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Biomedical subjects

Yu-Ju Chen

Publications and source records attributed to Yu-Ju Chen.

At least 19 recordsLinked to original sources
PubMed2006

Evaluation of serum amyloid A as a biomarker for gastric cancer.

BACKGROUND: Serum amyloid A (SAA) is a useful biomarker for gastric cancer in an animal model. We investigated the potential of SAA as a biomarker for gastric cancer in humans. METHODS: Serum levels of SAA from 96 gastric cancer patients were measured before and after curative gastrectomy; 32 patients with gastric ulcers and 52 healthy subjects were the control groups. The immunohistochemical study was performed to evaluate the protein expression over gastric cancer tissue slides. RESULTS: The mean SAA concentration was higher in gastric cancer patients (88.54 +/- 50.44 mg/l) than in healthy subjects (3.36 +/- 2.29 mg/l) and gastric ulcer patients (10.48 +/- 8.97 mg/l) (P < .05). The SAA concentration was associated with tumor stage (P = .0244) and location (P = .0016) but not with Lauren's histological type (P = .839). In the multivariate analysis, SAA level was correlated with tumor location (P < .0001) and lymph node status (P < .05). During follow-up, the mean SAA concentration increased significantly in 24 patients with tumor recurrence (P < .05) but did not change in 77 patients without recurrence. In the survival analysis, patients with SAA levels > 97 mg/l had a nearly fourfold increase in risk of death. Immunoreactivity was most prominent in blood vessel regions but not within cancer cells. CONCLUSIONS: These data not only demonstrated SAA was useful in predicting survival of patients with gastric cancer, but they also showed that SAA was a valuable tool for postoperative follow-up.

Adenocarcinoma↗
PubMed2006

Determination of SMN1/SMN2 gene dosage by a quantitative genotyping platform combining capillary electrophoresis and MALDI-TOF mass spectrometry.

BACKGROUND: Spinal muscular atrophy (SMA) is a common inherited and fatal neuromuscular disease caused by deletions and/or mutations that lead to altered concentrations of proteins encoded by the survival motor neuron genes SMN1 and SMN2. Because of the high incidence (at least 1 in 10,000 live births and a carrier frequency of 1 in 35 to 1 in 50) and severity of the disease, precise quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. METHODS: We developed a genotyping platform combining capillary electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to quantify absolute gene dosage. The absolute gene dosage can be determined by a multiplexed competitive PCR protocol followed by capillary electrophoresis analysis. The relative SMN1/SMN2 ratio can be analyzed by PinPoint assay followed by MALDI-TOF MS analysis. RESULTS: The complementary assays were evaluated in confirmed cases including 9 affected patients, 33 carriers, and 478 healthy individuals from the general population. We were able to determine all genotypes with different SMN1/SMN2 gene copy number ratios, which unambiguously diagnosed carrier status and the severity of SMA with 100% specificity. CONCLUSIONS: This quantitative genotyping platform is suitable for detection of SMA. The described approach may serve as a general quantitative genotyping method for molecular diagnosis of other inheritable diseases.

Cyclic AMP Response Element-Binding Protein↗
PubMed2006

The internalized CdSe/ZnS quantum dots impair the chondrogenesis of bone marrow mesenchymal stem cells.

Mesenchymal stem cells (MSCs) are capable of differentiating into multiple cell lineages and are useful for therapeutic applications. Labeling the MSCs with fluorescent probes is beneficial in tracing the fate of MSCs after implantation. We have introduced the CdSe/ZnS quantum dots (QDs) into the human bone marrow MSCs and examined the effects of QDs on the proliferation and chondrogenesis of the cells. The internalized QDs were found localized in perinuclear regions and remained there after a number of cell passages. The presence of QDs did not affect the proliferation of cells or the size of chondrospheres formed, when subjected to chondrogenesis induction. However, the expression of mRNA and protein of type II collagen and aggrecan in the chondrospheres was significantly inhibited in cells labeled with QDs, suggesting impaired chondrogenesis. Our results that the presence of QDs interferes with the chondrogenic differentiation of MSCs raise concerns in using the QDs as fluorescence tracers for stem cells.

