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Xian Chen

Publications and source records attributed to Xian Chen.

At least 19 recordsLinked to original sources
PubMed2026

A systematic literature review on low-grade myofibroblastic sarcoma of the trunk.

BACKGROUND: Low-grade myofibroblastic sarcoma (LGMS) is a rare malignant mesenchymal tumor, with primary trunk involvement being particularly uncommon. Due to its rarity, associated diagnostic challenges, and variability in management, a comprehensive evaluation of the available evidence is required. This study aims to systematically review the clinical characteristics, treatment strategies, and outcomes of truncal LGMS. METHODS: A systematic literature search was conducted using PubMed, Web of Science, and Embase for articles published from January 1998 to January 2026. The review included full-text articles involving patients with a pathologically confirmed diagnosis of truncal LGMS. The collected data included patient demographics, tumor features, treatment modalities, recurrence, and follow-up status. RESULTS: Of the 404 studies initially identified, 30 studies involving 59 patients with pathologically confirmed truncal LGMS met the inclusion criteria. Outcome analyses of therapeutic management and clinical course included 45 patients with complete follow-up data, including 42 surgically treated patients and 3 non-surgically managed patients. The final evidence base consisted solely of retrospective studies and case reports. No prospective studies or randomized controlled trials were identified. Consequently, a descriptive statistical analysis was conducted instead of a meta-analysis. CONCLUSION: Current evidence indicates that wide excision with negative margins may be a reasonable primary treatment option for truncal LGMS, with case-based reports showing numerically lower recurrence after wide excision, although the evidence is limited and potentially confounded by multiple factors. Radiotherapy or chemotherapy may be considered only on a highly individualized basis for selected unresectable, recurrent, metastatic, anatomically constrained, or margin-positive cases. Given the very limited sample size and heterogeneous treatment indications across published cases, treatment efficacy cannot be reliably estimated from the available data. Prolonged long-term regular follow-up is recommended for all patients, considering the risk of late recurrence.

Humans↗
PubMed2006

Toward automated biochemotype annotation for large compound libraries.

Combinatorial chemistry allows scientists to probe large synthetically accessible chemical space. However, identifying the sub-space which is selectively associated with an interested biological target, is crucial to drug discovery and life sciences. This paper describes a process to automatically annotate biochemotypes of compounds in a library and thus to identify bioactivity related chemotypes (biochemotypes) from a large library of compounds. The process consists of two steps: (1) predicting all possible bioactivities for each compound in a library, and (2) deriving possible biochemotypes based on predictions. The Prediction of Activity Spectra for Substances program (PASS) was used in the first step. In second step, structural similarity and scaffold-hopping technologies are employed. These technologies are used to derive biochemotypes from bioactivity predictions and the corresponding annotated biochemotypes from MDL Drug Data Report (MDDR) database. About a one million (982,889) commercially available compound library (CACL) has been tested using this process. This paper demonstrates the feasibility of automatically annotating biochemotypes for large libraries of compounds. Nevertheless, some issues need to be considered in order to improve the process. First, the prediction accuracy of PASS program has no significant correlation with the number of compounds in a training set. Larger training sets do not necessarily increase the maximal error of prediction (MEP), nor do they increase the hit structural diversity. Smaller training sets do not necessarily decrease MEP, nor do they decrease the hit structural diversity. Second, the success of systematic bioactivity prediction relies on modeling, training data, and the definition of bioactivities (biochemotype ontology). Unfortunately, the biochemotype ontology was not well developed in the PASS program. Consequently, "ill-defined" bioactivities can reduce the quality of predictions. This paper suggests the ways in which the systematic bioactivities prediction program should be improved.

Chemistry, Pharmaceutical↗
PubMed2006

Nanopore-based proteolytic reactor for sensitive and comprehensive proteomic analyses.

