Targeted Proteomics of the Secretory Pathway Reveals the Secretome of Mouse Embryonic Fibroblasts and Human Embryonic Stem Cells

Proteins endogenously secreted by human embryonic stem cells (hESCs) and those present in hESC culture medium are critical regulators of hESC self-renewal and differentiation. Current MS-based approaches for identifying secreted proteins rely predominantly on MS analysis of cell culture supernatants. Here we show that targeted proteomics of secretory pathway organelles is a powerful alternate approach for interrogating the cellular secretome. We have developed procedures to obtain subcellular fractions from mouse embryonic fibroblasts (MEFs) and hESCs that are enriched in secretory pathway organelles while ensuring retention of the secretory cargo. MS analysis of these fractions from hESCs cultured in MEF conditioned medium (MEF-CM) or MEFs exposed to hESC medium revealed 99 and 129 proteins putatively secreted by hESCs and MEFs, respectively. Of these, 53 and 62 proteins have been previously identified in cell culture supernatants of MEFs and hESCs, respectively, thus establishing the validity of our approach. Furthermore, 76 and 37 putatively secreted proteins identified in this study in MEFs and hESCs, respectively, have not been reported in previous MS analyses.The identification of low abundance secreted proteins via MS analysis of cell culture supernatants typically necessitates the use of altered culture conditions such as serum-free medium. However, an altered medium formulation might directly influence the cellular secretome. Indeed, we observed significant differences between the abundances of several secreted proteins in subcellular fractions isolated from hESCs cultured in MEF-CM and those exposed to unconditioned hESC medium for 24 h. In contrast, targeted proteomics of secretory pathway organelles does not require the use of customized media. We expect that our approach will be particularly valuable in two contexts highly relevant to hESC biology: obtaining a temporal snapshot of proteins secreted in response to a differentiation trigger, and identifying proteins secreted by cells that are isolated from a heterogeneous population.Human embryonic stem cells (hESCs)¹ are pluripotent cells isolated from the inner cell mass of a pre-implantation blastocyst stage embryo (1). They have potential applications in regenerative medicine, are an attractive source of human cells for drug evaluation, and are useful models for understanding human development. The self-renewal or differentiation of hESCs is controlled by endogenous proteins secreted by hESCs and by exogenous factors present in cell culture medium (2, 3). For instance, hESCs are routinely cultured on feeder layers of mouse embryonic fibroblasts (MEFs) or on Matrigel-coated plates in mouse embryonic fibroblast–conditioned medium (MEF-CM). In these cases, cytokines secreted by MEFs and present in MEF-CM, together with cytokines and extracellular matrix (ECM) proteins secreted by hESCs, form a localized microenvironment that regulates hESC fate.The comprehensive identification of proteins secreted by MEFs and hESCs—their cellular secretome—can help unravel the molecular mechanisms that regulate hESC fate. Yet the use of MS-based approaches for secretome analysis remains challenging. In general, secretome studies of various cell types have relied on MS analysis of cell culture supernatants (reviewed in Ref. 4). However, such an approach typically results in the identification of small numbers of extracellular proteins. This was indeed the case with MS analysis of conditioned medium (CM) from MEFs or other feeder cells that support the maintenance of undifferentiated hESCs (5–8). A low abundance of secreted proteins of interest and a high concentration of serum proteins in cell culture media significantly impede MS analysis. To overcome these limitations, Bendall et al. implemented an iterative-exclusion MS (IE-MS) strategy, in conjunction with the use of medium without serum or serum replacer, for the identification of proteins secreted by MEFs and hESCs (2). Using this approach, large numbers of previously unreported proteins secreted by MEFs and hESCs could be identified, showing that IE-MS is a powerful strategy for the identification of low abundance proteins. However, the use of medium without serum or serum replacer for secretomic analysis can be problematic. Specifically, the use of a “blank” or serum-free medium might alter cellular physiology and, consequently, the profile of secreted proteins. Indeed, we observe that hESCs are highly prone to apoptosis under such growth conditions. Moreover, an analysis of the cell culture supernatant is not specifically targeted toward endogenously secreted ECM proteins, which are also an important component of the cellular microenvironment. ECM proteins form a matrix that associates with the cell and might not be present in the cell culture supernatant. Moreover, many growth factors are known to be sequestered by ECM proteins and might not be released into the culture medium (9). Here we present a rigorous evaluation of an alternate strategy to interrogate the entire cellular secretome, including cytokines and ECM proteins. Notably, our approach does not require the use of customized media lacking serum and serum replacers, and it is compatible with cell culture systems utilizing media of unknown or poorly defined composition, such as CM from MEFs.To identify the secretome of MEFs and hESCs, we carried out an MS analysis of their subcellular fractions that were enriched in secretory pathway organelles. The secretory pathway comprises the endoplasmic reticulum (ER), the Golgi apparatus, and the associated transport vesicles. Detailed MS analysis of these organelles identifies the secretory cargo (i.e. proteins destined to be secreted) in addition to the secretory pathway proteome (10). Indeed, we have previously identified several secreted proteins in hESCs as a result of contamination by the ER and Golgi (11) in our subcellular fractions. In light of these reports, we hypothesized that targeted proteomic analysis of the secretory pathway is a viable approach for comprehensive characterization of the cellular secretome. Accordingly, we developed protocols to isolate subcellular fractions enriched in the ER and Golgi compartments from MEFs and hESCs, and we subsequently carried out MS analysis on these samples. Several proteins secreted by MEFs and hESCs could be identified in this manner. Strikingly, the numbers of proteins identified were comparable to those obtained with the highly efficient IE-MS approach. Furthermore, we also show that short-term changes in medium composition affect the profile and quantitative levels of several proteins that transit through the secretory pathway, including secreted and membrane proteins. Taken together, our results validate the use of targeted secretory pathway proteomics as a powerful alternate approach to interrogate the cellular secretome.     

