Biomedical subjects

Bin Qian

Publications and source records attributed to Bin Qian.

13 recordsLinked to original sources

PubMed2006

[Expression of epithelial-cadherin, CD44v6 and connexin43 in hepatocellular carcinoma].

OBJECTIVE: To study the expression of epithelial-cadherin (E-cad), CD44v6 and Cx43 in hepatocellular carcinoma (HCC) and its relationship with sex and age of patients, as well as tumor histopathologic grades. METHODS: Double immunofluorescent staining and laser scanning confocal microscopy was used to study the expression of E-cad, CD44v6 and Cx43 in 30 cases of normal liver tissue, 25 cases of benign hepatic lesions and 38 cases of HCC. In the HCC group, correlation of antigen expression with sex and age of patients and tumor histopathologic grades was studied by T-test. RESULTS: Significant decrease in expression of E-cad and Cx43 was noted in HCC group, as compared to normal liver tissue and benign hepatic lesion (P<0.05). On the other hand, CD44v6 expression was higher in HCC group than in the other two groups (P<0.05). In HCC group, the expression of E-cad and Cx43 did not correlate with sex, age and histopathologic grades (P>0.05). However, CD44v6 expression positively correlated with higher tumor histopathologic grades (P<0.05) but not sex and age of patients (P>0.05). In HCC group, the expression of E-cad positively correlated with that of Cx43, while the expression of CD44v6 negatively correlated with that of E-cad and Cx43. CONCLUSIONS: Tumor immunophenotype alters during development and progression of HCC. Low expression of E-cad and Cx43 and high expression of CD44v6 may be related to aggressive clinical behavior of HCC, moreover, high expression of CD44v6 correlated with high tumor grades. Detection of E-cad, CD44v6 and Cx43 expression may thus be useful in predicting prognosis of HCC.

Adult↗

PubMed2005

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.

The prediction of functional sites in newly solved protein structures is a challenge for computational structural biology. Most methods for approaching this problem use evolutionary conservation as the primary indicator of the location of functional sites. However, sequence conservation reflects not only evolutionary selection at functional sites to maintain protein function, but also selection throughout the protein to maintain the stability of the folded state. To disentangle sequence conservation due to protein functional constraints from sequence conservation due to protein structural constraints, we use all atom computational protein design methodology to predict sequence profiles expected under solely structural constraints, and to compute the free energy difference between the naturally occurring amino acid and the lowest free energy amino acid at each position. We show that functional sites are more likely than non-functional sites to have computed sequence profiles which differ significantly from the naturally occurring sequence profiles and to have residues with sub-optimal free energies, and that incorporation of these two measures improves sequence based prediction of protein functional sites. The combined sequence and structure based functional site prediction method has been implemented in a publicly available web server.

Algorithms↗

PubMed2005

Free modeling with Rosetta in CASP6.

We describe Rosetta predictions in the Sixth Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), focusing on the free modeling category. Methods developed since CASP5 are described, and their application to selected targets is discussed. Highlights include improved performance on larger proteins (100-200 residues) and the prediction of a 70-residue alpha-beta protein to near-atomic resolution.

Algorithms↗

PubMed2004

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.

Accurate high-resolution refinement of protein structure models is a formidable challenge because of the delicate balance of forces in the native state, the difficulty in sampling the very large number of alternative tightly packed conformations, and the inaccuracies in current force fields. Indeed, energy-based refinement of comparative models generally leads to degradation rather than improvement in model quality, and, hence, most current comparative modeling procedures omit physically based refinement. However, despite their inaccuracies, current force fields do contain information that is orthogonal to the evolutionary information on which comparative models are based, and, hence, refinement might be able to improve comparative models if the space that is sampled is restricted sufficiently so that false attractors are avoided. Here, we use the principal components of the variation of backbone structures within a homologous family to define a small number of evolutionarily favored sampling directions and show that model quality can be improved by energy-based optimization along these directions.

