PubMed Health⌕ Search

Biomedical subjects

Shui-Tein Chen

Publications and source records attributed to Shui-Tein Chen.

At least 19 recordsLinked to original sources

Enhanced detectability in proteome studies.

The discovery of candidate biomarkers from biological materials coupled with the development of detection methods holds both incredible clinical potential as well as significant challenges. However, the proteomic techniques still provide the low dynamic range of protein detection at lower abundances. This review describes the current development of potential methods to enhance the detection and quantification in proteome studies. It also includes the bioinformatics tools that are helpfully used for data mining of protein ontology. Therefore, we believe that this review provided many proteomic approaches, which would be very potent and useful for proteome studies and for further diagnostic and therapeutic applications.

Biomarkers↗

Toxicogenomics of A375 human malignant melanoma cells treated with arbutin.

Although arbutin is a natural product and widely used as an ingredient in skin care products, its effect on the gene expression level of human skin with malignant melanoma cells is rarely reported. We aim to investigate the genotoxic effect of arbutin on the differential gene expression profiling in A375 human malignant melanoma cells through its effect on tumorigenesis and related side-effect. The DNA microarray analysis provided the differential gene expression pattern of arbutin-treated A375 cells with the significant changes of 324 differentially expressed genes, containing 88 up-regulated genes and 236 down-regulated genes. The gene ontology of differentially expressed genes was classified as belonging to cellular component, molecular function and biological process. In addition, four down-regulated genes of AKT1, CLECSF7, FGFR3, and LRP6 served as candidate genes and correlated to suppress the biological processes in the cell cycle of cancer progression and in the downstream signaling pathways of malignancy of melanocytic tumorigenesis.

Arbutin↗

Synthesis of 2'-paclitaxel methyl 2-glucopyranosyl succinate for specific targeted delivery to cancer cells.

A novel glucose-conjugated paclitaxel 5 was synthesized using succinic acid as linker between 2'-paclitaxel and methyl 2'-glucopyranose. 5 has not only improved the pharmaceutical properties of paclitaxel, such as solubility and stability, but also enhanced the specific target delivery to MCF-7 cells without the cytotoxicity against normal cells. Therefore, the glucose conjugation may be potentially used in the targeted delivery of other drugs into cells via glucose transporters (GLUTs) for cancer therapy.

Antineoplastic Agents, Phytogenic↗

Unusually strong positive cooperativity in binding of peptides to latent membrane protein-1 DNA fragments of the Epstein-Barr viral gene.

The DNA-binding preferences of two oligopeptide amides, (His-Pro-Arg-Lys)(3)NH(2) (HR-12) and (Ser-Pro-Arg-Lys)(3)NH(2) (SP-12), have been examined by quantitative DNase I footprinting studies. Two different DNA fragments were investigated: a pair of 5'-(32)P-labeled duplexes from pBR322 with one or other of the complementary strands labeled and a corresponding pair of 5'-(32)P-labeled duplexes representing fragments of the latent membrane protein (LMP-1) gene from a pathogenic Epstein-Barr virus variant derived from nasopharyngeal carcinoma. The major objective was to examine molecular recognition and cooperative features associated with sequence-selective binding of synthetic peptides to the LMP-1 fragments. At various binding sites on the pBR322 fragments, Hill coefficients (n(H)) ranging from 1.9-2.2 were observed; these results indicate modest positive cooperativity between binding sites for both peptides. By contrast, unusually high values of n(H), ranging from 4.0-9.3, were observed at various binding sites on the LMP-1 fragments. Allosteric models can be constructed to interpret the observed cooperative interactions between different DNA recognition sites in the LMP-1 gene upon binding of the peptide ligands. It is noteworthy that these models feature a novel network of cooperativity interconnecting multiple DNA allosteric sites. The evidence of sequence selectivity and strong cooperativity discovered in this work may prove to be a general feature of peptide interactions with some nucleic acids.

Base Sequence↗

Proteomics analysis of a novel compound: cyclic RGD in breast carcinoma cell line MCF-7.