Comparative Proteomic Analysis of Supportive and Unsupportive Extracellular Matrix Substrates for Human Embryonic Stem Cell Maintenance

Human embryonic stem cells (hESCs) are pluripotent cells that have indefinite replicative potential and the ability to differentiate into derivatives of all three germ layers. hESCs are conventionally grown on mitotically inactivated mouse embryonic fibroblasts (MEFs) or feeder cells of human origin. In addition, feeder-free culture systems can be used to support hESCs, in which the adhesive substrate plays a key role in the regulation of stem cell self-renewal or differentiation. Extracellular matrix (ECM) components define the microenvironment of the niche for many types of stem cells, but their role in the maintenance of hESCs remains poorly understood. We used a proteomic approach to characterize in detail the composition and interaction networks of ECMs that support the growth of self-renewing hESCs. Whereas many ECM components were produced by supportive and unsupportive MEF and human placental stromal fibroblast feeder cells, some proteins were only expressed in supportive ECM, suggestive of a role in the maintenance of pluripotency. We show that identified candidate molecules can support attachment and self-renewal of hESCs alone (fibrillin-1) or in combination with fibronectin (perlecan, fibulin-2), in the absence of feeder cells. Together, these data highlight the importance of specific ECM interactions in the regulation of hESC phenotype and provide a resource for future studies of hESC self-renewal.     

Engineering tissue from human embryonic stem cells

Recent advances in human embryonic stem cell (hESC) biology now offer an alternative cell source for tissue engineers, as these cells are capable of proliferating indefinitely and differentiating to many clinically relevant cell types. Novel culture methods capable of exerting spatial and temporal control over the stem cell microenvironment allow for more efficient expansion of hESCs, and significant advances have been made toward improving our understanding of the biophysical and biochemical cues that direct stem cell fate choices. Effective production of lineage specific progenitors or terminally differentiated cells enables researchers to incorporate hESC derivatives into engineered tissue constructs. Here, we describe current efforts using hESCs as a cell source for tissue engineering applications, highlighting potential advantages of hESCs over current practices as well as challenges which must be overcome.     

