Biomedical subjects

Yunping Zhu

Publications and source records attributed to Yunping Zhu.

30 records · Page 2Linked to original sources

PubMed2004

Identification of genetic variants in base excision repair pathway and their associations with risk of esophageal squamous cell carcinoma.

The etiology of esophageal squamous cell carcinoma (ESCC) has been shown to be associated with genetic and certain environmental factors that produce DNA damage. Base excision repair (BER) genes are responsible for repair of DNA damage caused by reactive oxygen species and other electrophiles and therefore are good candidate susceptibility genes for ESCC. We first screened eight BER genes for new and potential functional polymorphisms by resequencing 27 DNA samples. We then identified and genotyped for important tagging single nucleotide polymorphisms (SNPs) in a case-control study of 419 patients with newly diagnosed esophageal cancer and 480 healthy controls by frequency matching on age and sex. The association between genotypes and ESCC risk was estimated by unconditional multivariate logistic regression analysis, and stepwise regression procedure was used for constructing the final logistic regression model. We identified 129 SNPs in the eight BER genes, including 18 SNPs that cause amino acid changes. In the final model, 4 SNPs, including 2 in the coding regions (ADPRT Val762Ala and MBD4 Glu346Lys) and others in noncoding regions (LIG3 A3704G and XRCC1 T-77C), remained as significant predictors for the risk of ESCC. The adjusted odd ratios were 1.25 [95% confidence interval (CI) 1.02-1.53] for the ADPRT 762Ala allele, 1.25 (95% CI 1.02-1.53) for the MBD4 346 Lys allele, 0.78 (95% CI 0.63-0.97) for the LIG3 3704G allele, and 1.38 (95% CI 1.01-1.89) for the XRCC1-77C allele. In addition, we observed a significant gene-gene interaction between XRCC1 Gln399Arg and ADPRT Val762Ala. The results suggest that the polymorphisms in five BER genes may be associated with the susceptibility to ESCC in a Chinese population.

ADP Ribose Transferases↗

PubMed2004

Characterization of a novel C-type lectin-like gene, LSECtin: demonstration of carbohydrate binding and expression in sinusoidal endothelial cells of liver and lymph node.

A new C-type lectin-like gene encodes 293 amino acids and maps to chromosome 19p13.3 adjacent to the previously described C-type lectin genes, CD23, dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN), and DC-SIGN-related protein (DC-SIGNR). The four genes form a tight cluster in an insert size of 105 kb and have analogous genomic structures. The new C-type lectin-like molecule, designated liver and lymph node sinusoidal endothelial cell C-type lectin (LSECtin), is a type II integral membrane protein of approximately 40 kDa in size with a single C-type lectin-like domain at the COOH terminus, closest in homology to DC-SIGNR, DC-SIGN, and CD23. LSECtin mRNA was only expressed in liver and lymph node among 15 human tissues tested, intriguingly neither expressed on hematopoietic cell lines nor on monocyte-derived dendritic cells (DCs). Moreover, LSECtin is expressed predominantly by sinusoidal endothelial cells of human liver and lymph node and co-expressed with DC-SIGNR. LSECtin binds to mannose, GlcNAc, and fucose in a Ca(2+)-dependent manner but not to galactose. Our results indicate that LSECtin is a novel member of a family of proteins comprising CD23, DC-SIGN, and DC-SIGNR and might function in vivo as a lectin receptor.

Base Sequence↗

PubMed2004

Proteomic analysis on structural proteins of Severe Acute Respiratory Syndrome coronavirus.

Recently, a new coronavirus was isolated from the lung tissue of autopsy sample and nasal/throat swabs of the patients with Severe Acute Respiratory Syndrome (SARS) and the causative association with SARS was determined. To reveal further the characteristics of the virus and to provide insight about the molecular mechanism of SARS etiology, a proteomic strategy was utilized to identify the structural proteins of SARS coronavirus (SARS-CoV) isolated from Vero E6 cells infected with the BJ-01 strain of the virus. At first, Western blotting with the convalescent sera from SARS patients demonstrated that there were various structural proteins of SARS-CoV in the cultured supernatant of virus infected-Vero E6 cells and that nucleocaspid (N) protein had a prominent immunogenicity to the convalescent sera from the patients with SARS, while the immune response of spike (S) protein probably binding with membrane (M) glycoprotein was much weaker. Then, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to separate the complex protein constituents, and the strategy of continuous slicing from loading well to the bottom of the gels was utilized to search thoroughly the structural proteins of the virus. The proteins in sliced slots were trypsinized in-gel and identified by mass spectrometry. Three structural proteins named S, N and M proteins of SARS-CoV were uncovered with the sequence coverage of 38.9, 93.1 and 28.1% respectively. Glycosylation modification in S protein was also analyzed and four glycosylation sites were discovered by comparing the mass spectra before and after deglycosylation of the peptides with PNGase F digestion. Matrix-assisted laser desorption/ionization-mass spectrometry determination showed that relative molecular weight of intact N protein is 45 929 Da, which is very close to its theoretically calculated molecular weight 45 935 Da based on the amino acid sequence deduced from the genome with the first amino acid methionine at the N-terminus depleted and second, serine, acetylated, indicating that phosphorylation does not happen at all in the predicted phosphorylation sites within infected cells nor in virus particles. Intriguingly, a series of shorter isoforms of N protein was observed by SDS-PAGE and identified by mass spectrometry characterization. For further confirmation of this phenomenon and its related mechanism, recombinant N protein of SARS-CoV was cleaved in vitro by caspase-3 and -6 respectively. The results demonstrated that these shorter isoforms could be the products from cleavage of caspase-3 rather than that of caspase-6. Further, the relationship between the caspase cleavage and the viral infection to the host cell is discussed.