Biocompatible Materials↗
PubMed2006

Multi-Q: a fully automated tool for multiplexed protein quantitation.

The iTRAQ labeling method combined with shotgun proteomic techniques represents a new dimension in multiplexed quantitation for relative protein expression measurement in different cell states. To expedite the analysis of vast amounts of spectral data, we present a fully automated software package, called Multi-Q, for multiplexed iTRAQ-based quantitation in protein profiling. Multi-Q is designed as a generic platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. To calculate peptide ratios, the software automatically processes iTRAQ's signature peaks, including peak detection, background subtraction, isotope correction, and normalization to remove systematic errors. Furthermore, Multi-Q allows users to define their own data-filtering thresholds based on semiempirical values or statistical models so that the computed results of fold changes in peptide ratios are statistically significant. This feature facilitates the use of Multi-Q with various instrument types with different dynamic ranges, which is an important aspect of iTRAQ analysis. The performance of Multi-Q is evaluated with a mixture of 10 standard proteins and human Jurkat T cells. The results are consistent with expected protein ratios and thus demonstrate the high accuracy, full automation, and high-throughput capability of Multi-Q as a large-scale quantitation proteomics tool. These features allow rapid interpretation of output from large proteomic datasets without the need for manual validation. Executable Multi-Q files are available on Windows platform at http://ms.iis.sinica.edu.tw/Multi-Q/.

Chromatography, Liquid↗
PubMed2006

Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells.

Gastric cancer is a leading cause of death worldwide, and patients have an overall 5-year survival rate of less than 10%. Using quantitative proteomic techniques together with microarray chips, we have established comprehensive proteome and transcriptome profiles of the metastatic gastric cancer TMC-1 cells and the noninvasive gastric cancer SC-M1 cell. Our qualitative protein profiling strategy offers the first comprehensive analysis of the gastric cancer cell proteome, identifying 926 and 909 proteins from SC-M1 and TMC-1 cells, respectively. Cleavable isotope-coded affinity tagging analysis allows quantitation of a total of 559 proteins (with a protein false-positive rate of <0.005), and 240 proteins were differentially expressed (>1.3-fold) between the SC-M1 and TMC-1 cells. We identified numerous proteins not previously associated with gastric cancer. Notably, a large subset of differentially expressed proteins was associated with tumor metastasis, including proteins functioning in cell-cell and cell-extracellular matrix (cell-ECM) adhesion, cell motility, proliferation, and tumor immunity. Gene expression profiling by DNA microarray revealed differential expression (of >2-fold) of about 1000 genes. The weak correlation observed between protein and mRNA profiles highlights the important complementarities of DNA microarray and proteomics approaches. These comparative data enabled us to map the disease-perturbed cell-cell and cell-ECM adhesion and Rho GTPase-mediated cytoskeletal pathways. Further validation of a subset of genes suggests the potential use of vimentin and galectin 1 as markers for metastasis. We demonstrate that combining proteomic and genomic approaches not only provides a rapid, robust, and sensitive platform to elucidate the molecular mechanisms underlying gastric cancer metastasis but also may identify candidate diagnostic markers and therapeutic targets.

Biomarkers, Tumor↗
PubMed2005

The inhibition of osteogenesis with human bone marrow mesenchymal stem cells by CdSe/ZnS quantum dot labels.

CdSe/ZnS quantum dots (QDs) have recently been used as cell tracers for long term imaging of live cells. A number of studies indicate that introduction of quantum dots to cells have no apparent deleterious effects on the morphology or growth of cells. In the present study, the human bone marrow mesenchymal stem cells (hBMSCs) were used as a model to examine the effects of QDs on the growth and osteogenic differentiation of the cells. The CdSe/ZnS QDs were delivered into hBMSCs by liposome-mediated transfection with high efficiency; analysis by transmission electron microscopy revealed that the internalized QDs could be located in the endosome-like vesicles. Uptake of QDs into hBMSCs did not affect the proliferation and cell cycle distribution of the cells. When induced to differentiate along the osteogenic lineage, the QD-containing-hBMSCs were shown to have mineral deposition on the extracellular matrix. However, the cells displayed lower alkaline phosphatase activity as compared to those without QDs. Analysis by reverse transcriptase polymerase chain reaction further demonstrated that the expression of two osteogenic markers, osteopontin and osteocalcin, was significantly inhibited. Together our results show that the presence of QDs in hBMSCs prevents the full response of the cells to induced osteogenic differentiation.