Rapid Fibroblast Removal from High Density Human Embryonic Stem Cell Cultures

Mouse embryonic fibroblasts (MEFs) were used to establish human embryonic stem cells (hESCs) cultures after blastocyst isolation¹. This feeder system maintains hESCs from undergoing spontaneous differentiation during cell expansion. However, this co-culture method is labor intensive, requires highly trained personnel, and yields low hESC purity⁴. Many laboratories have attempted to minimize the number of feeder cells in hESC cultures (i.e. incorporating matrix-coated dishes or other feeder cell types^5-8). These modified culture systems have shown some promise, but have not supplanted the standard method for culturing hESCs with mitomycin C-treated mouse embyronic fibroblasts in order to retard unwanted spontaneous differentiation of the hESC cultures. Therefore, the feeder cells used in hESC expansion should be removed during differentiation experiments. Although several techniques are available for purifying the hESC colonies (FACS, MACS, or use of drug resistant vectors) from feeders, these techniques are labor intensive, costly and/or destructive to the hESC. The aim of this project was to invent a method of purification that enables the harvesting of a purer population of hESCs. We have observed that in a confluent hESC culture, the MEF population can be removed using a simple and rapid aspiration of the MEF sheet. This removal is dependent on several factors, including lateral cell-to-cell binding of MEFs that have a lower binding affinity to the styrene culture dish, and the ability of the stem cell colonies to push the fibroblasts outward during the generation of their own "niche". The hESC were then examined for SSEA-4, Oct3/4 and Tra 1-81 expression up to 10 days after MEF removal to ensure maintenance of pluripotency. Moreover, hESC colonies were able to continue growing from into larger formations after MEF removal, providing an additional level of hESC expansion.     

Scalable GMP compliant suspension culture system for human ES cells

Suspension bioreactors are an attractive alternative to static culture of human embryonic stem cells (hESCs) for the generation of clinically relevant cell numbers in a controlled system. In this study, we have developed a scalable suspension culture system using serum-free defined media with spinner flasks for hESC expansion as cell aggregates. With optimized cell seeding density and splitting interval, we demonstrate prolonged passaging and expansion of several hESC lines with overall expansion, yield, viability and maintenance of pluripotency equivalent to adherent culture. Human ESCs maintained in suspension as aggregates can be passaged at least 20 times to achieve over 1×10(13) fold calculated expansion with high undifferentiation rate and normal karyotype. Furthermore, the aggregates are able to differentiate to cardiomyocytes in a directed fashion. Finally, we show that the cells can be cryopreserved in serum-free medium and thawed into adherent or suspension cultures to continue passaging and expansion. We have successfully used this method under cGMP or cGMP-equivalent conditions to generate cell banks of several hESC lines. Taken together, our suspension culture system provides a powerful approach for scale-up expansion of hESCs under defined and serum-free conditions for clinical and research applications.     

Scalable culture and cryopreservation of human embryonic stem cells on microcarriers

As a result of their pluripotency and potential for unlimited self‐renewal, human embryonic stem cells (hESCs) hold tremendous promise in regenerative medicine. An essential prerequisite for the widespread application of hESCs is the establishment of effective and efficient protocols for large‐scale cell culture, storage, and distribution. At laboratory scales hESCs are cultured adherent to tissue culture plates; these culture techniques are labor‐intensive and do not scale to high cell numbers. In an effort to facilitate larger scale hESC cultivation, we investigated the feasibility of culturing hESCs adherent to microcarriers. We modified the surface of Cytodex 3 microcarriers with either Matrigel or mouse embryonic fibroblasts (MEFs). hESC colonies were effectively expanded in a pluripotent, undifferentiated state on both Matrigel‐coated microcarriers and microcarriers seeded with a MEF monolayer. While the hESC expansion rate on MEF‐microcarriers was less than that on MEF‐plates, the doubling time of hESCs on Matrigel‐microcarriers was indistinguishable from that of hESCs expanded on Matrigel‐coated tissue culture plates. Standard hESC cryopreservation methodologies are plagued by poor viability and high differentiation rates upon thawing. Here, we demonstrate that cryopreservation of hESCs adherent to microcarriers in cryovials provides a higher recovery of undifferentiated cells than cryopreservation of cells in suspension. Together, these results suggest that microcarrier‐based stabilization and culture may facilitate hESC expansion and storage for research and therapeutic applications. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Innovation in the culture and derivation of pluripotent human stem cells

In recent years, substantial progress has been made in identifying culture conditions and specific molecular factors that maintain human embryonic stem cells (hESCs) in a self-renewing, pluripotent state. As science and medicine move closer to producing viable hESC-based therapeutics, effective methods of isolating and maintaining undifferentiated hESCs using clinically acceptable good manufacturing practices must be developed. In recent years, progress toward this goal has included the identification of molecular factors that induce or repress hESC self-renewal and the development of defined media that support long-term hESC expansion. In addition, the recent discovery of novel means to derive pluripotent cells that avoid embryo destruction, including induced pluripotent stem (iPS cells), may mitigate ethical concerns associated with the use of hESCs.     

