Proteomic identification of biomarkers expressed by human pluripotent stem cells

Development of chimeric antigen receptor T cells targeting cancer-expressing podocalyxin

Chimeric Antigen Receptor (CAR)-T cell therapy has revolutionized the treatment of CD19-positive B-cell malignancies. However, the field is rapidly evolving to target other antigens, such as podocalyxin (PODXL), a transmembrane protein implicated in tumor progression and poor prognosis in various cancers. This study explores the potential of PODXL-targeted CAR-T cells, utilizing a cancer-specific monoclonal antibody (CasMab) technique to enhance the specificity and safety of CAR-T cell therapy. We developed CAR-T cells based on the single-chain variable fragment (scFv) derived from the cancer-specific monoclonal antibody PcMab-6, which selectively targets glycosylation modifications on PODXL-expressing cancer cells. As a control, CAR-T cells were also generated from PcMab-47, a non-cancer-specific antibody for PODXL. In vitro experiments demonstrated that CAR-T cells based on PcMab-6 exhibited significant antitumor activity with reduced off-target effects on normal cells compared to PcMab-47-derived CAR-T cells. Additionally, to enhance the persistence and therapeutic efficacy of these CAR-T cells, we developed a humanized version of PcMab-6 scFv. The humanized CAR-T cells showed extended antitumor effects in vivo, demonstrating the potential for prolonged therapeutic activity. These findings underscore the utility of CasMab technology in generating highly specific and safer CAR-T cell therapies for solid tumors, highlighting the promise of humanized CAR-T cells for clinical application.

A cancer-specific anti-podocalyxin monoclonal antibody (60-mG2a-f) exerts antitumor effects in mouse xenograft models of pancreatic carcinoma

Overexpression of podocalyxin (PODXL) is associated with progression, metastasis, and poor outcomes in several cancers. PODXL also plays an important role in the development of normal tissues. For antibody-based therapy to target PODXL-expressing cancers using monoclonal antibodies (mAbs), cancer-specificity is necessary to reduce the risk of adverse effects to normal tissues. In this study, we developed an anti-PODXL cancer-specific mAb (CasMab), named as PcMab-60 (IgM, kappa) by immunizing mice with soluble PODXL, which is overexpressed in LN229 glioblastoma cells. The PcMab-60 reacted with the PODXL-overexpressing LN229 (LN229/PODXL) cells and MIA PaCa-2 pancreatic cancer cells in flow cytometry but did not react with normal vascular endothelial cells (VECs), whereas one of non-CasMabs, PcMab-47 showed high reactivity for not only LN229/PODXL and MIA PaCa-2 cells but also VECs, indicating that PcMab-60 is a CasMab. Next, we engineered PcMab-60 into a mouse IgG_2a-type mAb, named as 60-mG_2a, to add antibody-dependent cellular cytotoxicity (ADCC). We further developed a core fucose-deficient type of 60-mG_2a, named as 60-mG_2a-f, to augment its ADCC activity. In vivo analysis revealed that 60-mG_2a-f exerted antitumor activity in MIA PaCa-2 xenograft models at a dose of 100 μg/mouse/week administered three times. These results suggested that 60-mG_2a-f could be useful for antibody-based therapy against PODXL-expressing pancreatic cancers.

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PODXL is associated with poor outcomes in several cancers.

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We developed an anti-PODXL cancer-specific mAb (PcMab-60).

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A core fucose-deficient IgG_2a type of PcMab-60 (60-mG_2a-f) exerted antitumor activity in MIA PaCa-2 xenograft models.

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60-mG_2a-f could be useful for antibody-based therapy against PODXL-expressing pancreatic cancers.