Amino Acid Sequence↗

PubMed2003

Conversion of dose-volume constraints to dose limits.

The purpose of this study is to introduce two techniques for converting dose-volume constraints to dose limits for treatment planning optimization, and to evaluate their performance. The first technique, called dose-sorting, is based on the assumption that higher dose limits should be assigned to the constraint points receiving higher doses, and vice versa. The second technique, the hybrid technique, is a hybrid of the dose-sorting technique and the mixed integer linear programming (MILP) technique. Among all constraint points in an organ at risk, the dose limits for the points far from a dose-volume constraint are determined by dose-sorting, while the dose limits for the points close to a dose-volume constraint are determined by MILP. We evaluated the performance of the two new techniques for one treatment geometry by comparing them with the MILP technique. The dose-sorting technique had a high probability of finding the global optimum when no more than three organs at risk have dose-volume constraints. It was much faster than the MILP technique. The hybrid technique always found the global optimum when the MILP percentage (the percentage of constraint points for which the dose limits are determined by the MILP technique) was large enough, but its computation time increased dramatically with the MILP percentage. In conclusion, the dose-sorting technique and the hybrid technique with a low MILP percentage are clinically feasible.

Algorithms↗

PubMed2003

The potentiation role of hepatopoietin on activator protein-1 is dependent on its sulfhydryl oxidase activity.

Hepatopoietin (HPO) is a novel hepatotrophic growth factor that stimulates hepatocyte proliferation by two pathways. In the first, intracellular HPO specifically modulates the activator protein-1 (AP-1) pathway through JAB1 (Jun activation domain-binding protein 1), whereas in the second, extracellular HPO triggers the mitogen-activated protein kinase pathway by binding its specific receptor on the cell surface. In this report we demonstrate that HPO is a flavin-linked sulfhydryl oxidase, and the invariant CXXC (Cys-Xaa-Xaa-Cys) motif in HPO is essential for the enzyme activity of HPO but not for its dimerization nor for its binding ability with JAB1. Two intramolecular disulfides were identified in HPO by mass spectrometry, one of which is formed by the redox CXXC cysteine residues. HPO site-directed mutants (Cys/Ser) at active sites, which lost sulfhydryl oxidase activity, could not increase c-Jun phosphorylation and failed to potentiate JAB1-mediated AP-1 activation. However, the mutants still have mitogenic stimulation and mitogen-activated protein kinase activation effects on HepG2 cells. Thus, it can be concluded that the potentiation role of HPO on AP-1 is dependent on its sulfhydryl oxidase activity.

Amino Acid Sequence↗

PubMed2003

Haplotype structure and evidence for positive selection at the human IL13 locus.

Interleukin-13 (IL13) is believed to play an important role in the pathogenesis of atopy and allergic asthma. To better understand genetic variation at the IL13 locus, we resequenced a 5.1-kb genomic region spanning the entire locus and identified 26 single-nucleotide polymorphisms (SNPs) in 74 individuals from three major populations-Chinese, Caucasian, and African. Our survey suggests exceptionally high and significant geographic structure at the IL13 locus between African and outside Africa populations. This unusual pattern suggests that positive selection that acts in some local populations may have played a role on the IL13 locus. In support of this suggestion, we found a significant excess of high frequency-derived SNPs in the Chinese population and Caucasian population, respectively, as expected after a recent episode of positive selection. Further, the unusual haplotype structure indicates that different scenarios of the action of positive selection on the IL13 locus in different populations may exist. In the Caucasian population, the skewed haplotype distribution dominated by one common haplotype supports the hypothesis of simple directional selection. Whereas, in the Chinese population, the two-round hitchhiking hypothesis may explain the skewed haplotype structure with three dominant ones. These findings may provide insight into the likely relative roles of selection and population history in establishing present-day variation at the IL13 locus, and, motivate further studies of this locus as an important candidate in common diseases association studies.