Mechanics regulates fate decisions of human embryonic stem cells

Research on human embryonic stem cells (hESCs) has attracted much attention given their great potential for tissue regenerative therapy and fundamental developmental biology studies. Yet, there is still limited understanding of how mechanical signals in the local cellular microenvironment of hESCs regulate their fate decisions. Here, we applied a microfabricated micromechanical platform to investigate the mechanoresponsive behaviors of hESCs. We demonstrated that hESCs are mechanosensitive, and they could increase their cytoskeleton contractility with matrix rigidity. Furthermore, rigid substrates supported maintenance of pluripotency of hESCs. Matrix mechanics-mediated cytoskeleton contractility might be functionally correlated with E-cadherin expressions in cell-cell contacts and thus involved in fate decisions of hESCs. Our results highlighted the important functional link between matrix rigidity, cellular mechanics, and pluripotency of hESCs and provided a novel approach to characterize and understand mechanotransduction and its involvement in hESC function.     

Laminin-511 expression is associated with the functionality of feeder cells in human embryonic stem cell culture

Fibroblast feeder cells play an important role in supporting the derivation and long term culture of undifferentiated, pluripotent human embryonic stem cells (hESCs). The feeder cells secrete various growth factors and extracellular matrix (ECM) proteins into extracellular milieu. However, the roles of the feeder cell-secreted factors are largely unclear. Animal feeder cells and use of animal serum also make current feeder cell culture conditions unsuitable for derivation of clinical grade hESCs. We established xeno-free feeder cell lines using human serum (HS) and studied their function in hESC culture. While human foreskin fibroblast (hFF) feeder cells were clearly hESC supportive, none of the established xeno-free human dermal fibroblast (hDF) feeder cells were able to maintain undifferentiated hESC growth. The two fibroblast types were compared for their ECM protein synthesis, integrin receptor expression profiles and key growth factor secretion. We show that hESC supportive feeder cells produce laminin-511 and express laminin-binding integrins α3ß1, α6ß1 and α7ß1. These results indicate specific laminin isoforms and integrins in maintenance of hESC pluripotency in feeder-dependent cultures. In addition, several genes with a known or possible role for hESC pluripotency were differentially expressed in distinct feeder cells.     

Ghrelin promotes the differentiation of human embryonic stem cells in infarcted cardiac microenvironment

Ghrelin is broadly expressed in myocardial tissues, where it exerts different functions. It also has been found to have a wide variety of biological functions on cell differentiation and tissue development. The aim of this study was to investigate the effect of ghrelin on human embryonic stem cell (hESC) differentiation in infarcted cardiac microenvironment. The hESCs grown on feeder layers expressed several pluripotential markers including alkaline phosphatase (AKP). Four weeks after transplantation into rat infarcted hearts, the hESCs and their progeny cells survived and formed intracardiac grafts were 54.7% and 19.6% respectively in ghrelin- and phosphate-buffered saline (PBS)-treated groups. Double immunostaining with anti-human Sox9 and anti-HNA or anti-human fetal liver kinase-1 (Flk1) and anti β-tubulin showed that the human grafts were in development. However, double positive stains were only found in the ghrelin-treated group. In addition, the hESC injection protocol was insufficient to restore heart function of the acute myocardial infarction model. Our study, therefore, provides a new insight of ghrelin on promoting hESC survival and differentiation in rat infarcted cardiac microenvironment. This may give a clue for therapy for myocardial infarction by hESCs or progeny cells.     

Attachment and growth of human embryonic stem cells on microcarriers

The use of human embryonic stem cells (hESCs) for cell-based therapies will require large quantities of genetically stable pluripotent cells and their differentiated progeny. Traditional hESC propagation entails adherent culture and is sensitive to enzymatic dissociation. These constraints hamper modifying method from 2-dimensional flat-bed culture, which is expensive and impractical for bulk cell production. Large-scale culture for clinical use will require innovations such as suspension culture for bioprocessing. Here we describe the attachment and growth kinetics of both murine embryonic stem cells (mESCs) and hESCs on trimethyl ammonium-coated polystyrene microcarriers for feeder-free, 3-dimensional suspension culture. mESCs adhered and expanded according to standard growth kinetics. For hESC studies, we tested aggregate (collagenase-dissociated) and single-cell (TrypLE-dissociated) culture. Cells attached rapidly to beads followed by proliferation. Single-cell cultures expanded 3-fold over approximately 5 days, slightly exceeding that of hESC aggregates. Importantly, single-cell cultures were maintained through 6 passages with a 14-fold increase in cell number while still expressing the undifferentiated markers Oct-4 and Tra 1-81. Finally, hESCs retained their capacity to differentiate towards pancreatic, neuronal, and cardiomyocyte lineages. Our studies provide proof-of-principle of suspension-based expansion of hESCs on microcarriers, as a novel, economical and practical feeder-free means of bulk hESC production.     

