Collective cell traction force analysis on aligned smooth muscle cell sheet between three-dimensional microwalls.

During the past two decades, novel biomaterial scaffold for cell attachment and culture has been developed for applications in tissue engineering, biosensing and regeneration medicine. Tissue engineering of blood vessels remains a challenge owing to the complex three-layer histology involved. In order to engineer functional blood vessels, it is essential to recapitulate the characteristics of vascular smooth muscle cells (SMCs) inside the tunica media, which is known to be critical for vasoconstriction and vasodilation of the circulatory system. Until now, there has been a lack of understanding on the mechanotransduction of the SMC layer during the transformation from viable synthetic to quiescent contractile phenotypes. In this study, microfabricated arrays of discontinuous microwalls coated with fluorescence microbeads were developed to probe the mechanotransduction of the SMC layer. First, the system was exploited for stimulating the formation of a highly aligned orientation of SMCs in native tunica medium. Second, atomic force microscopy in combination with regression analysis was applied to measure the elastic modulus of a polyacrylamide gel layer coated on the discontinuous microwall arrays. Third, the conventional traction force assay for single cell measurement was extended for applications in three-dimensional cell aggregates. Then, the biophysical effects of discontinuous microwalls on the mechanotransduction of the SMC layer undergoing cell alignment were probed. Generally, the cooperative multiple cell-cell and cell-microwall interactions were accessed quantitatively by the newly developed assay with the aid of finite-element modelling. The results show that the traction forces of highly aligned cells lying in the middle region between two opposing microwalls were significantly lower than those lying adjacent to the microwalls. Moreover, the spatial distributions of Von Mises stress during the cell alignment process were dependent on the collective cell layer orientation. Immunostaining of the SMC sheet further demonstrated that the collective mechanotransduction induced by three-dimensional topographic cues was correlated with the reduction of actin and vinculin expression. In addition, the online two-dimensional LC-MS/MS analysis verified the modulation of focal adhesion formation under the influence of microwalls through the regulation in the expression of three key cytoskeletal proteins.

Proteomics based identification of cell migration related proteins in HBV expressing HepG2 cells.

Proteomics study was performed to investigate the specific protein expression profiles of HepG2 cells transfected with mutant HBV compared with wildtype HBV genome, aiming to identify the specific functions of SH3 binding domain (proline rich region) located in HBx. In addition to the cell movement and kinetics changes due to the expression of HBV genome we have observed previously, here we further targeted to explore the specific changes of cellular proteins and potential intracellular protein interactions, which might provide more information of the potential cellular mechanism of the differentiated cell movements. Specific changes of a number of proteins were shown in global protein profiling in HepG2 cells expressing wildtype HBV, including cell migration related proteins, and interestingly the changes were found recovered by SH3 binding domain mutated HBV. The distinctive expressions of proteins were validated by Western blot analysis.

Comparative proteomics analysis of engineered Saccharomyces cerevisiae with enhanced biofuel precursor production.

The yeast Saccharomyces cerevisiae was metabolically modified for enhanced biofuel precursor production by knocking out genes encoding mitochondrial isocitrate dehydrogenase and over-expression of a heterologous ATP-citrate lyase. A comparative iTRAQ-coupled 2D LC-MS/MS analysis was performed to obtain a global overview of ubiquitous protein expression changes in S. cerevisiae engineered strains. More than 300 proteins were identified. Among these proteins, 37 were found differentially expressed in engineered strains and they were classified into specific categories based on their enzyme functions. Most of the proteins involved in glycolytic and pyruvate branch-point pathways were found to be up-regulated and the proteins involved in respiration and glyoxylate pathway were however found to be down-regulated in engineered strains. Moreover, the metabolic modification of S. cerevisiae cells resulted in a number of up-regulated proteins involved in stress response and differentially expressed proteins involved in amino acid metabolism and protein biosynthesis pathways. These LC-MS/MS based proteomics analysis results not only offered extensive information in identifying potential protein-protein interactions, signal pathways and ubiquitous cellular changes elicited by the engineered pathways, but also provided a meaningful biological information platform serving further modification of yeast cells for enhanced biofuel production.

Proteomic analysis of vascular smooth muscle cells with S- and R-enantiomers of atenolol by iTRAQ and LC-MS/MS.