In studies of cell adhesion, migration, growth, differentiation, and apoptosis, synthetic peptides containing the RGD (Arg-Gly-Asp) motif have been extensively used as the inhibitors of integrin-ligand interactions. The RGD motif is an integrin-recognition motif found in many ligands, so that the RGD-containing peptides can be used to probe integrin functions in various biological systems. A linear RGD is a tripeptide consisting of a flexible structure that makes the motif bind to its receptor with inefficient chelating affinity. Therefore, we designed a cyclic-RGD peptide (Tpa-RGDWPC, cRGD) with rigid skeleton to closely bind with its receptor. The cRGD was obtained by solid-phase peptide synthesis method using Rink amide resin. We showed that the cRGD exerts more potency than linear RGD on inhibiting cell growth of MCF-7 breast carcinoma cells. This stimulated us to question how cRGD inhibits cell growth of MCF-7 cells. Moreover, understanding what molecular mechanism underlies the effect that RGD motif exerts on MCF-7 cells is also of considerable importance. We used proteomics and bioinformatics to survey the global changes in proteins after cRGD treatment in MCF-7 cells. The classification of these proteins is shown according to the different biological processes in which they are involved. Most of the proteins that appear to be strongly influenced by cRGD treatment are involved in metabolism, cell growth, responsive to external stimulus, cell communication, reproduction and cell death. This is the first report which monitors the protein expression profile of MCF-7 cells in response to treatment with RGD-containing peptides in a time-course analysis. The clustering data indicated temporal patterns of altered protein expression that can be categorized into early, intermediate and late response proteins. These patterns of protein expression may be important for predicting its response to cRGD. In summary, these results provide a molecular explanation for the properties of cRGD in breast cancer cells and present a valuable in-depth description of their possible impact on breast cancer therapy.

Antineoplastic Agents↗

Proteomic identification of alterations in metabolic enzymes and signaling proteins in hypokalemic nephropathy.

Hypokalemic nephropathy caused by prolonged K(+) deficiency is associated with metabolic alkalosis, polydipsia, polyuria, growth retardation, hypertension, and progressive tubulointerstitial injury. Its pathophysiology, however, remains unclear. We performed gel-based, differential proteomics analysis of kidneys from BALB/c mice fed with high-normal-K(+) (HNK), low-normal-K(+) (LNK), or K(+)-depleted diet for 8 wk (n = 6 in each group). Plasma K(+) levels were 4.62 +/- 0.35, 4.46 +/- 0.23, and 1.51 +/- 0.21 mmol/L for HNK, LNK, and KD mice, respectively (p < 0.0001; KD vs. others). With comparable amounts of food intake, the KD mice drank significantly more water than the other two groups and had polyuria. Additionally, the KD mice had growth retardation, metabolic alkalosis, markedly enlarged kidneys, renal tubular dilation, intratubular deposition of amorphous and laminated hyaline materials, and tubular atrophy. A total of 33 renal proteins were differentially expressed between the KD mice and others, whereas only eight proteins were differentially expressed between the HNK and LNK groups, as determined by quantitative intensity analysis and ANOVA with Tukey's post hoc multiple comparisons. Using MALDI-MS and/or quadrupole-TOF MS/MS, 30 altered proteins induced by K(+)-depletion were identified as metabolic enzymes (e.g., carbonic anhydrase II, aldose reductase, glutathione S-transferase GT41A, etc.), signaling proteins (14-3-3 epsilon, 14-3-3 zeta, and cofilin 1), and cytoskeletal proteins (gamma-actin and tropomyosin). Some of these altered proteins, particularly metabolic enzymes and signaling proteins, have been demonstrated to be involved in metabolic alkalosis, polyuria, and renal tubular injury. Our findings may lead to a new road map for research on hypokalemic nephropathy and to better understanding of the pathophysiology of this medical disease when the functional and physiological significances of these altered proteins are defined.

Animals↗

Lipopolysaccharide-stimulated responses in rat aortic endothelial cells by a systems biology approach.

The vascular endothelium plays an important role in regulating immune and inflammatory responses to resist pathogens infection. Although it has been known that lipopolysaccharide (LPS) is a critical inducer of sepsis or endotoxemia, the systematic responses of LPS-stimulation in endothelial cells (ECs) are still unclear. The present study aims to analyze the late-phase responses of LPS-induced rat aortic ECs by using systematic biology approaches, including rat cDNA microarray, 2-DE and MALDI-TOF MS/MS, and cytokine protein array. Furthermore, to improve the efficiency of analysis of the bulk systematic data of rat, we designed a set of bioinformatic tools to convert and integrate these rat data into the corresponding human genes or proteins IDs based on BioCarta, KEGG, and Gene Ontology databases. Using the systematic analysis, it was shown that LPS could promote some signaling or metabolic pathways as well as pathophysiologic phenomena of proliferation, atherogenesis, inflammation, and apoptosis through activated nuclear factor-kappaB pathway in ECs. Interestingly, ECs also activated the mediators of anti-inflammation, antiapoptosis, and antioxidation to protect themselves. Moreover, the expressions of altered genes, proteins, and their involvement in the hypothetical signaling pathway can provide further understanding of inflammation associated responses in ECs.