Expansion of human embryonic stem cells in defined serum-free medium devoid of animal-derived products

Human embryonic stem cells (hESCs) can serve as an unlimited cell source for cellular transplantation and tissue engineering due to their prolonged proliferation capacity and their unique ability to differentiate into derivatives of all three-germ layers. In order to reliably and safely produce hESCs, use of reagents that are defined, qualified, and preferably derived from a non-animal source is desirable. Traditionally, mouse embryonic fibroblasts (MEFs) have been used as feeder cells to culture undifferentiated hESCs. We recently reported a scalable feeder-free culture system using medium conditioned by MEFs. The base and conditioned medium (CM) still contain unknown bovine and murine-derived components, respectively. In this study, we report the development of a hESC culture system that utilizes a commercially available serum-free medium (SFM) containing human sourced and recombinant proteins supplemented with recombinant growth factor(s) and does not require conditioning with feeder cells. In this system, which employs human laminin coated surface and high concentration of hbFGF, the hESCs maintained undifferentiated hESC morphology and had a twofold increase in expansion compared to hESCs grown in MEF-CM. The hESCs also expressed surface markers SSEA-4 and Tra-1-60 and maintained expression of hTERT, Oct4, and Cripto genes similar to cells cultured in MEF-CM. In addition, hESCs maintained in this culture system were able to differentiate in vitro and in vivo into cells of all three-germ layers. The cells maintained a normal karyotype after prolonged culture in SFM. In summary, this study demonstrates that the hESCs cultured in defined non-conditioned serum-free medium (NC-SFM) supplemented with growth factor(s) retain the characteristics and replicative potential of hESCs. The use of defined culture system with NC-SFM on human laminin simplifies scale-up and allows for reproducible generation of hESCs under defined and controlled conditions that would serve as a starting material for production of hESC derived cells for therapeutic use.     

Mass Spectrometry–based Proteomic Analysis of the Matrix Microenvironment in Pluripotent Stem Cell Culture