Anti-podocalyxin antibody exerts antitumor effects via antibody-dependent cellular cytotoxicity in mouse xenograft models of oral squamous cell carcinoma

Podocalyxin (PODXL) overexpression is associated with progression, metastasis, and poor outcomes in cancers. We recently produced the novel anti-PODXL monoclonal antibody (mAb) PcMab-47 (IgG₁, kappa). Herein, we engineered PcMab-47 into 47-mG_2a, a mouse IgG_2a-type mAb, to add antibody-dependent cellular cytotoxicity (ADCC). We further developed 47-mG_2a-f, a core fucose-deficient type of 47-mG_2a to augment its ADCC. Immunohistochemical analysis of oral cancer tissues using PcMab-47 and 47-mG_2a revealed that the latter stained oral squamous cell carcinoma (OSCC) cells in a cytoplasmic pattern at a much lower concentration. PcMab-47 and 47-mG_2a detected PODXL in 163/201 (81.1%) and in 197/201 (98.0%) OSCC samples, respectively. 47-mG_2a-f also detected PODXL in OSCCs at a similar frequency as 47-mG_2a. In vitro analysis revealed that both 47-mG_2a and 47-mG_2a-f exhibited strong complement-dependent cytotoxicity (CDC) against CHO/hPODXL cells. In contrast, 47-mG_2a-f exhibited much stronger ADCC than 47-mG_2a against OSCC cells, indicating that ADCC and CDC of those anti-PODXL mAbs depend on target cells. In vivo analysis revealed that both 47-mG_2a and 47-mG_2a-f exerted antitumor activity in CHO/hPODXL xenograft models at a dose of 100 μg or 500 μg/mouse/week administered twice. 47-mG_2a-f, but not 47-mG_2a, exerted antitumor activity in SAS and HSC-2 xenograft models at a dose of 100 μg/mouse/week administered three times. Although both 47-mG_2a and 47-mG_2a-f exerted antitumor activity in HSC-2 xenograft models at a dose of 500 μg/mouse/week administered twice, 47-mG_2a-f also showed higher antitumor activity than 47-mG_2a. These results suggested that a core fucose-deficient anti-PODXL mAb could be useful for antibody-based therapy against PODXL-expressing OSCCs.

Embryonic stem cell proteomics

Human embryonic stem cells potentially represent an unlimited source of cells and tissues for regenerative medicine. Understanding signaling events that drive proliferation and specialization of these cells into various differentiated derivatives is of utmost importance for controlling their behavior in vitro. Major progress has been made in unraveling these signaling events with large-scale studies at the transcriptional level, but analysis of protein expression, interaction and modification has been more limited, since it requires different strategies. Recent advances in mass spectrometry-based proteomics indicate that proteome characterization can contribute significantly to our understanding of embryonic stem cell biology. In this article, we review mass spectrometry-based studies of human and mouse embryonic stem cells and their differentiated progeny, as well as studies of conditioned media that have been reported to support self-renewal of the undifferentiated cells in the absence of the more commonly used feeder cells. In addition, we make concise comparisons with related transcriptome profiling reports.

Podocalyxin is a glycoprotein ligand of the human pluripotent stem cell-specific probe rBC2LCN

In comprehensive glycome analysis with a high-density lectin microarray, we have previously shown that the recombinant N-terminal domain of the lectin BC2L-C from Burkholderia cenocepacia (rBC2LCN) binds exclusively to undifferentiated human induced pluripotent stem (iPS) cells and embryonic stem (ES) cells but not to differentiated somatic cells. Here we demonstrate that podocalyxin, a heavily glycosylated type 1 transmembrane protein, is a glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. When analyzed by DNA microarray, podocalyxin was found to be highly expressed in both iPS cells and ES cells. Western and lectin blotting revealed that rBC2LCN binds to podocalyxin with a high molecular weight of more than 240 kDa in undifferentiated iPS cells of six different origins and four ES cell lines, but no binding was observed in either differentiated mouse feeder cells or somatic cells. The specific binding of rBC2LCN to podocalyxin prepared from a large set of iPS cells (138 types) and ES cells (15 types) was also confirmed using a high-throughput antibody-overlay lectin microarray. Alkaline digestion greatly reduced the binding of rBC2LCN to podocalyxin, indicating that the major glycan ligands of rBC2LCN are presented on O-glycans. Furthermore, rBC2LCN was found to exhibit significant affinity to a branched O-glycan comprising an H type 3 structure (Ka, 2.5 × 10(4) M(-1)) prepared from human 201B7 iPS cells, indicating that H type 3 is a most probable potential pluripotency marker. We conclude that podocalyxin is a glycoprotein ligand of rBC2LCN on human iPS cells and ES cells.

