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author:("Yu, jingning")
1.  Targeting the ERK pathway reduces liver metastasis of Smad4-inactivated colorectal cancer 
Cancer Biology & Therapy  2013;14(11):1059-1067.
Transforming growth factor β (TGF-β)/Smad signaling is involved in colorectal carcinoma (CRC) development and progression. The frequent loss of SMAD4 is associated with liver metastasis and poor prognosis of CRC, but the underlying mechanism remains elusive. This study aimed to elucidate the role of Smad-independent TGF-β signaling in CRC metastasis. Immunohistochemistry showed that Smad4 level was negatively correlated with TNM stage and phospho-ERK level in human CRCs and liver metastasis samples. Knockdown of Smad4 in CT26 and HCT116 cells activated ERK pathway, altered the expression of MMP2 and COX-2, promoted cell motility, migration, and invasion in vitro, enhanced metastasis, and shortened the survival of metastatic tumor-bearing mice. MEK inhibitor U0126 and GSK1120212 inhibited the motility, migration, and invasion of Smad4 knockdown cells, inhibited metastasis, and prolonged the survival of metastatic tumor-bearing mice. Furthermore, MEK inhibitor could reverse the changes of phospho-ERK, MMP2, and COX-2 levels. In conclusion, our results indicate that ERK pathway plays a key oncogenic role in CRC with SMAD4 inactivation mutations, and implicate ERK as a potential therapeutic target for CRC liver metastasis.
PMCID: PMC3925661  PMID: 24025354
ERK pathway; Smad4; TGF-β; colorectal cancer; metastasis
2.  Cystic lymphangioma of adrenal gland: a clinicopathological study of 3 cases and review of literature 
Cystic lymphangioma of the adrenal gland is a rare and benign lesion, most often found incidentally during abdominal imaging studies, abdominal surgery or at autopsy. We aimed to retrospectively review all adrenal lymphangioma cases at our hospital, further document their lymphatic origin by immunohistochemical staining and discuss the differential diagnosis with other cystic adrenal gland lesions. A total of 3 adrenal lymphangioma cases were identified. All three patients were men and adults at time of diagnosis aged 41 years, 43 years, and 66 years, respectively. All were incidentally identified during investigating for unrelated reasons, two of which were discovered by routine radiologic check-up while the last one was found during imaging detection of ureteral cancer. The average size of an adrenal lymphangioma lesion was 3.2 cm (range, 2.5-4.6 cm). Histologically, all three cases showed a typical multicystic architecture with dilated spaces lined by flattened, bland, simple lining. The cystic spaces occasionally contained proteinaceous material but lacked red blood cell content. On immunohistochemical stains, D2-40 cytoplasmic staining was positive in all three lesions, whereas AE1/AE3 was negative, thus, confirming their lymphatic nature.
PMCID: PMC4152068  PMID: 25197378
Adrenal gland; lymphangioma; adrenal cyst; cystic neoplasm; D2-40; differential diagnosis
3.  RNA-Seq analysis reveals that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in curled-cotyledons mutant of soybean [Glycine max (L.) Merr.] 
BMC Genomics  2014;15(1):510.
Soybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the genetic dissection of embryo patterning and seed development. However, the molecular mechanisms underlying soybean cotyledon development are largely unexplored.
In this study, we characterised a soybean curled-cotyledon (cco) mutant. Compared with wild-type (WT), anatomical analysis revealed that the cco cotyledons at the torpedo stage became more slender and grew outward. The entire embryos of cco mutant resembled the “tail of swallow”. In addition, cco seeds displayed reduced germination rate and gibberellic acid (GA3) level, whereas the abscisic acid (ABA) and auxin (IAA) levels were increased. RNA-seq identified 1,093 differentially expressed genes (DEGs) between WT and the cco mutant. The KEGG pathway analysis showed many DEGs were mapped to the hormone biosynthesis and signal transduction pathways. Consistent with assays of hormones in seeds, the results of RNA-seq indicated auxin and ABA biosynthesis and signal transduction in cco were more active than in WT, while an early step in GA biosynthesis was blocked, as well as conversion rate of inactive GAs to bioactive GAs in GA signaling. Furthermore, genes participated in other hormone biosynthesis and signalling pathways such as cytokinin (CK), ethylene (ET), brassinosteroid (BR), and jasmonate acid (JA) were also affected in the cco mutant.