Asian People↗

PubMed2003

An initiator and its flanking elements function as a core promoter driving transcription of the Hepatopoietin gene.

Hepatopoietin (HPO)/ALR (augmenter of liver regeneration), as a versatile hepatotrophic growth factor and a cellular thiol oxidase, is involved in a wide variety of basic processes of various tissues, especially in liver and testis. Here, we studied the regulation of HPO gene expression. By sequential deletion of the HPO 5'-flanking region, the minimal promoter of the HPO gene was shown to span positions -22 to +42 relative to the transcriptional start point. Further transfection assay and mutation analysis showed that the core promoter contains a functional initiator. Interestingly, three tandem repeats of a CTGGAGGC element, surrounding the transcription start site and bound by specific nuclear factors, were found to be pivotal for the promoter activity. This initiator flanking element functions in an initiator-dependent fashion and is present in many initiator-containing genes. Taken together, our findings revealed that the initiator-like element and its flanking repeat sequence comprise a core promoter and drive the transcriptional initiation of the HPO gene in a combinatorial manner. The HPO gene promoter might represent a novel architecture for core promoters.

Base Sequence↗

PubMed2003

Identification of metastasis-associated proteins by proteomic analysis and functional exploration of interleukin-18 in metastasis.

Very little is currently known about mechanisms underlying cancer metastasis. In the present study, metastasis-associated proteomes were separated and identified by comparative proteomic analysis, and the metastasis-related function of candidate protein interleukin-18 (IL-18) was further elucidated. First, a pair of highly and poorly metastatic sublines (termed PLA801D and PLA801C, respectively), originating from the same parental PLA801 cell line, was identified by spontaneous tumorigenicity and metastasis in vivo and characterized by metastatic phenotypes analysis in vitro. Subsequently, a proteomic approach was used to compare the protein expression profiles between PLA801C and PLA801D sublines. Eleven proteins were identified and further verified by one-dimensional Western blotting, Northern blot and/or semiquantitative reverse transciptase polymerase chain reaction analysis. Compared with those in poorly metastatic PLA801C subline, cytokeratin 18, tissue transglutaminase, Rho GDP-dissociation inhibitor 1, tropomyosin, fibroblast type, IL-18 and annexin I were significantly up-regulated, while protein disulfide isomerase, heat shock protein 60, peroxiredoxin 1, chlorine intracellular channel protein 1 (CLI1) and creatine kinase, B chain were significantly down-regulated in the highly metastatic PLA801D subline. Intriguingly, all the identified candidate proteins except for CLI1 have been shown to be somehow associated with distinct aspects of tumor metastasis such as cell growth, motility, invasion, adhesion, apoptosis and tumor immunity, etc. Considering that IL-18 was present in highly metastatic PLA801D but absent in poorly metastatic PLA801C, the association of IL-18 with metastasis was further elucidated by introducing IL-18 sense/IL-18 antisense into PLA801C/PLA801D sublines simultaneously. The results demonstrated that ectopically expressed IL-18 promoted cell motility in vitro and down-regulated E-cadherin expression of PLA801C transfectants, while IL-18 antisense remarkably decreased cell invasion potency in vitro and notably increased E-cadherin expression of PLA801D transfectants, indicating that IL-18 might play a role in metastasis by inhibiting E-cadherin expression.

Animals↗

PubMed2002

Identification, characterization, and functional study of the two novel human members of the semaphorin gene family.

We cloned two novel human transmembrane semaphorins, (HSA)SEMA6C and (HSA)SEMA6D, that belong to the class VI subgroup of the semaphorin family. The genes for SEMA6C and SEMA6D are mapped on chromosome 1q12-21.1 and 15q21.1, respectively. Among the adult tissues, SEMA6C is expressed only in skeletal muscle, whereas SEMA6D is expressed abundantly in kidney, brain, and placenta and moderately in the heart and skeletal muscles. During murine development, neither SEMA6C nor SEMA6D was expressed in embryonic day 10.5 (E10.5) embryos, but both were highly expressed in the areas of the lateral ventricle, the striatum, the wall of the midbrain, the pons/midbrain junction, and the choroid plexus of E13 embryos. Were neurons, neither axons nor astrocytes, highly expressed both semaphorins. Three isoforms of SEMA6C and five isoforms of SEMA6D derived from alternative splicing were identified, and their expression was regulated in a tissue- and development-dependent manner. Deletion analysis indicated that a sema domain and a PSI domain are integrally necessary for correct post-translation modification and subcellular localization. The extracellular domain of SEMA6C inhibited axonal extension of nerve growth factor-differentiated PC12 cells and induced the growth cone collapse of chicken dorsal root ganglion, rat hippocampal neurons, and rat cortical neurons in a dose-responsive manner. SEMA6D acted like SEMA6C except it had no significant effect on the growth cones of rat cortical neurons.