Contribution of proteomics to the study of the role of cytokeratins in disease and physiopathology

Cytokeratins (CKs), the most abundant group of cytoskeletal intermediate filaments, and proteomics are strongly connected. On the one hand, proteomics has been extremely useful to uncover new features and functions of CKs, on the other, the highly abundant CKs serve as an exceptional tool to test new technological developments in proteomics. As a result, proteomics has contributed to finding valuable associations of CKs with diseases as diverse as cancer, cystic fibrosis, steatohepatitis, viral and bacterial infection, keratoconus, vitreoretinopathy, preeclampsia or the chronic fatigue syndrome, as well as to characterizing their participation in a number of physiopathological processes, including drug resistance, response to toxicants, inflammation, stem cell differentiation, embryo development, and tissue repair. In some cases, like in cystic fibrosis, CKs have been described as potential therapeutic targets. The development of a specific field of proteomics where CKs become the main subject of research aims and hypotheses is suggested.

Application of surface-enhanced laser desorption ionization time-of-flight mass spectrometry to the diagnosis and evaluation of interventional effect in patients with hepatocellular carcinoma

AIM: To establish a serum protein pattern model for diagnosing hepatocellular carcinoma (HCC) by using the surface-enhanced laser desorption ionization time-of-fligh mass spectrometry (SELDI-TOF-MS), and to evaluate the value of this model in predicting the effect of interventional treatment for HCC.

METHODS: Serum samples collected from patients with HCC (n = 60) and healthy people (n = 60) were used for SELDI-TOF-MS on CM10 chips. The proteomic spectra were analyzed by using the Biomarker Wizard software. The diagnosis model was established by using the Biomarker Pattern software.

RESULTS: Three significantly different protein peaks were found in serum samples between HCC patients and healthy controls. A protein peak at 6 992 Da showed higher expression and the other two protein peaks (4 182 Da, 5 710 Da) showed lower expression in HCC patients than in healthy people. The diagnostic model containing these three candidate biomarkers could distinguish patients with HCC from healthy controls with a sensitivity of 93.3% (28/30), a specificity of 90.0% (27/30), an accuracy of 91.7% (55/60), and a Youden index value of 0.833. The protein peak at 4 182 Da was significantly decreased one month after interventional treatment in HCC patients (P < 0.05).

CONCLUSION: The diagnostic model developed by using SELDI-TOF-MS allows efficiently identifying patients with HCC and may play a valuable role in the diagnosis of HCC. The protein peak at 4 182 Da is helpful for the evaluation of interventional curative effect in HCC patients.

Proteomic analysis of human mesenchymal stromal cells derived from adipose tissue undergoing osteoblast differentiation

BACKGROUND AIMS

Stem cells derived from human adipose tissue (ASC) have the capacity for renewal, are easily obtained and have plasticity properties that allow them to differentiate into several cell types, including osteoblast cells. With the aim of understanding the issue of the osteogenic process and finding reliable biomarkers in cells undergoing the osteogeneic differentiation process, this work took advantage of a proteomic approach to identify proteins involved in osteogenesis.

METHODS

For this purpose, ASC were analyzed under three conditions: S0, in the absence of stimulation; S1, with 2 weeks of osteogenic medium stimulation; and S2, with 4 weeks of osteogenic medium stimulation. The identification of ASC was carried out by flow cytometry using antibodies specific to known undifferentiated stem cell-surface markers. Cell viability, enzymatic activity, mineral deposition, collagen structure and production and gene analyzes were evaluated for each condition.