Our data suggest that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in cco, and changes in these pathways may partially contribute to the cco mutant phenotype, suggesting the involvement of multiple hormones in the coordination of soybean cotyledon development.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-510) contains supplementary material, which is available to authorized users.
PMCID: PMC4078243  PMID: 24952381
Soybean; RNA-seq; Plant hormone; Curled-cotyledon; Mutant
4.  Disturbance of Copper Homeostasis Is a Mechanism for Homocysteine-Induced Vascular Endothelial Cell Injury 
PLoS ONE  2013;8(10):e76209.
Elevation of serum homocysteine (Hcy) levels is a risk factor for cardiovascular diseases. Previous studies suggested that Hcy interferes with copper (Cu) metabolism in vascular endothelial cells. The present study was undertaken to test the hypothesis that Hcy-induced disturbance of Cu homeostasis leads to endothelial cell injury. Exposure of human umbilical vein endothelial cells (HUVECs) to concentrations of Hcy at 0.01, 0.1 or 1 mM resulted in a concentration-dependent decrease in cell viability and an increase in necrotic cell death. Pretreatment of the cells with a final concentration of 5 µM Cu in cultures prevented the effects of Hcy. Hcy decreased intracellular Cu concentrations. HPLC-ICP-MS analysis revealed that Hcy caused alterations in the distribution of intracellular Cu; more Cu was redistributed to low molecular weight fractions. ESI-Q-TOF detected the formation of Cu-Hcy complexes. Hcy also decreased the protein levels of Cu chaperone COX17, which was accompanied by a decrease in the activity of cytochrome c oxidase (CCO) and a collapse of mitochondrial membrane potential. These effects of Hcy were all preventable by Cu pretreatment. The study thus demonstrated that Hcy disturbs Cu homeostasis and limits the availability of Cu to critical molecules such as COX17 and CCO, leading to mitochondrial dysfunction and endothelial cell injury.
PMCID: PMC3799909  PMID: 24204604
5.  Extranodal Rosai-Dorfman disease involving appendix and mesenteric nodes with a protracted course: report of a rare case lacking relationship to IgG4-related disease and review of the literature 
Rosai-Dorfman disease (RDD), also known as sinus histiocytosis with massive lymphadenopathy, is a rare disease of unknown etiology that typically presents as nodal disease in young children. However, it also can present in various extranodal sites and can be difficult to recognize if not considered in the differential diagnosis. Here, we report a case of appendix involvement by extranodal RDD, which occurred in a 69-year-old woman with a long duration of 12 years for intermittent right lower quadrant pain. The patient underwent a right hemicolectomy for a clinical diagnosis of appendiceal cancer. A mixed inflammatory infiltration of mature lymphocytes, plasma cells and histiocytes exhibiting emperipolesis were indentified. Other areas had storiform fibrosis and sclerosis admixed with numerous plasma cells. These histologic features combination with immunoreactivity for CD68 and S100 protein were indicative of a diagnosis of extranodal RDD. We discuss the clinical, pathologic findings as well as differential diagnoses and consideration of a possible relationship of this entity to IgG4-related lesion.
PMCID: PMC3816829  PMID: 24228122
Rosai-Dorfman disease; extranodal disease; gastrointestinal tract; appendix; IgG4-related disease; differential diagnosis
6.  Angiofibroma of soft tissue: clinicopathologic study of 2 cases of a recently characterized benign soft tissue tumor 
Angiofibroma of soft tissue is a very recently characterized, histologically distinctive benign mesenchymal neoplasm of unknown cellular origin composed of 2 principal components, the spindle cell component and very prominent stromal vasculatures. It usually occurs in middle-aged adults, with a female predominance. Herein, we describe the clinical and pathologic details of 2 other examples of this benign tumor. Both patients were middle-aged male and presented with a slow-growing, painless mass located in the deep-seated soft tissue of thigh and left posterior neck region, respectively. Grossly, both tumors were well-demarcated, partial encapsulated of a grayish-white color with firm consistence. Histologically, one case showed morphology otherwise identical to those have been described before, whereas the other case showed in areas being more cellular than most examples of this subtype tumor had, with the lesional cells frequently exhibiting short fascicular, vaguely storiform and occasionally swirling arrangements, which posed a challenging differential diagnosis. Immunostains performed on both tumors did not confirm any specific cell differentiation with lesional cells only reactive for vimentin and focally desmin and negative for all the other markers tested. This report serves to broaden the morphologic spectrum of angiofibroma of soft tumor. Awareness of this tumor is important to prevent misdiagnosis as other more aggressive soft tissue tumor.