Alternative Splicing↗

PubMed2002

Preliminary results from a Phase II trail of conformal radiation therapy for pediatric patients with localised low-grade astrocytoma and ependymoma.

PURPOSE: To estimate the local control and patterns of failure for pediatric patients with low-grade astroglial tumors (LGA) and ependymoma (EP) treated with three-dimensional conformal radiation therapy (CRT) using an anatomically defined clinical target volume (CTV). METHODS AND MATERIALS: From an ongoing, prospective Phase II trial initiated in July 1997, 102 pediatric patients with LGA (n = 38) and EP (n = 64) have been treated with CRT using an anatomically defined CTV extending 1.0 cm beyond the gross tumor volume and a 0.5-cm margin (planning target volume) extending outside of the CTV. The prescribed dose was 54 Gy (LGA) and 59.4 Gy (EP). RESULTS: Patients with EP have been followed for a median of 17 months (range 3--43 months), and six failures have occurred. Patients with LGA have been followed for a median of 17 months (3--44 months), and four failures have occurred. Three-dimensional magnetic resonance (MR) studies performed to document treatment failure were registered with the MR and computed tomography (CT) data used in the treatment planning process. Failure occurred within the CTV for 5 patients with EP, including 3 with concurrent subarachnoid dissemination. One patient with EP developed metastatic disease with no evidence of local failure. Three patients with LGA failed within the CTV and one failed immediately outside of the CTV. CONCLUSIONS: Treatment of an anatomically defined CTV, encompassing 1.0 cm of non-involved brain beyond the margin of resection or neuroimaging-defined tumor, appears to be safe for pediatric patients with LGA and EP based on these preliminary data. Normal tissue sparing through the use of advanced radiation therapy treatment planning and delivery techniques should be beneficial to pediatric patients if the rate and patterns of failure are similar to conventional techniques and toxicity reduction can be objectively documented.

Adolescent↗

PubMed2002

Verification of multileaf collimator leaf positions using an electronic portal imaging device.

An automated method is presented for determining individual leaf positions of the Siemens dual focus multileaf collimator (MLC) using the Siemens BEAMVIEW(PLUS) electronic portal imaging device (EPID). Leaf positions are computed with an error of 0.6 mm at one standard deviation (sigma) using separate computations of pixel dimensions, image distortion, and radiation center. The pixel dimensions are calculated by superimposing the film image of a graticule with the corresponding EPID image. A spatial correction is used to compensate for the optical distortions of the EPID, reducing the mean distortion from 3.5 pixels (uncorrected) per localized x-ray marker to 2 pixels (1 mm) for a rigid rotation and 1 pixel for a third degree polynomial warp. A correction for a nonuniform dosimetric response across the field of view of the EPID images is not necessary due to the sharp intensity gradients across leaf edges. The radiation center, calculated from the average of the geometric centers of a square field at 0 degrees and 180 degrees collimator angles, is independent of graticule placement error. Its measured location on the EPID image was stable to within 1 pixel based on 3 weeks of repeated extensions/retractions of the EPID. The MLC leaf positions determined from the EPID images agreed to within a pixel of the corresponding values measured using film and ionization chamber. Several edge detection algorithms were tested: contour, Sobel, Roberts, Prewitt, Laplace, morphological, and Canny. These agreed with each other to within < or = 1.2 pixels for the in-air EPID images. Using a test pattern, individual MLC leaves were found to be typically within 1 mm of the corresponding record-and-verify values, with a maximum difference of 1.8 mm, and standard deviations of <0.3 mm in the daily reproducibility. This method presents a fast, automatic, and accurate alternative to using film or a light field for the verification and calibration of the MLC.

Algorithms↗

PubMed2002

Comparison of two algorithms for determining beam weights and wedge filters.

This article compares two algorithms for determining beam weights and wedge filters for conformal treatment planning. One algorithm, which is based on dose-gradient analysis, provides analytic formulas for determining beam weights, wedge angles, and collimator angles (i.e., wedge orientations) so that the dose distribution is homogeneous in the target volume. The second algorithm is based on the concept of the super-omni wedge (i.e., the arrangement of two pairs of orthogonal nominal wedged beams), numerically optimize beam weights, wedge angles, and collimator angles so that the dose requirements to targets and organs at risk are satisfied to the best. Three clinical cases were tested. For the first case, both algorithms resulted in comparable homogeneous dose distributions in the target volume. For the second case, the second algorithm resulted in much lower doses to the eyes plus a better homogeneous dose distribution in the target volume. For the third case, only the second algorithm was applicable, and the treatment plan it developed met the prescribed requirements. The results show that the first algorithm is better in terms of feasibility, whereas the second is better in terms of applicability and the quality of treatment plans.

Algorithms↗