The term "proteome" was first introduced by referring to the complete determination of proteins expressed in a given cell, tissue, or organism. In HPLC-based proteomics technique, the mixture of the cleaved peptides are bonded, separated sequentially on the multidimensional columns based on charge or hydrophobicity of the ionized analytes, and then eluted into the MS for identification. Among the developed stable isotope-based quantification methods, iTRAQ has recently gained popularity as its simple iTRAQ labeling procedures and up to eight labeled samples examined in a single experiment.

Metabolic engineering for enhanced fatty acids synthesis in Saccharomyces cerevisiae.

Microbial production of biofuel has attracted significant attention in recent years. The fatty acids are important precursors for the production of fuels and chemicals, and its biosynthesis is initiated by the conversion of acetyl-CoA to malonyl-CoA which requires acetyl-CoA as key substrate. Herein, the yeast Saccharomyces cerevisiae was proposed to be metabolically engineered for cytosol acetyl-CoA enhancement for fatty acid synthesis. By gene disruption strategy, idh1 and idh2 genes involved in citrate turnover in tricarboxylic acid cycle (TCA cycle) were disrupted and the citrate production level was increased to 4- and 5-times in mutant yeast strains. In order to convert accumulated citrate to cytosol acetyl-CoA, a heterologous ATP-citrate lyase (ACL) was overexpressed in yeast wild type and idh1,2 disrupted strains. The wild type strain expressing acl mainly accumulated saturated fatty acids: C14:0, C16:0 and C18:0 at levels about 20%, 14% and 27%, respectively. Additionally, the idh1,2 disrupted strains expressing acl mainly accumulated unsaturated fatty acids. Specifically in Δidh1 strain expressing acl, 80% increase in C16:1 and 60% increase in C18:1 was detected. In Δidh2 strain expressing acl, 60% increase in C16:1 and 45% increase in C18:1 was detected. In Δidh1/2 strain expressing acl, there was 92% increase in C16:1 and 77% increase in C18:1, respectively. The increased fatty acids from our study may well be potential substrates for the production of hydrocarbon molecules as potential biofuels.

Ultrasound assisted extraction of carbohydrates from microalgae as feedstock for yeast fermentation.

Recently, carbohydrates biomass from microalgae is considered as a promising and inexpensive feedstock for biofeuls production by microorganism fermentation. The main obstacle of the process is microalgae pretreatment and carbohydrates extraction from algal cell. In this study, comparison of three pretreatment methods was performed and the results showed that ultrasonic assisted extraction (UAE) was very effective. The effects of four parameters (ultrasonic power, extraction time, flow rate and algal cell concentration, respectively) on extraction efficiency were also investigated. Additionally, in order to identify significant factors for glucose yield, combination of these four parameters was examined by using fractional factorial design (FFD) and the regression model was obtained. Meanwhile, the refined model was confirmed as a good fitting model via analysis of variance (ANOVA). After extraction, glucose obtained from microalgae was used as substrate for Rhodosporidium toruloides fermentation and yeast biomass was much higher than that of control culture.

Comparative proteomics profile of lipid-cumulating oleaginous yeast: an iTRAQ-coupled 2-D LC-MS/MS analysis.

Accumulation of intracellular lipid in oleaginous yeast cells has been studied for providing an alternative supply for energy, biofuel. Numerous studies have been conducted on increasing lipid content in oleaginous yeasts. However, few explore the mechanism of the high lipid accumulation ability of oleaginous yeast strains at the proteomics level. In this study, a time-course comparative proteomics analysis was introduced to compare the non-oleaginous yeast Saccharomyces cerevisiae, with two oleaginous yeast strains, Cryptococcus albidus and Rhodosporidium toruloides at different lipid accumulation stages. Two dimensional LC-MS/MS approach has been applied for protein profiling together with isobaric tag for relative and absolute quantitation (iTRAQ) labelling method. 132 proteins were identified when three yeast strains were all at early lipid accumulation stage; 122 and 116 proteins were found respectively within cells of three strains collected at middle and late lipid accumulation stages. Significantly up-regulation or down-regulation of proteins were experienced among comparison. Essential proteins correlated to lipid synthesis and regulation were detected. Our approach provides valuable indication and better understanding for lipid accumulation mechanism from proteomics level and would further contribute to genetic engineering of oleaginous yeasts.

Epigallocatechin-3-gallate induced modulation of cell deadhesion and migration on thermosensitive poly(N-isopropylacrylamide).