RESULTS

Phenotypic modifications were observed during the in vitro osteogenic differentiation process by two-dimensional (2-D) differential image gel electrophoresis (DIGE). The proteins were identified by mass espectrometry in tandem (MS/MS) analyzes using Matrix-assisted laser desorption/ionization with TOF/TOF is a tandem mass spectrometry method where two time-of-flight mass spectrometers are used consecutively (MALDI-TOF/TOF). A total of 51 differentially expressed proteins was identified when comparing the three observed conditions. Sixteen different spots were identified in the S0 stage compared with S2, while 28 different spots were found in S2 compared with S0. S1 expressed seven different spots compared with S0 and S2.

CONCLUSIONS

These findings suggest the involvement of several proteins directly related to the osteogenic pathway, which can be used to improve understanding of the osteogenic process.

The human cancer and stem cell marker podocalyxin interacts with the glucose-3-transporter in malignant pluripotent stem cells

Podocalyxin, an integral plasma membrane cell-adhesion glycoprotein, is a marker of human pluripotent and multipotent stem cells. Podocalyxin is also a marker of many types of cancers and its expression correlates with an aggressive and poor-prognosis tumor phenotype. The function of podocalyxin in stem cells and malignant cells is unknown. Protein sequence data obtained from purified podocalyxin protein isolated from embryonal carcinoma cancer stem cells reveals peptide sequence data for the glucose-3-transporter. Protein-precipitation experiments of embryonal carcinoma protein extracts identify a podocalyxin/glucose-3-transporter protein complex. Cell imaging studies demonstrate co-localization of podocalyxin and glucose-3-transporter and confirm the interaction in vivo. Finally, siRNA podocalyxin-knockdown experiments show decreased expression levels of the glucose-3-transporter. These findings suggest a novel interaction of the glucose-3-transporter and the cell-adhesion protein podocalyxin. In pluripotent stem cells and in human cancer disease, podocalyxin may function in part to regulate and maintain the cell surface expression of the glucose-3-transporter.

Clinical diagnosis for discogenic low back pain

Discogenic lower back pain (DLBP) is the most common type of chronic lower back pain (LBP), accounting for 39% of cases, compared to 30% of cases due to disc herniation, and even lower prevalence rates for other causes, such as zygapophysial joint pain. Only a small proportion (approximately 20%) of LBP cases can be attributed with reasonable certainty to a pathologic or anatomical entity. Thus, diagnosing the cause of LBP represents the biggest challenge for doctors in this field. In this review, we summarize the process of obtaining a clinical diagnosis of DLBP and discuss the potential for serum-based diagnosis in the near future. The use of serum biomarkers to diagnose DLBP is likely to increase the ease of diagnosis as well as produce more accurate and reproducible results.

Mass Spectrometry in Diagnostic Oncoproteomics

Diagnostic oncoproteomics is the application of proteomic techniques for the diagnosis of malignancies. A new mass spectrometric technology involves surface enhanced laser desorption ionization combined with time-of flight mass analysis (SELDI-TOF-MS), using special protein chips. After the description of the relevant principles of the technique, including approaches to proteomic pattern diagnostics, applications are reviewed for the diagnosis of ovarian, breast, prostate, bladder, pancreatic, and head and neck cancers, and also several other malignancies. Finally, problems and prospects of the approach are discussed.

Promising diagnostic biomarkers for primary biliary cirrhosis identified with magnetic beads and MALDI-TOF-MS

(PBC) is not a rare disease worldwide. Most patients are diagnosed at the advanced stage, primarily because there are not yet any valid biomarkers available for early diagnosis. Useful biomarkers are absolutely necessary for early detection of PBC. Fortunately, the use of MALDI-TOF-MS and pattern recognition software has been successful in finding specific markers for the early detection of the disease. To screen for potential protein biomarkers in the serum for diagnosing PBC, MALDI-TOF-MS combined with magnetic beads and pattern recognition software was used to investigate 119 serum samples from 44 patients with PBC, 32 controls with other hepatic disease, and 43 healthy controls. A total of 69 discriminant m/z peaks were identified as being associated with PBC. Of them, the m/z peaks at 3445, 4260, 8133, and 16,290 were used to construct a model for the diagnosis of PBC. This diagnostic model can distinguish PBC from non-PBC controls with a sensitivity of 93.3% and a specificity of 95.1%. In our blind test, it demonstrated good sensitivity and specificity: 92.9% and 82.4%, respectively. These results indicate that useful serum biomarkers for PBC can be discovered by MALDI-TOF-MS combined with the use of magnetic beads and pattern recognition software. The pattern of multiple markers provides a powerful and reliable diagnostic method for PBC with high sensitivity and specificity.