Various silica-based microreactors have been designed that use enzyme immobilization to address technical concerns in proteolysis including inefficient and incomplete protein digestion. Most of current designs for proteolytic reactors can improve either protease stability or proteolysis efficiency of individual protein(s). However, the desired features such as rapid digestion, larger sequence coverage, and high sensitivity have not been achieved by a single microreactor design for broad range proteins with diverse physical properties. Here, unlike conventional enzyme immobilization strategies, we describe a novel proteolytic nanoreactor based on the unique three-dimensional nanopore structure of our newly synthesized mesoporous silica (MPS), FDU-12, which integrates substrate enrichment, "reagent-free" protein denaturation, and efficient proteolytic digestion. In our design, protein substrates were first captured by MPS nanopore structure and were concentrated from the solution. Following the pH change and applying trypsin, the denaturation and concurrent proteolysis of broad-range proteins were efficiently achieved. In minutes, many more sample peptides from the in-nanopore digestion of protein mixtures were detected by mass spectrometry, resulting in the identifications of a broad range of diverse proteins with high sequence coverage. The unique features of FDU-12 nanostructure that allow rapid, complete proteolysis and resulting enhanced sequence coverage of individual proteins were investigated by using Raman spectroscopy and comparative studies with respect to other MPSs.

Animals↗
PubMed2006

Finite element contact analysis of the hip joint.

The hip joint plays an important role in the musculoskeletal system; however, current knowledge of the mechanics of the hip joint, especially with regard to the distribution of stress, remains limited. In experimental research, difficulties arise during reproduction of physiological conditions of daily activities and practicable measurement of locations inside the hip joint without violating the physiological environment. On the other hand, numerical approaches, such as finite element analysis, have become useful tools in the field of biomechanics. In finite element contact analysis of the hip joint, due to discretization of contact surfaces, computational instability might occur when the contact nodes move near the edges of the contact elements. In this study, to overcome this problem, a contact smoothing approach was introduced by applying Gregory patches. Contact analysis of the hip joint was then performed for three representative daily activities; i.e., walking, rising up from a chair and knee bending. The effectiveness of the adopted smoothing approach was verified by comparing the results with those obtained experimentally. The distribution and history of contact stress, which have heretofore been scarcely reported, were also obtained and the implications associated with osteoarthritis were discussed.

Algorithms↗
PubMed2006

The dynamic alterations of H2AX complex during DNA repair detected by a proteomic approach reveal the critical roles of Ca(2+)/calmodulin in the ionizing radiation-induced cell cycle arrest.

By using DNA nuclease digestion and a quantitative "dual tagging" proteomic approach that integrated mass spectrometry, stable isotope labeling, and affinity purification, we studied the histone H2AX-associating protein complex in chromatin in mammalian cells in response to ionizing radiation (IR). In the non-irradiated control cells, calmodulin (CaM) and the transcription elongation factor facilitates chromatin transcription (FACT) were associated with H2AX. Thirty minutes after exposing cells to IR the CaM and FACT complexes dissociated, whereas two DNA repair proteins, poly(ADP-ribose) polymerase-1 and DEAH box polypeptide 30 isoform 1, interacted with H2AX. Two hours and 30 min after exposure, none of the above proteins were in the complex. H2B, nucleophosmin/B23, and calreticulin were associated with H2AX in both non-irradiated and irradiated cells. The results suggest that the H2AX complex undergoes dynamic changes upon induction of DNA damage and during DNA repair. The genuine interactions between H2AX and H2B, nucleophosmin/B23, calreticulin, poly(ADP-ribose) polymerase-1, and CaM under each condition were validated by immunoprecipitation/Western blotting and mammalian two-hybrid assays. Because multiple Ca(2+)-binding proteins were found in the H2AX complex, the roles of Ca(2+) were examined. The results indicate that Ca(2+)/CaM plays important roles in regulating IR-induced cell cycle arrest, possibly through mediating chromatin structure. The dataset presented here demonstrates that sensitive profiling of the dynamics of functional cellular protein-protein interactions can successfully lead to the dissection of important metabolic or signaling pathways.

Calcium-Binding Proteins↗
PubMed2006

Use of arterially perfused rabbit ventricular wedge in predicting arrhythmogenic potentials of drugs.