Epigallocatechin-3-gallate (EGCG), which is the main polyphenolic constituent of green tea, has emerged as a promising candidate for potential applications in selected anticancer therapeutics. Generally, tumor metastasis is known to be correlated with the alterations in cell adhesion and migration of normal cells. Nevertheless, the effect of EGCG on the biophysical responses of tumor cell adhering on extracellular matrix remains obscure. In this study, a thermosenstive poly(N-isopropylacrylamide) (PIPAAm) system was developed to elucidate the potential anti-tumor effect of EGCG on the deadhesion and migration of HepG2 cells. First, both XPS and ELISA validated the coating of laminin (LA) on PIPAAm. Second, a change of nanotopology of LA layer on PIPAAm across the lower solution critical temperature (LCST) was detected with AFM. HepG2 cells seeded on LA-coated PIPAAm surface was shown to go through deadhesion by lowering the temperature below the LCST. Interestingly, EGCG was shown to decelerate the thermally triggered deadhesion of HepG2 cell on LA coated PIPAAm. Moreover, the inhibition of cell deadhesion in EGCG treated cells was shown to be driven by actin remodeling. Interestingly, the modulation of cell deadhesion on LA coated PIPAAm by EGCG leads to the reduction of cell motility as shown by real-time cell migration assay. Overall, the use of PIPAAm system demonstrated the promise of EGCG as anticancer therapy through the suppression of cell deadhesion and migration.

HBx expression activates RhoA GTPase: impact on cell migration.

HBV (hepatitis B virus) remains a global health concern, especially in developing countries. It has been associated with the development of HCC (hepatocellular carcinoma). One of the four viral proteins, HBx, interacts with cellular proteins, which are involved in a series of cellular processes including cell migration. The Rho GTPases (guanine nucleotide triphosphatases) family of proteins is involved in the regulation of the reorganization of actin and cell migration. We have reported that HBV replication activates Rac1 through SH3 binding. Here, we reported that RhoA was activated by HBx in vitro. The cell motility was enhanced in HepG2 cells co-transfected with HBx and RhoA, compared with those transfected with RhoA alone. Our results were consistent with the recently reported role of RhoA in promoting cell motility and may provide new insights on the mechanism of HBV-associated HCC.

Proteomic analysis of HBV-associated HCC: insights on mechanisms of disease onset and biomarker discovery.

The development of hepatocellular carcinoma (HCC) can be considered as an end-stage outcome of chronic hepatitis B virus (HBV) infection. Early prognostic markers are needed to allow effective treatments and prevent HCC from developing. Proteomics analysis has been used to identify markers from clinical samples from HCC patients. This approach can be further improved by identifying early biomarkers before the onset of HCC. One way would be to use the cell-based HBV replication system, which is reflective of the early stage of virus infection and thus secreted proteins identified at this stage may have relevance in HCC prognosis. In this review, we focus the discussion on the current status of proteomics analysis of cellular proteins and HCC biomarker identification, with a special highlight on the potential of the cell-based HBV replication system for the identification of prognostic HCC biomarkers.

iTRAQ-coupled 2D LC-MS/MS analysis of secreted proteome of HBV-replicating HepG2 cells: potential in biomarkers for prognosis of HCC.

Hepatitis B virus (HBV) infection remains a major health concern with more than 350 million carriers in the world. It is associated with acute and chronic liver diseases including hepatocellular carcinoma (HCC). The early detection of severe liver diseases related to HBV is crucial for the effective treatment. This work aims to investigate the secreted proteins in our recently established cell-based HBV replication system, using isobaric tags for relative and absolute quantitation (iTRAQ)-coupled 2D LC-MS/MS proteomics approach. Such proteins are reflective of early events of HBV infection and thus may have potential as prognostic biomarkers for development of liver diseases.

DLEC1 Expression Is Modulated by Epigenetic Modifications in Hepatocelluar Carcinoma Cells: Role of HBx Genotypes.

Deleted in Lung and Esophageal Cancer 1 (DLEC1) is a functional tumor suppressor gene (TSG). It has been found to be silenced in a variety of human cancers including hepatocellular carcinoma (HCC). The silencing of DLEC1 can be modulated by epigenetic modifications, such as DNA hypermethylation and histone hypoacetylation. In the case of HCC, hepatitis B virus X protein (HBx) has been implicated in methylation of target promoters resulting in the down-regulation of tumor suppressor genes, which in turn contributes to the development of HCC. In the present study, we first established a cell system in which epigenetic modifications can be modulated using inhibitors of either DNA methylation or histone deacetylation. The cell system was used to reveal that the expression of DLEC1 was upregulated by HBx in a genotype-dependent manner. In particular, HBx genotype A was found to decrease DNA methylation of the DLEC1 promoter. Our results have provided new insights on the impact of HBx in HCC development by epigenetic modifications.