Models, Molecular↗

PubMed2004

CCAAT/enhancer-binding protein alpha (C/EBPalpha) activates transcription of the human microsomal epoxide hydrolase gene (EPHX1) through the interaction with DNA-bound NF-Y.

Microsomal epoxide hydrolase (mEH) plays a central role in xenobiotic metabolism as well as mediating the sodium-dependent uptake of bile acids into the liver, where these compounds regulate numerous biological processes such as cholesterol metabolism and hepatocyte signaling pathways. Little is known, however, about the factors that control the constitutive and inducible expression of the mEH gene (EPHX1) that is altered during development and in response to numerous xenobiotics. In previous studies we have established that GATA-4 binding to the EPHX1 core promoter is critical for EPHX1 expression. The -80/+25 bp core promoter also contained a reversed CCAAT box (-5/-1 bp), integrity of which was required for maximal basal EPHX1 transcription in HepG2 cells. Transient transfection of CCAAT/enhancer-binding protein alpha (C/EBPalpha) substantially stimulated EPHX1 promoter activity. Electrophoretic mobility shift assays, however, revealed that nuclear factor Y (NF-Y), but not C/EBPalpha, directly bound to this site although increased expression of NF-Y had no effect on EPHX1 promoter activity. These results suggested that C/EBPalpha activated EPHX1 expression through its interaction with NF-Y bound to the CCAAT box. The existence of a C/EBPalpha[NF-Y] complex was supported by electrophoretic mobility shift assays using antibodies against NF-Y and C/EBPalpha as well as by the ability of a dominant-negative NF-Y expression vector to inhibit promoter activity. The interaction between these transcription factors was established by co-immunoprecipitation analysis and glutathione S-transferase pull-down assays, whereas the association of the two factors and the interaction of NF-Y with the CCAAT box in vivo was confirmed by chromatin immunoprecipitation assays. C/EBPalpha-dependent EPHX1 activation was also supported by reconstitution studies in HeLa cells that lack this protein. These results establish that EPHX1 expression is regulated by C/EBPalpha interacting with DNA-bound NF-Y.

CCAAT-Binding Factor↗

PubMed2004

Performance of an iterated T-HMM for homology detection.

MOTIVATION: Much information about new protein sequences is derived from identifying homologous proteins. Such tasks are difficult when the evolutionary relationships are distant. Some modern methods achieve better results by building a model of a set of related sequences, and then identifying new proteins that fit the model. A further advance was the development of iterative methods that refine the model as more homologs are discovered. These methods are generally limited by ad hoc methods of sequence weighting, neglect of underlying evolutionary relationships and the representation of the set with a single one-size-fits-all model. These limitations are avoided through the use of a Tree hidden Markov model (T-HMM) approach. Our previous work described how a non-iterative version of the T-HMM method could identify distant homologs with superior performance compared with other non-iterated approaches, and described how this method was particularly appropriate for being implemented as an iterative algorithm. RESULTS: We describe an iterative version of the T-HMM algorithm, and evaluate its performance for the detection of distant homologs. Significant improvement over other commonly used methods is found. AVAILABILITY: The software (C++, Perl) is available from the corresponding author.

Algorithms↗

PubMed2004

Regulation of human microsomal epoxide hydrolase gene (EPHX1) expression by the transcription factor GATA-4.