INTRODUCTION: A growing number of drugs have reportedly been associated with delayed ventricular repolarization and a potentially fatal but rare arrhythmia, torsade de pointes (TdP). There is obviously a call for a validated proarrhythmia model that distinguishes proarrhythmic drugs from nonarrhythmogenic drugs. METHODS: In this article, we validated the arterially perfused rabbit left ventricular wedge preparation model and examined its use in predicting proarrhythmic potentials of drugs. A fairly detailed methodological description about this technically challenging model was given, aiming to help others establish the assay successfully. Parameters commonly used in the action potential studies were verified and critical experimental conditions (e.g. stability and reproducibility of recordings) were examined. Six commercially available compounds with various proarrhythmic potentials were administered in the model to evaluate their correlations with individual clinical outcomes. RESULTS: Our study indicated that, in a successful experiment, the action potential duration (APD) can be stably maintained for several hours without intervention. Dofetilide, DL-sotalol, cisapride, risperidone and moxifloxacin increased endo- and epicardial APD(90), QT interval and T(P-E) (peak-to-end time of the T wave) in a reverse use-dependent manner within clinically relevant concentration ranges. Phase 2 early afterdepolarizations (EADs) were observed at 1.6, 2.3, 16.7, 37.5 and 7.9 fold, respectively, their corresponding unbound therapeutic concentrations. In contrast, fluoxetine at up to 3 microM (approximately 35 fold unbound therapeutic mean plasma concentration after 60 mg/day, p.o. for 5 weeks) had only a mild prolonging effect on APD(90) and QT with essentially no effect on T(P-E). DISCUSSION: Our results strongly support the usefulness of this model in predicting a compound's arrhythmogenic potential in humans within clinically relevant concentration ranges, and the experimental results with this model need to be interpreted in light of each drug's pharmacokinetic and pharmacodynamic behavior in clinic.

Action Potentials↗
PubMed2006

Flightless I homolog negatively modulates the TLR pathway.

To date, much of our knowledge about the signaling networks involved in the innate immune response has come from studies using nonphysiologic model systems rather than actual immune cells. In this study, we used a dual-tagging proteomic strategy to identify the components of the MyD88 signalosome in murine macrophages stimulated with lipid A. This systems approach revealed 16 potential MyD88-interacting partners, one of which, flightless I homolog (Fliih) was verified to interact with MyD88 and was further characterized as a negative regulator of the TLR4-MyD88 pathway. Conversely, a reduction in endogenous Fliih by small-interfering RNA enhanced the activation of NF-kappaB, as well as cytokine production by LPS. Results from immunoprecipitation and a two-hybrid assay further indicated that Fliih directly interfered with the formation of the TLR4-MyD88 signaling complex. These results in turn suggest a new basis for the regulation of the TLR pathway by Fliih.

Actins↗
PubMed2006

[Cloning the lvgA gene of Legionella pneumophila and detecting its expression in Escherichia coli].

In order to clone lvgA gene (Legionella virulence gene) of Legionella pneumophila and detect its expression in prokaryotic cell, we amplified the lvgA gene from the total cell DNA of Legionella pneumophila with PCR,and then inserted it into the coloning vector pUC18. The recombinant plasmid pUlvgA was obtained. After the recombinant plasmid pUlvgA was identified with restriction enzyme analysis, polymerase chain reaction and nucleotide sequencing analysis, the lvgA gene was subcloned into the prokaryotic expression vector pGEX-4T-1. The prokaryotic expression recombinant plasmid pGlvgA was constructed. After IPTG induction, the E. coli JM109 containing the recombinant plasmid pGlvgA expressed fusion protein. The expression of lvgA was subsequently detected by SDS-polyacrylamine gel electrophoresis and Western-blot analysis. The results indicated that the lvgA gene of 627 bp long was amplified, the recombinant plasmids pUlvgA and pGlvgA were constructed successfully, and the GST-LvgA fusion protein of approximately 36 KDa in size was expressed in prokaryotic cell efficiently as expected.

Bacterial Proteins↗
PubMed2006

[Legionella pneumophila lvgA and Hsp60 gene splicing and the fusion gene expression in E.coli].