HBV X protein interacts with cytoskeletal signaling proteins through SH3 binding.

The aim of this study was to investigate interactions between cellular SH3-containing proteins and the proline-rich domain in Hepatitis B Virus (HBV) X protein (HBx) The proline-rich domain of HBx (amino acids 19-58) as well as the relevant site-directed mutagenesis (proline to alanine residues) were cloned into pGEX-5X-1 and expressed as GST-PXXP and GST-AXXA probes. Panomics SH3 domain arrays were probed using both GST-PXXP and GST-AXXA to identify potential interacting SH3 domain containing proteins. The specific interactions were confirmed by the immunoprecipitation of the full-length SH3 domain-containing protein. We report here the binding assay which demonstrated interaction between PXXP domain in HBx and the SH3-domain containing proteins, in particular various signaling proteins involved in cytoskeletal reorganization. Our findings were consistent with similar virus-host interactions via SH3 binding for other viruses such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV) Further characterization of the proline-rich binding to SH3 domains could yield important information for the design of novel therapeutic measures against downstream disease causative effects of HBx in the liver cells.

Protein profile in HBx transfected cells: a comparative iTRAQ-coupled 2D LC-MS/MS analysis.

The x protein of HBV (HBx) has been involved in the development of hepatocellular carcinoma (HCC), with a possible link to individual genotypes. Nevertheless, the underlying mechanism remains obscure. In this study, we aim to identify the HBx-induced protein profile in HepG2 cells by LC-MS/MS proteomics analysis. Our results indicated that proteins were differentially expressed in HepG2 cells transfected by HBx of various genotypes. Proteins associated with cytoskeleton were found to be either up-regulated (MACF1, HMGB1, Annexin A2) or down-regulated (Lamin A/C). These may in turn result in the decrease of focal adhesion and increase of cell migration in response to HBx. Levels of other cellular proteins with reported impact on the function of extracellular matrix (ECM) proteins and cell migration, including Ca(2+)-binding proteins (S100A11, S100A6, and S100A4) and proteasome protein (PSMA3), were affected by HBx. The differential protein profile identified in this study was also supported by our functional assay which indicated that cell migration was enhanced by HBx. Our preliminary study provided a new platform to establish a comprehensive cellular protein profile by LC-MS/MS proteomics analysis. Further downstream functional assays, including our reported cell migration assay, should provide new insights in the association between HCC and HBx.

Hepatitis B virus induced coupling of deadhesion and migration of HepG2 cells on thermo-responsive polymer.

The unique physical property of thermo-responsive polymer (TRP) has recently prompted its increasing applications in tissue engineering. On the other hand, TRP has not been exploited for potential applications in quantitative cell screening against external stimulations. In this study, TRP is applied as a model system for elucidating the effect of HBV replication on the biophysical responses of HepG2 cells transfected by wild type HBV genome. Moreover, mutant HBV genome is designed to assess the specific activity of the SH3-binding domain of HBx during HBV replication. The adhesion contact recession and geometry transformation of HepG2 cells transfected with empty vector (pcDNA3.1 cells), wild type HBV (wtHBV cells) and mutant HBV genome (mHBV cells) are probed during the thermal transformation across lower solution critical temperature of TRP. In comparison with pcDNA3.1 cells and mHBV cells, the initial rate of reduction in degree of deformation and average adhesion energy for wtHBV cells is significantly increased. Interestingly, migration speed and persistence time of cells are found to be correlated with the cell deadhesion kinetics. Immuno-fluorescence microscopy demonstrates that HBV replication reduces the actin concentration and focal adhesions at cell periphery during the initial 30 min cell deadhesion. The results strongly suggested that HBV infection triggers the dynamic responses of HepG2 cells through the cytoskeleton remodeling and subsequent mechanochemical transduction. Overall, it is shown that TRP provides a convenient platform for quantifying biological stimulations on adherent cells.

HBX-mediated migration of HBV-replicating HepG2 cells: insights on development of hepatocellular carcinoma.

Hepatitus B virus (HBV) is a major cause of the development of hepatpcellular carcinoma (HCC). One of the significant characteristics of tumor progression is cell migration which is reflective of cytoskeletal dynamics. The Rho GTPases contribute to a multiple cellular processes, including the cellular cytoskeletal reorganization and motility. It has been found that some Rho GTPases have oncogenic activity and can promote cancer cell invasion. Here we discuss one of the Rho GTPases, Rac1 can be activated by HBV replication and such activation results in the high motility of HBV-replicating cells. The enhanced cell motility can be interestingly alleviated by the mutation at the sites of proline rich domain located in HBX. Our findings may provide new insights on the mechanism of HCC development associated with chronic HBV infection.

iTRAQ-coupled 2-D LC-MS/MS analysis of protein profile associated with HBV-modulated DNA methylation.