Bone Marrow Cells↗
PubMed2005

Nanoprobe-based affinity mass spectrometry for selected protein profiling in human plasma.

In recent decades, magnetic nanoparticles have emerged as a promising new platform in biomedical applications, particularly bioseparations. We have developed an immunoassay using antibody-conjugated magnetic nanoparticles as an efficient affinity probe to simultaneously preconcentrate and isolate targeted antigens from biological media. We combined this probe with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI MS) to profile proteins in diluted human plasma. The nanoparticles were designed to detect several disease-associated proteins and could be used directly in MALDI MS without an elution step, thereby facilitating multiple antigen screening and the characterization of antigen variants. Plasma antigens bound rapidly (approximately 10 min) to the antibody-conjugated nanoparticles, allowing the assay to be performed within 20 min. With sensitivity of detection in the femtomole range, the nanoscale immunoassay is superior to assays using microscale particles. We applied our method to comparative protein profiling of patients with gastric cancer and healthy individuals and found differential protein expression levels associated with the disease as well as individuals. Given the flexibility of manipulating functional groups on the nanoprobes, their low cost, robustness, and simplicity of the assay, our approach shows promise for targeted proteome profiling in clinical settings.

Antibodies↗
PubMed2005

Molecular identification of canine podocalyxin-like protein 1 as a renal tubulogenic regulator.

GP135 is an apical membrane protein expressed in polarized MDCK epithelial cells. When cultured in three-dimensional collagen gel, MDCK cells form branching tubules in response to hepatocyte growth factor stimulation in a manner that simulates the embryonic renal development. During this process, GP135 displays transient loss of membranous localization but reappears at the cell surface when nascent lumen emerges from the developing tubules. Despite being used for decades as the canonical hallmark of apical surface, the molecular identity and the significance of the dynamic expression of GP135 during the tubulogenic process remain elusive. For exploring the function of GP135, the full-length cDNA encoding GP135 was obtained. Sequence alignments and features analysis confirm GP135 as a canine homolog of podocalyxin, confirming the finding of an earlier independent study. Immunohistochemical assays on canine kidney sections identified both glomerular and tubular distribution of GP135 along the nephron. Mutant MDCK cells expressing siRNA targeted at two regions of GP135 show defects in hepatocyte growth factor-induced tubulogenesis. Re-expression of full-length and an O-linked glycosylation abbreviated construct of GP135 could recapitulate the tubulogenesis process lacking in siRNA knockdown cells; however, a deletion construct devoid of the cytoplasmic domain failed to rescue the phenotype. In summary, the data identify the MDCK apical domain marker GP135 as a tubular form of podocalyxin and provide evidence for its importance in renal tubulogenesis.

Animals↗
PubMed2005

Parallel minisequencing followed by multiplex matrix-assisted laser desorption/ionization mass spectrometry assay for beta-thalassemia mutations.

Beta-thalassemia is a common monogenic disease caused by mutations in the human beta-globin gene (HBB), many of which are differentially represented in human subpopulations stratified by ethnicity. This study describes an efficient and highly accurate method to screen for the eight most-common disease-causing mutations, covering more than 98% of HBB alleles in the Taiwanese population, using parallel minisequencing and multiplex assay by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The MALDI-TOF MS was optimized for sensitivity and resolution by "mass tuning" the PinPoint assay for eight HBB SNPs. Because of the close proximity and clustering of mutations in HBB, primer extension reactions were conducted in parallel. Efficient sequential desalting using POROS and cationic exchange chromatography allowed for an unambiguous multiplex genotyping by MALDI-TOF MS. The embellishing SNP assay allowed for highly accurate identification of the eight most-common beta-thalassemia mutations in homozygous normal control, carrier, and eight heterozygous carrier mixtures, as well as the diagnosis of a high-risk family. The results demonstrated a flexible strategy for rapid identification of clustering SNPs in HBB with a high degree of accuracy and specificity. It can be adapted easily for high-throughput diagnosis of various hereditary diseases or to establish family heritage databases for clinical applications.