Microsomal epoxide hydrolase (mEH) is a bifunctional protein that plays a crucial role in the metabolism of numerous xenobiotics as well as in mediating the hepatic sodium-dependent uptake of bile acids that are involved in numerous physiological processes including the regulation of cholesterol metabolism. The transcription factors and nuclear receptors that control the constitutive and inducible expression of the mEH gene (EPHX1), however, have not been described. To characterize these factors, a series of 5'-deletion constructs have been transfected into human liver-derived HepG2 cells as well as non-hepatic HeLa cells. Promoter activity analysis indicated the presence of a positive regulatory element in the -80/-70 bp region. Sequence analysis revealed a putative GATA site at -79/-74 bp as well as an additional site at -31/-26 bp. Electrophoretic mobility shift assays with an anti-GATA-4 antibody confirmed that GATA-4 bound to these two sites with a dissociation constant of 1.56 nM (-79 site) and 0.65 nM (-31 site). Coexpression of GATA-4 stimulated EPHX1 promoter activity up to 7.5-fold in a dose-dependent manner. Endogenous EPHX1 message in HepG2 cells was also significantly increased by overexpression of GATA-4. Mutating the -79 element resulted in a 65% loss of promoter activity, while mutating the -31 element had no effect on basal activity but greatly reduced the response to additional GATA-4. In HeLa cells, which do not express GATA-4, EPHX1 activity was negligible; however, activity could be reconstituted by the addition of exogenous GATA-4. These results demonstrate that GATA-4 plays a critical role in regulating EPHX1 expression.

Binding Sites↗

PubMed2003

Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs.

Related proteins with similar biological functions generally share common features, allowing us to extract the common sequence features. These common features enable us to build statistical models that can be used to classify proteins, to predict new members, and to study the sequence-function relationship of this protein function group. Although evolution underlies the basis of multiple sequence analysis methods, most methods ignore phylogenetic relationships and the evolutionary process in building these statistical models. Previously we have shown that a phylogenetic tree-based profile hidden Markov model (T-HMM) is superior in generating a profile for a group of similar proteins. In this study we used the method to generate common features of G protein-coupled receptors (GPCRs). The profile generated by T-HMM gives high accuracy in GPCR function classification, both by ligand and by coupled G protein.

Animals↗

PubMed2003

Detecting distant homologs using phylogenetic tree-based HMMs.

It is often desired to identify further homologs of a family of biological sequences from the ever-growing sequence databases. Profile hidden Markov models excel at capturing the common statistical features of a group of biological sequences. With these common features, we can search the biological database and find new homologous sequences. Most general profile hidden Markov model methods, however, treat the evolutionary relationships between the sequences in a homologous group in an ad-hoc manner. We hereby introduce a method to incorporate phylogenetic information directly into hidden Markov models, and demonstrate that the resulting model performs better than most of the current multiple sequence-based methods for finding distant homologs.

Algorithms↗

PubMed2003

Inhibition of human m-epoxide hydrolase gene expression in a case of hypercholanemia.

Microsomal epoxide hydrolase (mEH) is a bifunctional protein that plays a central role in carcinogen metabolism and is also able to mediate the sodium-dependent uptake of bile acids into hepatocytes. Studies have identified a subject (S-1) with extremely elevated serum bile salt levels in the absence of observable hepatocellular injury, suggesting a defect in bile acid uptake. In this individual, mEH protein and mEH mRNA levels were reduced by approximately 95% and 85%, respectively, whereas the expression and amino acid sequence of another bile acid transport protein (NTCP) was unaffected. Sequence analysis of the mEH gene (EPHX1) revealed a point mutation at an upstream HNF-3 site (allele I) and in intron 1 (allele II), which resulted in a significant decrease in EPHX1 promoter activity in transient transfection assays. Gel shift assays using a radiolabeled oligonucleotide from each region resulted in specific transcription factor binding patterns, which were altered in the presence of the mutation. These studies demonstrate that the expression of mEH is greatly reduced in a patient with hypercholanemia, suggesting that mEH participates in sodium-dependent bile acid uptake in human liver where its absence may contribute to the etiology of this disease.

Alleles↗

PubMed2002

Optimization of a new score function for the generation of accurate alignments.

The accuracy of the alignments of protein sequences depends on the score matrix and gap penalties used in performing the alignment. Most score functions are designed to find homologs in the various databases rather than to generate accurate alignments between known homologs. We describe the optimization of a score function for the purpose of generating accurate alignments, as evaluated by using a coordinate root-mean-square deviation (RMSD)-based merit function. We show that the resulting score matrix, which we call STROMA, generates more accurate alignments than other commonly used score matrices, and this difference is not due to differences in the gap penalties. In fact, in contrast to most of the other matrices, the alignment accuracies with STROMA are relatively insensitive to the choice of gap penalty parameters.