The development of hepatocellular carcinoma (HCC) is believed to be associated with multiple risk factors, including the infection of hepatitis B virus (HBV). Based on the analysis of individual genes, evidence has indicated the association between HCC and HBV and has also been expanded to epigenetic regulation, with an involvement of HBV in the DNA methylation of the promoter of cellular target genes leading to changes in their expression. Proteomic study has been widely used to map a comprehensive protein profile, which in turn could provide a better understanding of underlying mechanisms of disease onset. In the present study, we performed a proteomic profiling by using iTRAQ-coupled 2-D LC/MS-MS analysis to identify cellular genes down-regulated in HBV-producing HepG2.2.15 cells compared with HepG2 cells. A total of 15 proteins including S100A6 and Annexin A2 were identified by our approach. The significance of these cellular proteins as target of HBV-mediated epigenetic regulation was supported by our validation assays, including their reactivation in cells treated with 5-aza-2'-deoxycytidine (a DNA methyltransferase inhibitor) by real-time RT-PCR and Western blot analysis, as well as the DNA methylation status analysis by bisulfite genome sequencing. Our approach provides a comprehensive analysis of cellular target proteins to HBV-mediated epigenetic regulation and further analysis should facilitate a better understanding of its involvement in HCC development.

HBx genotype D represses GSTP1 expression and increases the oxidative level and apoptosis in HepG2 cells.

Epigenetics has been implicated in human cancer development. Epigenetic factors include HBx protein, which is able to induce hypermethylation and suppresses tumor suppressor genes. One of such tumor suppressor genes, GSTP1, shows reduced expression in many human cancers. Hypermethylation of GSTP1 is the most studied mechanism of its silence. In the present study, we reported that GSTP1 expression was completely depleted in HBV integrated HepG2.2.15 cells due to the hypermethylation in its promoter region. And it was HBx, especially HBx genotype D, that played the key role in repressing GSTP1 expression. Further functional studies like ROS assay and apoptosis detection were also used to confirm this repression. Our findings should facilitate the understanding of HBV and their influences on the epigenetic modulations for epigenetic tumorigenesis during HBV-mediated hepatocellular carcinogenesis.

Syncytin-A mediates the formation of syncytiotrophoblast involved in mouse placental development.

Syncytin-A, a new mouse endogenous retroviral envelope protein expressed in placenta, can mediate cell fusion in vitro. But its physiological function was still unknown. We proposed a role for syncytin-A in syncytiotrophoblast (SynT) formation derived from the differentiation of trophoblast stem (TS) cells during placental development. To evaluate this hypothesis, we analyzed the involvement of syncytin-A in the differentiation of mouse TS cells. After withdrawing fibroblast growth factor 4 (FGF4), TS cells can fuse to form SynT cells. We found syncytin-A mRNA and protein expression are colinear with fusion index increase during TS cell differentiation. Expression of syncytin-A is localized in SynT cells through in situ immunofluorescent staining. By using specific antibody and antisense oligonucleotides, we demonstrated that inhibition of syncytin-A lead to obvious decrease of SynT cell formation. These results present evidence in support of the direct role for syncytin-A in mouse TS cell fusion and differentiation involved in placental development.

Cellular transcription modulator SMARCE1 binds to HBV core promoter containing naturally occurring deletions and represses viral replication.

Suppression of hepatitis B virus (HBV) replication, a causative agent for chronic hepatitis, is an effective approach to controlling disease progression. Host factors have a significant effect on viral replication efficiency and need to be better characterized. We have reported association between clinical virus load and deletions in HBV viral promoter. We showed here that HBV genome with such deletions led to decreased replication compared with wild type virus. Consistently, the promoter with deletion showed lower activity. A cellular transcription regulator recognizing the promoter with deletion was revealed in gel shift assay and subsequently identified as SMARCE 1 through DNA-protein array assay. The ability of SMARCE 1 in modulating the replication efficiency of HBV was further demonstrated. Taken together, our studies show a direct dependence of HBV on a host factor to modulate its replication efficiency, and provided a new platform for molecular characterization of mechanisms of disease outcome as a result of binding of new transcription factors to rearranged promoter sequences.