PMCID: PMC3796244  PMID: 24133600
Soft tissue tumor; benign; angiofibroma; fibrovasular tumor; differential diagnosis
7.  Lymphoid papillary hyperplasia of the palatine tonsil: a Chinese case report 
Lymphoid papillary hyperplasia is a rare abnormality of the tonsils with a predilection for affecting young Asian girls. Herein, we report a 31-year-old Chinese woman presented as right lateral recurrent tonsillar hypertrophy with odynophagia and dysphagia over the past 5 years, worsening over a period of for half a year. Clinically, this lesion was similar to papillomatosis or lymphoid polyposis. However, histopathologic study showed a distinctive form of lymphoid hyperplasia with considerable distinct finger-like projections composed of many phyllodes which contained remarkable follicular lymphoid hyperplasia. This is the only Chinese case of lymphoid papillary hyperplasia of the palatine tonsils that has been reported in the most recent English literature so far. The importance of recognizing this disorder rests in the fact that in spite of the clinical features suggestive of both a benign and a malignant tumor, however, the process is a benign tumor-like proliferation, probably non-neoplastic, could easily be cured by tonsillectomy.
PMCID: PMC3759507  PMID: 24040465
Palatine tonsils; lymphoid hyperplasia; papilloma; lymphoid polyposis
8.  Hybrid Multilevel Sparse Reconstruction for a Whole Domain Bioluminescence Tomography Using Adaptive Finite Element 
Quantitative reconstruction of bioluminescent sources from boundary measurements is a challenging ill-posed inverse problem owing to the high degree of absorption and scattering of light through tissue. We present a hybrid multilevel reconstruction scheme by combining the ability of sparse regularization with the advantage of adaptive finite element method. In view of the characteristics of different discretization levels, two different inversion algorithms are employed on the initial coarse mesh and the succeeding ones to strike a balance between stability and efficiency. Numerical experiment results with a digital mouse model demonstrate that the proposed scheme can accurately localize and quantify source distribution while maintaining reconstruction stability and computational economy. The effectiveness of this hybrid reconstruction scheme is further confirmed with in vivo experiments.
PMCID: PMC3603587  PMID: 23533542
9.  Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays 
BMC Molecular Biology  2011;12:49.
The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP) and methylated DNA (MeDIP) represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription.
To allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease.
The high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation to pursue mechanistic, functional and diagnostic information at genes of interest in health and disease.
PMCID: PMC3247195  PMID: 22098709
10.  A Finite Element Mesh Aggregating Approach to Multiple-Source Reconstruction in Bioluminescence Tomography 
A finite element mesh aggregating approach is presented to reconstruct images of multiple internal bioluminescence sources. Rather than assuming independence between mesh nodes, the proposed reconstruction strategy exploits spatial structure of nodes and aggregation feature of density distribution on the finite element mesh to adaptively determine the number of sources and to improve the quality of reconstructed images. With the proposed strategy integrated in the regularization-based reconstruction process, reconstruction algorithms need no a priori knowledge of source number; even more importantly, they can automatically reconstruct multiple sources that differ greatly in density or power.
PMCID: PMC3227523  PMID: 22144980
11.  Inhibition of Human Vascular NADPH Oxidase by Apocynin Derived Oligophenols 
Bioorganic & medicinal chemistry  2009;17(14):5146-5152.
Enzymatic oxidation of apocynin, which may mimic in vivo metabolism, affords a large number of oligomers (apocynin oxidation products, AOP) that inhibit vascular NADPH oxidase. In vitro studies of NADPH oxidase activity were performed to identify active inhibitors, resulting in a trimer hydroxylated quinone (IIIHyQ) that inhibited NADPH oxidase with an IC50 = 31 nM. Apocynin itself possessed minimal inhibitory activity. NADPH oxidase is believed to be inhibited through prevention of the interaction between two NADPH oxidase subunits, p47phox and p22phox. To that end, while apocynin was unable to block the interaction of his-tagged p47phox with a surface immobilized biotinalyted p22phox peptide, the IIIHyQ product strongly interfered with this interaction (apparent IC50 = 1.6 μM). These results provide evidence that peroxidase-catalyzed AOP, which consist of oligomeric phenols and quinones, inhibit critical interactions that are involved in the assembly and activation of human vascular NADPH oxidase.
PMCID: PMC2723721  PMID: 19523836

Results 1-11 (11)