also MAb productivities were determined. Collected supernatants from the reactors were concentrated by a cross-flow filtration system. In conclusion, cells were not adapted to SFM in RB and STR. Therefore, less MAb titer in both STR and RB systems with SFM was observed compared to the cultures containing fetal bovine serum-supplemented medium. A higher MAb titer was gained in the membrane-aerated system compared to those in STR and RB. Although the highest MAb titer was obtained in the static membrane bioreactor system, the highest productivity was obtained in STR operated in semicontinuous mode with overlay aeration.     

Improved biocompatibility of phosphorylcholine end-capped poly(butylene succinate)

In this work, the biocompatibility of a biomimetic, fully biodegradable ionomer phosphorylcholine (PC)-functionalized poly(butylene succinate) (PBS-PC) was investigated by means of hemolysis, platelet adhesion, protein adsorption and cytotox- icity experiments. The reference materials were poly(butylene succinate) (PBS) and chloroethylphosphoryl functionalized poly(butylene succinate) (PBS-Cl). The hemolysis rates (HR) of the leaching solutions of PBS, PBS-Cl and PBS-PC were all lower than the safe value, and the rate of PBS-PC was reduced to 1.07%. Scanning electron microscopy (SEM) measurements showed that platelet adhesion and aggregation were significant on both PBS and PBS-Cl surface. In contrast, very few platelets were observed on PBS-PC surface. Bicinchoninic acid (BCA) measurements revealed that the adsorption amounts of bovine serum albumin (BSA) and bovine plasma fibrinogen (BPF) on PBS-PC surface were 52% and 72% reduction respectively compared with those on PBS surface. Moreover, non-cytotoxicity of both PBS-PC particles and its leaching solution was sug- gested by MTT assay using mouse L929 fibroblast cells. All the results demonstrated that the biocompatibility of PBS could be greatly improved by PC end-capping strategy. This PC functionalized polyester may have potential applications in biological environments as a novel carrier for controlled drug release and scaffold for tissue engineering.     

Scanning-force techniques to monitor time-dependent changes in topography and adhesion force of proteins on surfaces

Scanning-force microscopy (SFM) investigations were conducted to probe the influences of the interactions of proteins with surfaces relevant in medicine. These interactions are an important feature in the area of biofilm formation. The adsorption of proteins leads to changes in topography, which was monitored for the build up of protein layers of hen egg-white lysozyme and bovine serum albumin (BSA) on mica in real time in phosphate-buffered aqueous solution over a time period of 10 min. Phase imaging was additionally applied to compare material contrasts and to evaluate this method for further application in this field. The adhesion forces that develop on a time scale below 20 s between a protein-modified SFM tip and titanium surfaces (TiO(2), TiAl6V4 and TiAl6Nb7) were investigated. The influences of the parameters loading force and interaction time between the protein and the surface were monitored as well as the influence of protein structure. The interaction time dependency of the adhesion force could be described with a kinetic model of two consecutive first-order reactions. For the maximal adhesion force a correlation to the ratio of the amino acids cysteine, proline and glycine has been proposed.     

Photoluminescence Lifetime Imaging of Synthesized Proteins in Living Cells Using an Iridium–Alkyne Probe

Designing probes for real‐time imaging of dynamic processes in living cells is a continuous challenge. Herein, a novel near‐infrared (NIR) photoluminescence probe having a long lifetime was exploited for photoluminescence lifetime imaging (PLIM) using an iridium‐alkyne complex. This probe offers the benefits of deep‐red to NIR emission, a long Stokes shift, excellent cell penetration, low cytotoxicity, and good resistance to photobleaching. This example is the first PLIM probe applicable to the click reaction of copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) with remarkable lifetime shifts of 414 ns, before and after click reaction. The approach fully eliminates the background interference and distinguishes the reacted probes from the unreacted probes, thus enabling the wash‐free imaging of the newly synthesized proteins within single living cells. Based on the unique properties of the iridium complexes, it is anticipated to have applications for imaging other processes within living cells.     

The First Zero‐Length Mass Spectrometry‐Cleavable Cross‐Linker for Protein Structure Analysis

Combining the properties of a zero‐length cross‐linker with cleavability by tandem mass spectrometry (MS/MS) poses great advantages for protein structure analysis using the cross‐linking/MS approach. These include a reliable, automated data analysis and the possibility to obtain short‐distance information of protein 3D‐structures. We introduce 1,1′‐carbonyldiimidazole (CDI) as an easy‐to‐use and commercially available, low‐cost reagent that ideally fulfils these features. CDI bridges primary amines and hydroxy groups in proteins with the lowest possible spacer length of one carbonyl unit (ca. 2.6 Å). The cross‐linking reaction can be conducted under physiological conditions in the pH range between 7.2 and 8. Urea and carbamate cross‐linked products are cleaved upon collisional activation during MS/MS experiments generating characteristic product ions, greatly improving the unambiguous identification of cross‐links. Our innovative analytical concept is exemplified and applied for bovine serum albumin (BSA), wild‐type tumor suppressor p53, an intrinsically disordered protein, and retinal guanylyl cyclase activating protein‐2 (GCAP‐2).     

Electrochemical Sensors Continuously Monitor Magnesium Biodegradation under Cell Culture Conditions

Magnesium (Mg) and its alloys have increasingly been considered as implant materials for orthopedic, craniofacial, and cardiovascular applications. These materials generally have mechanical properties close to those of human bone and they biodegrade in aqueous environments. The biodegradation properties can be tailored to fit the desired application by changing the alloying elements and/or by addition of surface coatings. To test and compare the biodegradation properties of different materials, immersion tests in solutions ranging from simple salt solutions to complex biological media are commonly done that yield some information about the biodegradation rate and the biodegradation products on the surface after completion of the test. Here we report on a method that allows the continuous real‐time monitoring of the biodegradation process using electrochemical sensors for pH and H₂ during immersion of Mg samples in the cell culture medium DMEM/F12 with different concentrations of fetal bovine serum and in the presence of living cells. The sensors effectively indicated the biodegradation behavior of Mg samples in real‐time. This system could be very useful for immersion tests and even supporting biocompatibility testing of implant materials.