Differences in protein profiles of the isolates of Entamoeba histolytica and E. dispar by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS) ProteinChip assays

Surface-enhanced laser desorption ionization time of flight mass spectrometry (SELDI-TOF MS) ProteinChip assays with weak cationic exchange chips were used for protein profiling of different isolates of Entamoeba histolytica and E. dispar. When SELDI-TOF MS spectra of cell lysates from E. histolytica strain HM-1:IMSS were compared with those from four other laboratory strains (200:NIH, HK-9, DKB, and SAW755CR) grown under the same culture conditions, different peak patterns of SELDI-TOF MS were observed among these strains, independent of their zymodeme types. Similarly, five Japanese isolates of E. histolytica grown under the same culture conditions revealed different peak patterns among themselves. The SELDI-TOF MS spectra of cell lysates from two isolates of E. dispar strain AS16IR and CYNO 09:TPC showed the presence of peaks specific for E. dispar isolates and the absence of peaks common to E. histolytica isolates. This is not only the first use of SELDI-TOF MS ProteinChip technology for protein profiling of different strains of Entamoeba but also the use for parasitic protozoa. The SELDI-TOF MS spectra show a realistic view of proteins with a biological status of E. histolytica and E. dispar isolates, contributing to show their phenotypic differences of proteins and provide a unique means of distinguishing them.

Proteome of mesenchymal stem cells

Proteomics has evolved, in recent years, into effective tools for basic and applied stem cell research, and has been extensively used to facilitate the identification of changes in signal transduction components, especially with regard to plasticity, proliferation, and differentiation. Several recent reports have also employed proteomic strategies to characterize human mesenchymal stem cells (hMSC) and their differentiated derivatives. Although these approaches have yielded valuable data, the results highlight the fact that only the limited numbers of proteins are characterized at the protein level in these cells, thus necessitating expandable MSC proteome dataset. This review presents, for the first time, an expandable list of MSC proteins, which will function as a starting point for the generation of a comprehensive reference map of their proteome. Also, the better way to bridge current gap between genomics and proteomics study such as integrated proteomic and transcriptomic analyses is discussed.

Concise review: trends in stem cell proteomics

Gene expression analyses of stem cells (SCs) will help to uncover or further define signaling pathways and molecular mechanisms involved in the maintenance of self-renewal, pluripotency, and/or multipotency. In recent years, proteomic approaches have produced a wealth of data identifying proteins and mechanisms involved in SC proliferation and differentiation. Although many proteomics techniques have been developed and improved in peptide and protein separation, as well as mass spectrometry, several important issues, including sample heterogeneity, post-translational modifications, protein-protein interaction, and high-throughput quantification of hydrophobic and low-abundance proteins, still remain to be addressed and require further technical optimization. This review summarizes the methodologies used and the information gathered with proteome analyses of SCs, and it discusses biological and technical challenges for proteomic study of SCs. Disclosure of potential conflicts of interest is found at the end of this article.

Proteome analysis of the culture environment supporting undifferentiated mouse embryonic stem and germ cell growth

The therapeutical interest of pluripotent cells and ethical issues related to the establishment of human embryonic stem cell (ESC) or embryonic germ cell (EGC) lines raise the understanding of the mechanism underlying pluripotency to a fundamental issue. Establishing a protein pluripotency signature for these cells can be complicated by the presence of unrelated proteins produced by the culture environment. Here, we have analyzed the environment supporting ESC and EGC growth, and established 2-D reference maps for each constituent present in this culture environment: mouse embryonic fibroblast feeder cells, culture medium (CM) and gelatin. The establishment of these reference maps is essential prior to the study of ESC and EGC specific proteomes. Indeed, these maps can be subtracted from ESC or EGC maps to allow focusing on spots specific for ESCs or EGCs. Our study led to the identification of 110 unique proteins from fibroblast feeder cells and 23 unique proteins from the CM, which represent major contaminants of ESC and EGC proteomes. For gelatin, no collagen-specific proteins were identified, most likely due to difficulties in resolution and low quantities. Furthermore, no differences were observed between naive and conditioned CM. Finally, we compared these reference maps to ESC 2-D gels and isolated 17 ESC specific spots. Among these spots, proteins that had already been identified in previous human and mouse ESC proteomes were identified but no apparent ESC-specific pluripotency marker could be identified. This work represents an essential step in furthering the knowledge of environmental factors supporting ESC and EGC growth.