Amino Acid Sequence↗

PubMed2002

Primary cutaneous CD30-positive anaplastic large cell lymphoma analysis.

OBJECTIVE: To examine 10 cases with primary cutaneous CD30-positive anaplastic large cell lymphoma (ALCL), analyze their clinical manifestations and pathological and immunohistochemical features, and improve early diagnosis of this disease. METHODS: We studied the morphological characteristics of primary cutaneous CD30-positive ALCL using histopathological methods. Leukocyte common antigen (LCA), CD20, CD30, CD45RO, CD68, epithelial membrane antigen (EMA), cytokeratin (CK) and HMB45 antibodies were used to determine the expression of their respective antigens from routine paraffin samples of the patients. RESULTS: Ten patients (7 men and 3 women, aged 31 to 84 years) complained of subcutaneous masses or papular eruptions over their lower trunks and extremities. Histopathologically, the lesions were composed of numerous large round or oval pleomorphic cells. The cytoplasm was usually abundant, amphophilic or basophilic, and finely vacuolated. Nuclei were commonly eccentrically localized and lobated or horseshoed in shape, and multinucleated giant cells and Reed-Sternberg-like cells were seen. Nucleoli were generally multiple and large. Of the 10 patients, tumor cells displayed positive antigen expression of CD30 in all cases, positive CD45RO in 6 cases, positive CD20 in only 1 case, but negative CD45RO and CD20 expressions in 3 cases. Two patients died at 7 weeks and 3.4 years of follow-up, respectively. CONCLUSION: Our study highlights the importance of histopathologic features and positive CD30 staining for differentiation of this disease from other malignant skin tumors.

Adult↗

PubMed2000

Expressions of chromogranin A and cathepsin D in human primary hepatocellular carcinoma.

AIM:To determine the expression and clinical significance of chromogranin A and cathepsin D in hepatocellular carcinoma (HCC).METHODS:Double immunofluorescence stain-ing techniques combined with laser confocal scanning microscopy (LSCM) was used to investigate chromogranin A and cathepsin D expressions in 85 HCC patients.RESULTS:Cathepsin D was expressed in 3 normal liver tissues, while in HCC the staining showed regional variation and the fraction of strongly stained cells increased as the tumors became less differentiated and usually clinically more malignant.Cells which showed strong positivity for cathepsin D were present in 71/85(83.5%) cases. Strong expression of cathepsin D in cancer cells was related to histopathological features. They were more common in grade 3-4 (26/28, 92.9%) and grade 2 (46/53, 86.8%) tumors than in grade 1 tumors (1/4, 25.0%)(P <0.01). No significant correlation was found between age and cathepsin D expression. In patients with positive cathepsin D reaction, the mean age was 52.1± 2.8 years (range 32-68 years) and in the group with negative reaction, the mean age was 51.3± 4.5 years (range 28-71 years). No obvious relationship was observed between CgA expression in cancer cells and the histopathological features. The CgA positive rate was 75.0% (3/4) in grade 1, 71.7% (38/53) in grade 2,and 71.4% (20/28) in grade 3-4(P >0.05) tumors. The coexpression of CgA and cathepsin D was found by double labeled immunofluorescence staining techniques. The processing of cathepsin D was disturbed in HCC cells and accumulated in the cells.Cathepsin D had proteolytic activity and autocrine mitogenic effect, suggesting their functions in invasion. These findings demonstrated that the expression of cathepsin D in HCC had prognostic value.CONCLUSION:Chromogranin A and cathepsin D are expressed in a high proportion of HCC and the existence of cathepsin D in HCC might be related to processing of CgA. This is clearly a subject for further studies because of its potential clinical applications.

Journal Article↗