Animals↗

Proteomic identification of altered proteins in skeletal muscle during chronic potassium depletion: Implications for hypokalemic myopathy.

Prolonged potassium depletion is a well-known cause of myopathy. The pathophysiology of hypokalemic myopathy, however, remains unclear. We performed a gel-based, differential proteomics study to define altered proteins in skeletal muscles during chronic potassium depletion. BALB/c mice were fed with normal chow (0.36% K+) or K+-depleted (KD) diet (<0.001% K+) for 8 weeks (n = 5 in each group). Left gastrocnemius muscles were surgically removed from each animal. Histopathological examination showed mild-degree infiltration of polymornuclear and mononuclear cells at the interstitium of the KD muscles. Extracted proteins were resolved with two-dimensional electrophoresis (2-DE), and visualized with Coomassie Brilliant Blue R-250 stain. Quantitative intensity analysis revealed 16 up-regulated protein spots in the KD muscles, as compared to the controls. These differentially expressed proteins were subsequently identified by peptide mass fingerprinting and by quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS). Most of the altered proteins induced by chronic potassium depletion were muscle enzymes that play significant roles in several various metabolic pathways. Other up-regulated proteins included myosin-binding protein H, alpha-B Crystallin, and translationally controlled tumor protein (TCTP). These findings may lead to a new roadmap for research on hypokalemic myopathy, to better understanding of the pathophysiology of this medical disease, and to biomarker discovery.

Amino Acid Sequence↗

Toxicogenomics of kojic acid on gene expression profiling of a375 human malignant melanoma cells.

Kojic acid is a natural product and normally used as a food additive and preservative, a skin-whitening agent in cosmetics, a plant growth regulator and a chemical intermediate. Using DNA microarray technology, the overall biological effects of kojic acid on the gene expression profiling of a human skin A375 malignant melanoma cells were examined. After treatment with kojic acid, a total of 361 differentially expressed genes were distinctively changed with 136 up-regulated genes and 225 down-regulated genes. We used the bioinformatics tool to search the gene ontology and category classification of differentially expressed genes that provided the useful information of expressed genes belonging to cellular component, molecular function and biological process in regulation of melanogenesis. Seven down-regulated genes of APOBEC1, ARHGEF16, CD22, FGFR3, GALNT1, UNC5C and ZNF146 that were typically validated by the real-time quantitative PCR (RT-qPCR) analysis technology showed to be the tumor suppressor genes in melanoma cancer cells. Thus, microarray technology coupled with RT-qPCR offered a high throughput method to explore the number of differentially expressed genes responding to kojic acid and their biological functions, and led to more understanding of kojic acid effects on skin cancer therapy and related side effects. Moreover, the differentially expressed genes may become useful markers of skin malignant melanoma for further diagnostic and therapeutic applications.

Antioxidants↗

A screening platform for compounds with potential immuno-regulatory activities using human cord blood mononuclear cells.

A systematic and combinatorial approach was adopted using human umbilical cord blood mononuclear cells (hUCB-MNCs) to screen for potential immuno-regulatory compounds. The hUCB-MNCs contain several types of immunogenic cells, which are a suitable material to mimic the in vivo immuno-response after drug treatment. hUCB-MNCs were treated with various natural products such as quercetin, astaxanthin, caffeic acid, bilobalide, eugenol, rutin and gamma-dodecalactone (gamma-DDL). Phenotypic expression analysis revealed that the subpopulation of CD3(+) T cells, CD56(+) NK cells and CD1a(+) dendritic cells apparently increased after being treated with gamma-DDL for 6 days. The expression of CD56 reached a maximum at 72 h with a dose-dependent relationship. The NK cells activation marker (CD69) also elevated following gamma-DDL treatment. These results demonstrated that the gamma-DDL has immuno-regulatory effects to enhance cord blood NK cells population and bioactivities. Such a high-throughput methodology using hUCB-MNCs may be an effective platform for systematically screening potential immuno-regulatory compounds.

4-Butyrolactone↗

Protein microarray using alpha-amino acids as metal tags on chips.