The cellular microenvironment comprises soluble factors, support cells, and components of the extracellular matrix (ECM) that combine to regulate cellular behavior. Pluripotent stem cells utilize interactions between support cells and soluble factors in the microenvironment to assist in the maintenance of self-renewal and the process of differentiation. However, the ECM also plays a significant role in shaping the behavior of human pluripotent stem cells, including embryonic stem cells (hESCs) and induced pluripotent stem cells. Moreover, it has recently been observed that deposited factors in a hESC-conditioned matrix have the potential to contribute to the reprogramming of metastatic melanoma cells. Therefore, the ECM component of the pluripotent stem cell microenvironment necessitates further analysis.In this study we first compared the self-renewal and differentiation properties of hESCs grown on Matrigel™ pre-conditioned by hESCs to those on unconditioned Matrigel™. We determined that culture on conditioned Matrigel™ prevents differentiation when supportive growth factors are removed from the culture medium. To investigate and identify factors potentially responsible for this beneficial effect, we performed a defined SILAC MS-based proteomics screen of hESC-conditioned Matrigel™. From this proteomics screen, we identified over 80 extracellular proteins in matrix conditioned by hESCs and induced pluripotent stem cells. These included matrix-associated factors that participate in key stem cell pluripotency regulatory pathways, such as Nodal/Activin and canonical Wnt signaling. This work represents the first investigation of stem-cell-derived matrices from human pluripotent stem cells using a defined SILAC MS-based proteomics approach.The two defining characteristics of human embryonic stem cells (hESCs),¹ self-renewal and pluripotency, are maintained by a delicate balance of intracellular and extracellular signaling processes. Extracellular regulation is primarily the result of changes in the microenvironment surrounding the cells during growth in vitro or in vivo. HESCs interact with this “niche ” through support cells, extracellular matrix (ECM) components, and autocrine/paracrine signaling (reviewed in Refs. 1–3). Modulation of any of these supportive elements individually or in combination has been used extensively to alter hESC behavior (1–3).The culture of hESCs, as well as that of human induced pluripotent stem cells (hiPSCs), is conventionally performed on a layer of irradiated mouse embryonic fibroblast cells (MEFs). These MEFs are believed to promote the maintenance of hESCs and hiPSCs through the secretion of beneficial support proteins and cytokines into the soluble microenvironment. A number of proteomic studies have been conducted that examine the secretome of feeder-cell layers in an attempt to elucidate proteins and pathways essential for hESC and hiPSC survival (4–7). Alternatively, hESCs and hiPSCs can be cultured in feeder-free conditions in the absence of support cells. In feeder-free conditions, hESCs and hiPSCs are most often grown on the basement membrane matrix Matrigel™ in medium that has been previously conditioned by MEFs (MEF-CM). Matrigel™ is a gelatinous mixture that is secreted by Engelbreth-Holm-Swarm mouse sarcoma cells (8). Although recent studies have proposed that a variety of defined matrices can support the growth of hESCs and hiPSCs, few of these can maintain a wide range of stem cell lines and therefore are typically not used in place of Matrigel™. The properties of Matrigel™ that make it such an effective matrix for hESC and hiPSC culture remain poorly understood. Because of the complexity of matrices like Matrigel™, the majority of proteomic studies that examine the hESC and hiPSC microenvironment have focused on contributions from support cells and soluble extracellular factors.The ECM is typically a complex network of structural proteins and glycosaminoglycans that function to support cells through the regulation of processes such as adhesion and growth factor signaling (9). Thus, it is not surprising that the generation of a well-defined matrix capable of facilitating hESC and hiPSC self-renewal has remained difficult (10). Previous proteomic investigations of Matrigel™ and other matrices supportive of hESC maintenance in vitro have revealed the presence of numerous growth, binding, and signaling proteins (11, 12). Further examination of how hESCs and hiPSCs interact with these complex matrices would provide critical information about what role the ECM plays in the organization of processes involved in the regulation of self-renewal and pluripotency.A recent study has established the ability of hESC-derived matrix microenvironments to alter tumorigenic properties through the reprogramming of metastatic melanoma cells (13). Importantly, this effect was found to be dependent on the exposure of metastatic cells to hESC-derived conditioned Matrigel™. Culture of metastatic melanoma cells in hESC-conditioned medium did not promote the reprogramming effect. These data suggest that the proteins responsible for this effect were integrated in the matrix. With the use of immunochemical techniques, it was later found that the left-right determination (Lefty) proteins A and B that were deposited in the matrix by hESCs during conditioning were at least in part responsible for the cellular change observed in metastatic cells (14). The Lefty A and B proteins are antagonists of transforming growth factor (TGF)-β signaling that act directly on Nodal protein, a critical regulator of the stem cell phenotype (15, 16). Subsequent studies of conditioned matrix utilizing mESCs implicated the bone morphogenic protein (BMP) 4 antagonist Gremlin as a primary regulator of the observed changes in metastatic cells (17). Collectively, these studies were all biased by a targeted analysis of potential effectors of metastatic cells. A comprehensive proteomic analysis of conditioned matrix could potentially reveal other factors involved in metastatic cell reprogramming. Furthermore, proteomic examination of hESC and hiPSC conditioned matrix could expose factors important in the regulation of self-renewal and pluripotency by the microenvironment in vitro.To this end, we have analyzed both types of human pluripotent stem cells, hESCs and hiPSCs, via a mass spectrometry (MS)-based proteomics approach to identify proteins deposited during growth in feeder-free conditions in vitro on Matrigel™. To investigate the hESC- and hiPSC-derived matrix, the metabolic labeling technique known as stable isotope labeling with amino acids in cell culture (SILAC) was used (18). SILAC facilitates the identification of hESC- and hiPSC-derived proteins that would otherwise be confounded by the presence of mouse-derived protein background from Matrigel™. From the proteomic analysis of three cells lines, namely, the hESC lines H9 and CA1 and the hiPSC line BJ-1D, we identified a total of 621, 1355, and 1350 total unique proteins, respectively. This work represents the first analysis of a hESC- and hiPSC-derived conditioned matrix and resulted in the identification of at least one novel microenvironmental contributor responsible for the regulation of human pluripotent stem cells.     