Base Sequence↗
PubMed2005

Study of the preferred modification sites of the quinone methide intermediate resulting from the latent trapping device of the activity probes for hydrolases.

Use of activity probes has been demonstrated to be a powerful tool in modern chemical proteomic study. Previously we have designed and synthesized a series of mechanism-based activity probes that utilized quinone methide chemistry. Here, we characterized the trend of chemical reactivity for the reactive quinone methide intermediate 3 (QM-3) resulting from the latent trapping device. In a competition assay, the labeling of PTP1B by probe 1a was blocked by externally added cysteine without affecting the catalytic activity of the enzyme. Further sequencing analysis on the trypsin-digested peptides of probe 1a-labeled PTP1B using tandem mass spectrometry revealed that all six cysteine residues of PTP1B are capable of being modified by probe 1a. These results indicated that the sulfhydryl group of cysteine residue is the preferred nucleophile for the reactive QM-3. Our finding provides the first example in understanding the preferred amino acid residues modified by the reactive QM-3, which is also the key structural unit responsible for forming covalent bonds in many biochemical applications.

Binding Sites↗
PubMed2005

Structural characterization of sialic acid synthase by electrospray mass spectrometry--a tetrameric enzyme composed of dimeric dimers.

Sialic acid synthase (NeuB) encoded by the neuB gene catalyzes the condensation of N-acetylmannosamine and phospho(enol)pyruvate to form N-acetylneuraminic acid. The enzyme is essential for the biosynthesis of polysialic acid, a capsular sugar polymer functioning as a virulent factor and antiphagocytic barrier. This report demonstrates the first characterization on the quaternary structure of NeuB from Escherichia coli (EcNeuB) and Streptococcus agalactiae (SaNeuB) by nanoflow electrospray ionization mass spectrometry (ESI-MS). Under non-denaturing conditions, Tris buffer was observed to induce a higher ratio of tetramer/dimer of NeuB in the ESI mass spectra, providing supportive evidence for the existence of a "structurally-specific" tetramer. The instrument parameters were found to significantly affect the ratio of detected tetramer/dimer in ESI mass spectra. The harshest conditions, including high desolvation voltages and pressure in the collision cell, led to enhanced detection of the 160 kDa tetramer. The prevalence of dimeric form is likely the cause in loss of tetramer stability in gas-phase arising from insufficient collisional cooling, which implies an asymmetric assembly, possibly composed of dimeric dimers. Most interestingly, the hypothesis was further supported by chemical cross-linking of SaNeuB, in which the reaction of shorter linker yielded mainly the dimer whereas that of longer linker produced both dimer and tetramer. Furthermore, the ESI-MS analysis can reflect dramatic change of pH-dependent quaternary structure in association with enzyme activity, suggesting the tetrameric form may be the primary species responsible for the enzyme catalysis.

Dimerization↗
PubMed2004

Plasma proteome of severe acute respiratory syndrome analyzed by two-dimensional gel electrophoresis and mass spectrometry.

We have investigated the plasma proteome by using 2D gel electrophoresis and MS from patients with severe acute respiratory syndrome (SARS). A complete proteomic analysis was performed on four patients with SARS in different time courses, and a total of 38 differential spots were selected for protein identification. Most of the proteins identified are acute phase proteins, and their presence represents the consequence of serial cascades initiated by SARS-coronavirus infection. There are several proteins that have never been identified in plasma before using 2D gel electrophoresis, among which peroxiredoxin II was chosen for further study by analyzing additional 20 plasma samples from patients with probable and suspected SARS and patients with fever, respectively. The results showed that the level of plasma peroxiredoxin II in patients with SARS is significantly high and could be secreted by T cells. Taken together, our findings indicate that active innate immune responses, along with the oxidation-associated injuries, may play a major role in the pathogenesis of SARS.

Acute-Phase Proteins↗
PubMed2004

Nuclear efflux of heterogeneous nuclear ribonucleoprotein C1/C2 in apoptotic cells: a novel nuclear export dependent on Rho-associated kinase activation.