Application of proteomic technology to neural stem cell science and neurology

There is widespread recognition of the potential that stem cells hold for the treatment and repair of a large number of disorders affecting the human CNS. Therefore, stem cell research will go hand in hand with progress in specific areas of neuroscience. Proteomics has great potential to make important contributions to the basic understanding of neurological processes, and to deliver much needed cellular biomarkers in both of these fields. This review focuses on the importance of proteomic research in neuroscience, in particular the application of biomarker discovery in stem cells and degenerative diseases of the CNS.

The pitfalls of proteomics experiments without the correct use of bioinformatics tools

The elucidation of the entire genomic sequence of various organisms, from viruses to complex metazoans, most recently man, is undoubtedly the greatest triumph of molecular biology since the discovery of the DNA double helix. Over the past two decades, the focus of molecular biology has gradually moved from genomes to proteomes, the intention being to discover the functions of the genes themselves. The postgenomic era stimulated the development of new techniques (e.g. 2-DE and MS) and bioinformatics tools to identify the functions, reactions, interactions and location of the gene products in tissues and/or cells of living organisms. Both 2-DE and MS have been very successfully employed to identify proteins involved in biological phenomena (e.g. immunity, cancer, host-parasite interactions, etc.), although recently, several papers have emphasised the pitfalls of 2-DE experiments, especially in relation to experimental design, poor statistical treatment and the high rate of 'false positive' results with regard to protein identification. In the light of these perceived problems, we review the advantages and misuses of bioinformatics tools - from realisation of 2-DE gels to the identification of candidate protein spots - and suggest some useful avenues to improve the quality of 2-DE experiments. In addition, we present key steps which, in our view, need to be to taken into consideration during such analyses. Lastly, we present novel biological entities named 'interactomes', and the bioinformatics tools developed to analyse the large protein-protein interaction networks they form, along with several new perspectives of the field.

Application of surface enhanced laser desorption ionization time-of-flight mass spectrometry technology in the diagnosis of hepatocellular carcinoma

AIM: To explore tumor markers for the diagnosis of hepatocellular carcinoma (HCC) through detecting the serum protein spectrum differently expressed between hepatitis B virus (HBV) carriers and HCC patients.

METHODS: We detected the serum protein spectrum in 27 HCC patients, 27 HBV carriers and 25 healthy controls using surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) technique, and the diagnosis model was established through analyzing the detected data by biomarker patterns software (BPS) 5.0.

RESULTS: The protein peaks, which could discriminate HBV carriers from HCC patients and healthy individuals, as well as healthy individuals from HCC patients, were detected. A diagnosis model based on the detected data was established with the specificity of 93%, 96%, 84%, and sensitivity of 85%, 96%, 89%, respectively. In addition, the 8141-Da protein in HCC patients had a higher expression than that in HBV carriers (P < 10^-5); the expression of 3448-Da protein was higher both in HCC patients and HBV carriers than that in healthy controls (P < 10^-5), but it had no significant difference between HCC patients and HBV carriers (P > 0.05), indicating that 3448-Da protein might be a potential marker for HBV infection; 7771-Da protein was differently expressed between the three groups of patients.

CONCLUSION: With a high specificity and sensitivity, the detection of serum protein spectrum can be performed easily and quickly by SELDI-TOF-MS technique, which provides a serological way for the diagnosis of HCC.