Improving Survival of Disassociated Human Embryonic Stem Cells by Mechanical Stimulation Using Acoustic Tweezing Cytometry

Dissociation-induced apoptosis of human embryonic stem cells (hESCs) hampers their large-scale culture. Herein we leveraged the mechanosensitivity of hESCs and employed, to our knowledge, a novel technique, acoustic tweezing cytometry (ATC), for subcellular mechanical stimulation of disassociated single hESCs to improve their survival. By acoustically actuating integrin-bound microbubbles (MBs) to live cells, ATC increased the survival rate and cloning efficiency of hESCs by threefold. A positive correlation was observed between the increased hESC survival rate and total accumulative displacement of integrin-anchored MBs during ATC stimulation. ATC may serve as a promising biocompatible tool to improve hESC culture.     

An In Vitro Mechanism Study on the Proliferation and Pluripotency of Human Embryonic Stems Cells in Response to Magnesium Degradation

Magnesium (Mg) is a promising biodegradable metallic material for applications in cellular/tissue engineering and biomedical implants/devices. To advance clinical translation of Mg-based biomaterials, we investigated the effects and mechanisms of Mg degradation on the proliferation and pluripotency of human embryonic stem cells (hESCs). We used hESCs as the in vitro model system to study cellular responses to Mg degradation because they are sensitive to toxicants and capable of differentiating into any cell types of interest for regenerative medicine. In a previous study when hESCs were cultured in vitro with either polished metallic Mg (99.9% purity) or pre-degraded Mg, cell death was observed within the first 30 hours of culture. Excess Mg ions and hydroxide ions induced by Mg degradation may have been the causes for the observed cell death; hence, their respective effects on hESCs were investigated for the first time to reveal the potential mechanisms. For this purpose, the mTeSR®1 hESC culture media was either modified to an alkaline pH of 8.1 or supplemented with 0.4–40 mM of Mg ions. We showed that the initial increase of media pH to 8.1 had no adverse effect on hESC proliferation. At all tested Mg ion dosages, the hESCs grew to confluency and retained pluripotency as indicated by the expression of OCT4, SSEA3, and SOX2. When the supplemental Mg ion dosages increased to greater than 10 mM, however, hESC colony morphology changed and cell counts decreased. These results suggest that Mg-based implants or scaffolds are promising in combination with hESCs for regenerative medicine applications, providing their degradation rate is moderate. Additionally, the hESC culture system could serve as a standard model for cytocompatibility studies of Mg in vitro, and an identified 10 mM critical dosage of Mg ions could serve as a design guideline for safe degradation of Mg-based implants/scaffolds.     

Noggin maintains pluripotency of human embryonic stem cells grown on Matrigel

Objective:  Spontaneous differentiation of human embryonic stem cell (hESC) cultures is a major concern in stem cell research. Physical removal of differentiated areas in a stem cell colony is the current approach used to keep the cultures in a pluripotent state for a prolonged period of time. All hESCs available for research require unidentified soluble factors secreted from feeder layers to maintain the undifferentiated state and pluripotency. Under experimental conditions, stem cells are grown on various matrices, the most commonly used being Matrigel.
Materials and Methods:  We propose an alternative method to prevent spontaneous differentiation of hESCs grown on Matrigel that uses low amounts of recombinant noggin. We make use of the porosity of Matrigel to serve as a matrix that traps noggin and gradually releases it into the culture to antagonize bone morphogenetic proteins (BMP). BMPs are known to initiate differentiation of hESCs and are either present in the conditioned medium or are secreted by hESCs themselves.
Results:  hESCs grown on Matrigel supplemented with noggin in conditioned medium from feeder layers (irradiated mouse embryonic fibroblasts) retained both normal karyotype and markers of hESC pluripotency for 14 days. In addition, these cultures were found to have increased cell proliferation of stem cells as compared to hESCs grown on Matrigel alone.
Conclusion:  Noggin can be utilized for short term prevention of spontaneous differentiation of stem cells grown on Matrigel.     