OBJECTIVE: To fuse Legionella virulence gene (lvgA) with heat shock protein 60 gene (Hsp60) by PCR and detect the fusion gene expression in E.coli. METHODS: The fragments of lvgA and Hsp60 genes having matching sequences at their ends to be fused were amplified from the genomic DNA of Legionella pneumophila by PCR, and the PCR products were mixed, denatured, reannealed, so that the strands with matching sequences at their 3' ends overlapped to serve as primers for each other. Extension of this overlap by DNA polymerase produced recombinant products. After amplification with outer primers, sufficient product of the fusion gene was harvested, which was inserted into the prokaryotic expression vector pGEX-4T-1 to construct the prokaryotic expression recombinant plasmid. After identification with restriction enzyme analysis, polymerase chain reaction and nucleotide sequence analysis, the E.coli BL21 containing the recombinant plasmid pGlvgA/Hsp60 was induced with IPTG and the expression of lvgA/Hsp60 was detected by SDS-PAGE and Western blot analysis. RESULTS: The lvgA/Hsp60 fusion gene of 2,292 bp was amplified and the recombinant plasmid pGlvgA/Hsp60 was constructed successfully. A 117-kD GST-lvgA-Hsp60 fusion protein was detected in the E.coli containing the recombinant plasmid. CONCLUSION: The recombinant plasmid for Legionella pneumophila lvgA/Hsp60 fusion gene is constructed successfully and this fusion protein can be expressed in prokaryotic cells efficiently, which make possible the immunological characterization of this fusion gene.

Alternative Splicing↗
PubMed2005

Mesoporous silica nanoreactors for highly efficient proteolysis.

Protein digestion inside the nanoreactor channels of mesoporous silica (SBA-15) is reported, and evaluated by using peptide-mass mapping. Both proteases and substrates were efficiently captured within these biocompatible nanoreactors. After 10 minutes, the mass spectrum of the protein digests released from the mesoporous-silica-based nanoreactors revealed the presence of eight peptides covering 58% of the protein sequence with an intense signal (signal/noise ratio > 70). In comparison, the conventional overnight in-solution digestion of proteins under otherwise identical conditions generated only three peptides (27% sequence coverage). We propose that this order-of-magnitude increase in the proteolytic reaction rate is mainly attributed to two factors: substrate enrichment within mesoporous silica channels and enzyme immobilization. The surface properties and macrostructure of the mesoporous silica were studied to reveal their significant influence on proteolytic reactions.

Hydrolysis↗
PubMed2005

Precise proteomic identification using mass spectrometry coupled with stable isotope labeling.

Stable isotope labeling (SIL) can assist mass spectrometry to improve its specificity and throughput in protein identification, de novo sequencing, and characterization of post translational modifications. This Education article summarizes the unique characteristics of stable isotope-assisted mass spectrometry for accurate protein identification without requirements for ultrahigh mass accuracy. Some applications are discussed here to demonstrate the general experimental procedures, data interpretation, and the improvements in accuracy and throughput compared to the use of mass spectrometry alone.

Animals↗
PubMed2005

Novel potent human ether-a-go-go-related gene (hERG) potassium channel enhancers and their in vitro antiarrhythmic activity.

A variety of drugs has been reported to cause acquired long QT syndrome through inhibition of the IKr channel. Screening compounds in early discovery and development stages against their ability to inhibit IKr or the hERG channel has therefore become an indispensable procedure in the pharmaceutical industry. In contrast to numerous hERG channel blockers discovered during screening, only (3R,4R)-4-[3-(6-methoxyquinolin-4-yl)-3-oxo-propyl]-1-[3-(2,3,5-trifluoro-phenyl)-prop-2-ynyl]-piperidine-3-carboxylic acid (RPR260243) has been reported so far to enhance the hERG current. In this article, we describe several potent mechanistically distinct hERG channel enhancers. One example is PD-118057 (2-{4-[2-(3,4-dichloro-phenyl)-ethyl]-phenylamino}-benzoic acid) which produced average increases of 5.5 +/- 1.1, 44.8 +/- 3.1, and 111.1 +/- 21.7% in the peak tail hERG current at 1, 3, and 10 muM, respectively, in human embryonic kidney 293 cells. PD-118057 did not affect the voltage dependence and kinetics of gating parameters, nor did it require open conformation of the channel. In isolated guinea pig cardiomyocytes, PD-118057 showed no major effect on I(Na), I(Ca,L), I(K1), and I(Ks). PD-118057 shortened the action potential duration and QT interval in arterially perfused rabbit ventricular wedge preparation in a concentration-dependent manner. The presence of 3 muM PD-118057 prevented action potential duration and QT prolongation caused by dofetilide. "Early after-depolarizations" induced by dofetilide were also completely eliminated by 3 microM PD-118057. Although further investigation is warranted to evaluate the therapeutic value and safety profile of these compounds, our data support the notion that hERG activation by pharmaceuticals may offer a new approach in the treatment of delayed repolarization conditions, which may occur in patients with inherited or acquired long QT syndrome, congestive heart failure, and diabetes.