Effect of 5-azacytidine on the protein expression of porcine bone marrow mesenchymal stem cells in vitro

Bone marrow-derived mesenchymal stem cells (MSCs) are pluripotent stem cells that show a vital potential in the clinical application for cell transplantation. In the present paper, proteomic techniques were used to approach the protein profiles associated with porcine bone marrow MSCs and investigate the regulation of MSC proteins on the effect of 5-azacytidine (5-aza). Over 1,700 protein species were separated from MSCs according to gel analysis. Compared with the expression profiling of control MSCs, there were 11 protein spots up-regulated and 26 down-regulated in the protein pattern of 5-aza-treated cells. A total of 21 proteins were successfully identified by MALDI-TOF-MS analysis, among which some interesting proteins, such as alpha B-crystallin, annexin A2, and stathmin 1, had been reported to involve in cell proliferation and differentiation through different signaling pathways. Our data should be useful for the future study of MSC differentiation and apoptosis.

Following the Differentiation of Human Pluripotent Stem Cells by Proteomic Identification of Biomarkers

Following the differentiation of cultured stem cells is often reliant on the expression of genes and proteins that provide information on the developmental status of the cell or culture system. There are few molecules, however, that show definitive expression exclusively in a specific cell type. Moreover, the reliance on a small number of molecules that are not entirely accurate biomarkers of particular tissues can lead to misinterpretation in the characterization of the direction of cell differentiation. Here we describe the use of technology that examines the mass spectrum of proteins expressed in cultured cells as a means to identify the developmental status of stem cells and their derivatives in vitro. This approach is rapid and reproducible and it examines the expression of several different biomarkers simultaneously, providing a profile of protein expression that more accurately corresponds to a particular type of cell differentiation.

Proteomic analysis of neural differentiation of mouse embryonic stem cells

Mouse embryonic stem cells (mESCs) can differentiate into different types of cells, and serve as a good model system to study human embryonic stem cells (hESCs). We showed that mESCs differentiated into two types of neurons with different time courses. To determine the global protein expression changes after neural differentiation, we employed a proteomic strategy to analyze the differences between the proteomes of ES cells (E14) and neurons. Using 2-DE plus LC/MS/MS, we have generated proteome reference maps of E14 cells and derived dopaminergic neurons. Around 23 proteins with an increase or decrease in expression or phosphorylation after differentiation have been identified. We confirmed the downregulation of translationally controlled tumor protein (TCTP) and upregulation of alpha-tubulin by Western blotting. We also showed that TCTP was further downregulated in derived motor neurons than in dopaminergic neurons, and its expression level was independent of extracellular Ca(2+) concentration during neural differentiation. Potential roles of TCTP in modulating neural differentiation through binding to Ca(2+), tubulin and Na,K-ATPase, as well as the functional significance of regulation of other proteins such as actin-related protein 3 (Arp3) and Ran GTPase are discussed. This study demonstrates that proteomic tools are valuable in studying stem cell differentiation and elucidating the underlying molecular mechanisms.

Proteomic fingerprints distinguish microglia, bone marrow, and spleen macrophage populations

Mononuclear phagocytes (MP; dendritic cells, monocytes, tissue macrophages, and microglia) maintain tissue homeostasis and provide a first line of defense against invading pathogens. In specific circumstances, MPs also induce inflammatory responses and as such affect disease onset and progression. Despite intensive research into MP biology, little is known of the functional and molecular properties of individual MP subtypes. Using a novel proteomics platform, unique protein patterns and protein identities were observed among populations of spleen and bone marrow macrophages and microglia. Cells were obtained from C57BL/6 mice and were cultivated in macrophage colony-stimulating factor. MP subtypes were indistinguishable by morphological or antigenic criteria. Protein profiling by Surface Enhanced Laser Desorption Ionization-Time of Flight (SELDI-TOF) ProteinChip assays with weak cationic exchange chips showed unique MP spectral profiles. Corresponding protein fractions were recovered by high performance liquid chromatography and identified by liquid chromatography tandem mass spectrometry. The results provide a unique means to distinguish microglia from other MP subtypes.