Procedures for synthesizing alpha-amino acids on a chip for coordination with transitional metal ions and a His-Tagged protein have been successfully developed as a stable protein microarray. Using the recombinant His-Tagged 3CL-protease (3CLpro) as a model for attachment to chips containing D-/L-Glu, Asp, Orn, Ser via different transitional metal ions, it was found that the Orn chip was the best of affinity binding and stability by which Zn2+ was the best metal ion for affinity while Co2+ was the best metal ion for stability. Thus, this protein microarray can be alternatively used as a high throughput screening method for rapid detection against SARS CoV 3CLpro and/or efficient purification of other Tagged proteins.

Amino Acids↗

A new application of microwave technology to proteomics.

Two-dimensional electrophoresis (2-DE) combined with mass spectrometry has significantly improved the possibilities of large-scale identification of proteins. However, 2-DE is limited by its inability to speed up the in-gel digestion process. We have developed a new approach to speed up the protein identification process utilizing microwave technology. Proteins excised from gels are subjected to in-gel digestion with endoprotease trypsin by microwave irradiation, which rapidly produces peptide fragments. The peptide fragments were further analyzed by matrix-assisted laser desorption/ionization technique for protein identification. The efficacy of this technique for protein mapping was demonstrated by the mass spectral analyses of the peptide fragmentation of several proteins, including lysozyme, albumin, conalbumin, and ribonuclease A. The method reduced the required time for in-gel digestion of proteins from 16 hours to as little as five minutes. This new application of microwave technology to protein identification will be an important advancement in biotechnology and proteome research.

Albumins↗

Different techniques for urinary protein analysis of normal and lung cancer patients.

Many components in urine are useful in clinical diagnosis and urinary proteins are known as important components to define many diseases such as proteinuria, kidney, bladder and urinary tract diseases. In this study, we focused on the comparison of different sample preparation methods for isolating urinary proteins prior to protein analysis of pooled healthy and lung cancer patient samples. Selective method was used for preliminary investigation of some putative urinary protein markers. Urine samples were passed first through a gel filtration column (PD-10 desalting column) to remove high salts and subsequently concentrated. Remaining interferences were removed by ultrafiltration or four precipitation methods. The analysis of urinary proteins by high-performance liquid chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed many similarities in profiles among preparation methods and a few profiles were different between normal and lung cancer patients. In contrast, the results of two-dimensional gel electrophoresis (2-DE) showed more distinctly different protein patterns. Our finding showed that the sequential preparation of urinary proteins by gel filtration and ultrafiltration could retain most urinary proteins which demonstrated the highest protein spots on 2-D gels and able to identify preliminary urinary protein markers related to cancer. Although sequential preparation of urine samples by gel filtration and protein precipitation resulted in low amounts of proteins on 2-D gels, high Mr proteins were easily detected. Therefore, there are alternative choices for urine sample preparation for studying the urinary proteome and identifying urinary protein markers important for further preclinical diagnostic and therapeutic applications.

Acetone↗

Functional proteomics and correlated signaling pathway of the thermophilic bacterium Bacillus stearothermophilus TLS33 under cold-shock stress.

The thermophilic bacterium Bacillus stearothermophilus TLS33 was examined under cold-shock stress by a proteomic approach to gain a better understanding of the protein synthesis and complex regulatory pathways of bacterial adaptation. After downshift in the temperature from 65 degrees C, the optimal growth temperature for this bacterium, to 37 degrees C and 25 degrees C for 2 h, we used the high-throughput techniques of proteomic analysis combining 2-DE and MS to identify 53 individual proteins including differentially expressed proteins. The bioinformatics database was used to search the biological functions of proteins and correlate these with gene homology and metabolic pathways in cell protection and adaptation. Eight cold-shock-induced proteins were shown to have markedly different protein expression: glucosyltransferase, anti-sigma B (sigma(B)) factor, Mrp protein homolog, dihydroorthase, hypothetical transcriptional regulator in FeuA-SigW intergenic region, RibT protein, phosphoadenosine phosphosulfate reductase and prespore-specific transcriptional activator RsfA. Interestingly, six of these cold-shock-induced proteins are correlated with the signal transduction pathway of bacterial sporulation. This study aims to provide a better understanding of the functional adaptation of this bacterium to environmental cold-shock stress.

Amino Acid Sequence↗

Proteomics viewed on stress response of thermophilic bacterium Bacillus stearothermophilus TLS33.