Animals↗
PubMed2005

PUMA overexpression induces reactive oxygen species generation and proteasome-mediated stathmin degradation in colorectal cancer cells.

Increased amounts of reactive oxygen species (ROS) induce apoptosis in mammalian cells. PUMA (P53 up-regulated modulator of apoptosis), a mitochondrial proapoptotic BH3-only protein, induces rapid apoptosis through a Bax- and mitochondria-dependent pathway. However, the molecular basis of PUMA-induced apoptosis is largely not understood. Using a combination of biophysical and biochemical methods and PUMA-inducible colorectal cells, DLD-1.PUMA, we showed that (a) PUMA-induced apoptosis is dose and time dependent; (b) PUMA-induced apoptosis is directly associated with ROS generation; (c) diphenyleneiodonium chloride, a ROS blocker, or BAX-inhibiting peptide, a suppressor of BAX translocation, decreased ROS generation and apoptosis in DLD-1.PUMA cells; (d) overexpression of PUMA induced up-regulation (>1.34-fold) of peroxiredoxin 1 and down-regulation (by 25%) of stathmin through proteasome-mediated degradation; and (e) hydrogen peroxide down-regulated stathmin and disrupted the cellular microtubule network. Our findings indicate that PUMA induces apoptosis, in part, through the BAX-dependent generation of superoxide and hydrogen peroxide. ROS overproduction and oxidative stress induce proteome-wise alterations, such as stathmin degradation and disorganization of the cell microtubule network, in apoptotic cells.

Apoptosis↗
PubMed2005

Pentamidine reduces hERG expression to prolong the QT interval.

Pentamidine, an antiprotozoal agent, has been traditionally known to cause QT prolongation and arrhythmias; however, its ionic mechanism has not been illustrated. In a stable HEK-293 cell line, we observed a concentration-dependent inhibition of the hERG current with an IC50 of 252 microM. In freshly isolated guinea-pig ventricular myocytes, pentamidine showed no effect on the L-type calcium current at concentrations up to 300 microM, with a slight prolongation of the action potential duration at this concentration. Since the effective concentrations of pentamidine on the hERG channel and APD were much higher than clinically relevant exposures (approximately 1 microM free or lower), we speculated that this drug might not prolong the QT interval through direct inhibition of I(Kr) channel. We therefore incubated hERG-HEK cells in 1 and 10 microM pentamidine-containing media (supplemented with 10% serum) for 48 h, and examined the hERG current densities in the vehicle control and pentamidine-treated cells. In all, 36 and 85% reductions of the current densities were caused by 1- and 10-microM pentamidine treatment (P<0.001 vs control), respectively. A similar level of reduction of the hERG polypeptides and a reduced intensity of the hERG protein on the surface membrane in treated cells were observed by Western blot analysis and laser-scanning confocal microscopy, respectively. Taken together, our data imply that chronic administration of pentamidine at clinically relevant exposure reduces the membrane expression of the hERG channel, which may most likely be the major mechanism of QT prolongation and torsade de pointes reported in man.

Animals↗
PubMed2005

QT prolongation and proarrhythmia by moxifloxacin: concordance of preclinical models in relation to clinical outcome.