Using a proteomic approach, we searched for protein changes dependent on Rho-associated kinase (ROCK) during phorbol-12-myristate-13-acetate (PMA)-induced apoptosis. We found that heterogeneous nuclear ribonucleoprotein C1 and C2 (hnRNP C1/C2), two nuclear restricted pre-mRNA binding proteins, are translocated to the cytosolic compartment in a ROCK-dependent manner in PMA-induced pro-apoptotic cells, where nuclear envelopes remain intact. The subcellular localization change of hnRNP C1/C2 appears to be dependent on ROCK-mediated cytoskeletal change and independent of caspase execution and new protein synthesis. Such a ROCK-dependent translocation is also seen in TNFalpha-induced apoptotic NIH3T3 cells. By overexpressing the dominant active form of ROCK, we showed that a ROCK-mediated signal is sufficient to induce translocation of hnRNP C1/C2. Deletion experiments indicated that the C-terminal 40-amino-acid region of hnRNP C1/C2 is required for ROCK-responsive translocation. By using nuclear yellow fluorescent protein (YFP) fusion, we determined that the C-terminal 40-amino-acid region of hnRNP C1/C2 is a novel nuclear export signal responsive to ROCK-activation. We conclude that a novel nuclear export is activated by the ROCK signaling pathway to exclude hnRNP C1/C2 from nucleus, by which the compartmentalization of specific hnRNP components is disturbed in apoptotic cells.

3T3 Cells↗
PubMed2004

Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath).

Copper ions switch the oxidation of methane by soluble methane monooxygenase to particulate methane monooxygenase in Methylococcus capsulatus (Bath). Toward understanding the change in cellular metabolism related to this transcriptional and metabolic switch, we have undertaken genomic sequencing and quantitative comparative analysis of the proteome in M. capsulatus (Bath) grown under different copper-to-biomass ratios by cleavable isotope-coded affinity tag technology. Of the 682 proteins identified, the expressions of 60 proteins were stimulated by at least 2-fold by copper ions; 68 proteins were down-regulated by 2-fold or more. The 60 proteins overexpressed included the methane and carbohydrate metabolic enzymes, while the 68 proteins suppressed were mainly responsible for cellular signaling processes, indicating a role of copper ions in the expression of the genes associated with the metabolism of the organism downstream of methane oxidation. The study has also provided a complete map of the C1 metabolism pathways in this methanotroph and clarified the interrelationships between them.

Bacterial Proteins↗
PubMed2004

Purification, tandem mass characterization, and inhibition studies of oxidosqualene-lanosterol cyclase enzyme from bovine liver.

The oxidosqualene-lanosterol cyclase (OSC) from bovine liver has been isolated from the microsomal membrane fraction and purified to homogeneity by ultracentrifugation, Q-Sepharose, hydroxyapatite, and HiTrap heparin chromatographies. The purified protein required Triton X-100 to retain its highest activity. The cyclase had a molecular mass of approximately 70 and approximately 140 kDa, as evidenced by a single protein band on silver-stained SDS-PAGE and Coomassie-stained PAGE, respectively. Results from Edman degradation of OSC suggested that it might have a blocked N-terminus. Further peptide mapping coupled with tandem mass spectrometric determination identified three peptide fragments, ILGVGPDDPDLVR, LSAEEGPLVQSLR, and NPDGGFATYETK, which are highly homologous to human, rat, and mouse OSCs. The purified cyclase showed pH and temperature optima at pH 7.4 and 37 degrees C, respectively. The apparent K(M) and k(cat)/K(M) values were estimated to be 11 microM and 1.45 mM(-1)min(-1), respectively. Inhibition studies using both Ro48-8071 and N-(4-methylenebenzophenonyl)pyridinium bromide showed potent inhibition of OSC with an IC(50) of 11 nM and 0.79 microM, respectively. Results from DTNB modification and DTNB coupled with Ro48-8071 competition study suggest that two sulfhydryl groups are involved in the catalysis but not located in the substrate binding pocket or catalytic active site. The purified OSC was maximally inactivated by diethyl pyrocarbonate near neutral pH and re-activated by hydroxylamine, indicating the modification of histidine residues. The stoichiometry of histidine modification and the extent of inactivation showed that two essential histidine residues per active site are necessary for complete bovine liver OSC activity.

Amino Acid Sequence↗