Thermophilic bacterium Bacillus stearothermophilus TLS33, isolated from a hot spring in Chiang Mai, Thailand, usually produces many enzymes that are very useful for industrial applications. However, the functional properties and mechanisms of this bacterium under stress conditions are rarely reported and still need more understanding on how the bacterium can survive in stress environments. In this study, we examined the oxidative stress induced proteins of this bacterium by proteomic approach combining two-dimensional electrophoresis and mass spectrometry. When the bacterium encountered oxidative stress, peroxiredoxin, as an antioxidant enzyme, is one of the interesting stressed proteins which appeared to be systematically increased with different pI. There are four isoforms of peroxiredoxin, denoted as Prx I, Prx II, Prx III and Prx IV, which are observed at the same molecular weight of 27 kDa but differ in pI values of 5.0, 4.87, 4.81 and 4.79, respectively. The H2O2 concentration directly increased Prx II, Prx III and Prx IV intensities, but decreased Prx I intensity. These shifting of peroxiredoxin isoforms may occur by a post-translational modification. Otherwise, the longer time of oxidative stress had not affected the expression level of peroxiredoxin isoforms. Therefore, this finding of peroxiredoxin intends to know the bacterial adaptation under oxidative stress. Otherwise, this protein plays an important role in many physiological processes and able to use in the industrial applications.

Amino Acid Sequence↗

Proteomic profiling of cholangiocarcinoma cell line treated with pomiferin from Derris malaccensis.

Pomiferin, a prenylated isoflavonoid from Derris malaccensis with strong anti-fungal and anti-oxidant activities, showed cytotoxic activity towards human cholangiocarcinoma cells (HuCCA-1), with IC(50) of 0.9 microg/mL. Pomiferin caused apoptosis, detectable by DNA fragmentation. Two-dimensional PAGE showed increased expression of 12 proteins, namely glucose-regulated protein 75 (grp 75), calcyclin (S100A6), degraded cytokeratin 19, ATP synthase D, ribosomal protein P0, degraded cytokeratin 18 (two spots pI/MW 6.03/29.9 and pI/MW 4.66/21.5), cofilin, annexin A1, triose phosphate isomerase, peroxiredoxin-1, calgizzarin, and profilin. In contrast, cytokeratins (CK) 7, 18 and 19 were down-regulated, and were shown by 1-DE immunodetection to be degraded.

Apoptosis↗

Polysaccharides of Ganoderma lucidum alter cell immunophenotypic expression and enhance CD56+ NK-cell cytotoxicity in cord blood.

In our previous study, a fucose-containing glycoprotein fraction (F3), isolated from the water-soluble extracts of Ganoderma lucidum, was shown to stimulate mice spleen cell proliferation and cytokine expression. We now further investigate the effect of F3 on the immunophenotypic expression in mononuclear cells (MNCs). When human umbilical cord blood (hUCB) MNCs were treated with F3 (10-100 microg/mL) for 7days, the population of CD14+CD26+ monocyte/macrophage, CD83+CD1a+ dendritic cells, and CD16+CD56+ NK-cells were 2.9, 2.3, and 1.5 times higher than those of the untreated controls (p<0.05). B-cell population has no significant change. T cell growth was, however, slightly inhibited and CD3 marker expression decreased approximately 20% in the presence of higher concentrations of F3 (100 microg/mL). We also found that F3 is not harmful to human cells in vitro, and after F3 treatment, NK-cell-mediated cytotoxicity was significantly enhanced by 31.7% (p<0.01) at effector/target cell ratio (E/T) 20:1, but was not altered at E/T 5:1.

CD56 Antigen↗

GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data.

UNLABELLED: Inferring genetic network architecture from time series data generated from high-throughput experimental technologies, such as cDNA microarray, can help us to understand the system behavior of living organisms. We have developed an interactive tool, GeneNetwork, which provides four reverse engineering models and three data interpolation approaches to infer relationships between genes. GeneNetwork enables a user to readily reconstruct genetic networks based on microarray data without having intimate knowledge of the mathematical models. A simple graphical user interface enables rapid, intuitive mapping and analysis of the reconstructed network allowing biologists to explore gene relationships at the system level. AVAILABILITY: Download from http://genenetwork.sbl.bc.sinica.edu.tw/. SUPPLEMENTARY INFORMATION: Supplement documentation of algorithms for the four approaches is downloadable at the above location.

Algorithms↗