Moxifloxacin, a fluoroquinolone antibiotic associated with QT prolongation, has been recommended as a positive control by regulatory authorities to evaluate the sensitivity of both clinical and preclinical studies to detect small but significant increases in QT interval measurements. In this study, we investigated effects of moxifloxacin on the hERG current in HEK-293 cells, electrocardiograms in conscious telemetered dogs, and repolarization parameters and arrhythmogenic potentials in the arterially perfused rabbit ventricular wedge model. Moxifloxacin inhibited the hERG current with an IC50 of 35.7 microM. In conscious telemetered dogs, moxifloxacin significantly prolonged QTc at 30 and 90 mg kg(-1), with mean serum Cmax of 8.52 and 22.3 microg ml(-1), respectively. In the wedge preparation, moxifloxacin produced a concentration-dependent prolongation of the action potential duration, QT interval, and the time between peak and end of the T wave, an indicator for transmural dispersion of repolarization. Phase 2 early after-depolarizations were observed in one of five experiments at 30 microM and five of five experiments at 100 microM. The arrhythmogenic potential was also concentration-dependent, and 100 microM ( approximately 18-fold above the typical unbound Cmax exposure in clinical usage) appeared to have a high risk of inducing torsade de pointes (TdP). Our data indicated a good correlation among the concentration-response relationships in the three preclinical models and with the available clinical data. The lack of TdP report by moxifloxacin in patients without other risk factors might be attributable to its well-behaved pharmacokinetic profile and other dose-limiting effects.

Action Potentials↗
PubMed2005

The study of Chinese medicinal herbal formula Shen San Fang in the treatment of experimental IgA nephropathy.

IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide, yet there is no effective or specific therapy. Shen San Fang (S3F) is a traditional Chinese herbal medicinal formula that has been used in China for many years to treat patients with hematuria. The aim of this study is to test the therapeutic value of S3F in an experimental model of IgAN. IgAN was induced in Lewis rats by continuous oral immunization with bovine gamma-globulin (BGG) in the drinking water for 8 weeks, followed by intravenous injection of 1 mg BGG daily for 3 successive days. The rats were randomly divided into four groups (five rats/group): control, control receiving S3F, induction of IgAN, and IgAN receiving S3E S3F decoction was fed to rats beginning week 4 from the first day of oral sensitization with BGG. The S3F treatment was continued until the rats were sacrificed or for a 4-week period. Hematuria, renal immunohistochemistry for IgA and transforming growth factor-beta 1 (TGF-beta1), renal histopathology, and renal content of TGF-beta1 were measured. Rats developing IgAN had marked hematuria, profound mesangial proliferation and mesangial expansion, intense and diffuse glomerular IgA deposition, increased glomerular TGF-beta1 expression, and raised renal TGF-beta1 levels. S3F treatment resulted in a significant reduction of hematuria, decreased mesangial IgA deposition, weaker immunostaining of TGF-beta1 in glomerulus, and a lower renal TGF-beta1 concentration. Our animal data suggests a therapeutic value for the Chinese medicinal formula S3F in experimental IgAN. This beneficial effect was due to reduced glomerular IgA deposition and TGF-beta1 expression. Our preliminary findings hold promise for future human therapy.

Animals↗
PubMed2005

Proteomics analysis of stage-specific proteins expressed in human squamous cell lung carcinoma tissues.

There is a growing interest in applying proteomics to gain insight into the mechanism of tumorigenesis, develop new markers for molecular diagnosis and accelerate drug development. In an attempt to find new stage-specific tumor markers, patients suffering from squamous cell lung carcinomas (SQCLC) at different pathologic stages have been selected to achieve differential protein expression patterns. Two-dimensional polyacrylamide gel electrophoresis (2-DE) profiles of human SQCLC and normal tissue were compared. Differential protein spots were identified with peptide mass fingerprinting (PMF) based on matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and database searching. A total of 63 unique proteins were identified in this experiment. Among them, peroxiredoxin 1 (PRDX1) expression level was significantly increased from stage I to III, and had a slight decrease at stage IV; whereas, a lasting decrease in the expression level of tropomyosins 3 (TPM3), was observed with the malignant progression from I stage to IV stage. These results provide further insight into malignant transformation in SQCLC and proteins may serve as new biomarkers for early diagnosis.

Biomarkers, Tumor↗