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells

Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful quantitative proteomics platform for comprehensive characterization of complex biological systems. However, the potential of SILAC-based approaches has not been fully utilized in human embryonic stem cell (hESC) research mainly because of the complex nature of hESC culture conditions. Here we describe complete SILAC labeling of hESCs with fully preserved pluripotency, self-renewal capabilities, and overall proteome status that was quantitatively analyzed to a depth of 1556 proteins and 527 phosphorylation events. SILAC-labeled hESCs appear to be perfectly suitable for functional studies, and we exploited a SILAC-based proteomics strategy for discovery of hESC-specific surface markers. We determined and quantitatively compared the membrane proteomes of the self-renewing versus differentiating cells of two distinct human embryonic stem cell lines. Of the 811 identified membrane proteins, six displayed significantly higher expression levels in the undifferentiated state compared with differentiating cells. This group includes the established marker CD133/Prominin-1 as well as novel candidates for hESC surface markers: Glypican-4, Neuroligin-4, ErbB2, receptor-type tyrosine-protein phosphatase ζ (PTPRZ), and Glycoprotein M6B. Our study also revealed 17 potential markers of hESC differentiation as their corresponding protein expression levels displayed a dramatic increase in differentiated embryonic stem cell populations.Human embryonic stem cells (hESCs)¹ are stem cells derived from the blastocyst inner cell mass. They are pluripotent; thus they are able to differentiate into any human cell type. The self-renewal capacity and pluripotency make hESCs an ideal system to study the processes of cell development and differentiation. Moreover hESC research is highly relevant for regenerative medicine, which aims at replacing or restoring tissue damaged by disease or injury through transplantation of functional hESCs (1,2). However, factors responsible for maintaining the undifferentiated and pluripotent nature of hESCs are still largely unknown. Before hESCs can be used for transplantation into the human body, reliable and reproducible protocols for differentiating them into specific cell types are needed. To create such protocols we need to develop a thorough understanding of the mechanisms maintaining the undifferentiated pluripotent nature of hESCs and those guiding their differentiation into specific lineages.A number of factors involved in the maintenance of pluripotency have been described over the last few years (3). It has also been demonstrated that overexpression of some of these factors in somatic cells is sufficient to turn them into pluripotent stem cells very similar to hESCs (4–8). However, it is apparent that the processes occurring during such transformation are extremely complex. A large number of factors and pathways are involved in maintaining the pluripotent state and regulating self-renewal and differentiation. The process of specific hESC differentiation into distinct cell types is even less understood. Most current attempts to directionally differentiate hESCs are based on sequential application of empirically selected growth factors and consequent selection for markers expressed in the target cell types (9). A more systematic approach is needed to improve our understanding of the pathways that control the conversion of precursors into specific cell types, progressing toward the goal of reproducing these processes in vitro for the generation of functional cells and tissues for transplantation.Comprehensive quantitative analysis of the hESC proteome would mean an important advance in understanding the nature of “stemness,” pluripotency, and differentiation. Several studies targeting various aspects of the hESC proteome have already been reported (for reviews, see Refs. 10 and 11). The task, however, is so enormous that further detailed analysis and novel strategies are necessary and will be of high interest and importance. In this regard, MS-based quantitative proteomics and in particular stable isotope labeling by amino acids in cell culture (SILAC) may greatly facilitate the process of defining the mechanisms of hESC self-renewal and differentiation. With SILAC, the entire proteome of a given cell population is metabolically labeled by heavy, non-radioactive isotopic variants of amino acids, thus making it distinguishable by MS analysis (12). Thereafter two or more distinctly SILAC-labeled cell populations can be mixed and analyzed in one MS experiment that allows accurate quantitation of proteins from the different cellular states (13). This versatile strategy has been demonstrated to be very useful for comprehensive characterization of complex biological phenomena (14–21) including in-depth comparison of signaling pathways to identify control points determining cell fate of adult mesenchymal stem cells (22).Here we report a procedure for complete SILAC labeling of human ES cells. We show that these SILAC-encoded hESCs have preserved self-renewing undifferentiated status as well as pluripotent capabilities based on analysis of known markers. In addition, we further compared the overall proteomes and phosphoproteomes of SILAC-labeled hESCs and equivalent cells grown under conventional culture conditions. We next compared the membrane proteomes of undifferentiated and differentiated hESCs in a quantitative manner. Our analysis identified 811 membrane proteins, which to our knowledge is the largest data set of ES cell membrane proteome. This study also revealed 23 membrane proteins with large changes in their expression levels during the differentiation. Six of those cell surface molecules displayed more than 3-fold higher levels in the self-renewing cells, whereas the remaining 17 were identified as more abundant in the differentiated population. These may be useful as specific hESC markers for the corresponding ES cell state and help to shed light on the mechanisms for self-renewal and differentiation.