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1.  Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line 
BMC Genomics  2015;16(1):76.
Background
Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both expressed in B cells, and have been demonstrated to redundantly activate transcription of genes required for B cell differentiation and function. It was hypothesized that Spi-B and PU.1 occupy a similar set of regions within the genome of a B lymphoma cell line.
Results
To compare binding regions of Spi-B and PU.1, murine WEHI-279 lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) was performed. Analysis for high-stringency enriched genomic regions demonstrated that PU.1 occupied 4528 regions and Spi-B occupied 3360 regions. The majority of regions occupied by Spi-B were also occupied by PU.1. Regions bound by Spi-B and PU.1 were frequently located immediately upstream of genes associated with immune response and activation of B cells. Motif-finding revealed that both transcription factors were predominantly located at the ETS core domain (GGAA), however, other unique motifs were identified when examining regions associated with only one of the two factors. Motifs associated with unique PU.1 binding included POU2F2, while unique motifs in the Spi-B regions contained a combined ETS-IRF motif.
Conclusions
Our results suggest that complementary biological functions of PU.1 and Spi-B may be explained by their interaction with a similar set of regions in the genome of B cells. However, sites uniquely occupied by PU.1 or Spi-B provide insight into their unique functions.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1303-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1303-0
PMCID: PMC4334403
PU.1; Spi-B; ChIP-seq; Motif; B cell; Gene regulation
2.  Lesion discrimination with breath-hold hepatic diffusion-weighted imaging: A meta-analysis 
AIM: To investigate the diagnostic capability of breath-hold diffusion-weighted imaging (DWI) for differentiation between malignant and benign hepatic lesions.
METHODS: A total of 614 malignant liver lesions (132 hepatocellular carcinomas, 468 metastases and 14 intrahepatic cholangiocarcinomas) and 291 benign liver lesions (102 hemangiomas, 158 cysts, 24 focal nodular hyperplasia, 1 angiomyolipoma and 6 hepatic adenomas) were included from seven studies (eight sets of data).
RESULTS: The pooled sensitivity and specificity of breath-hold DWI were 0.93 [95% confidence interval (CI): 0.91-0.95] and 0.87 (95%CI: 0.83-0.91), respectively. The positive likelihood ratio and negative likelihood ratio were 7.28 (95%CI: 4.51-11.76) and 0.09 (95%CI: 0.05-0.17), respectively. The P value for χ2 heterogeneity for all pooled estimates was < 0.05. From the fitted summary receiver operating characteristic curve, the area under the curve and Q* index were 0.96 and 0.91, respectively. Publication bias was not present (t = 0.49, P = 0.64). The meta-regression analysis indicated that evaluated covariates including magnetic resonance imaging modality, echo time, mean age, maximum b factor, and number of b factors were not sources of heterogeneity (all P > 0.05).
CONCLUSION: Breath-hold DWI is useful for differentiating between malignant and benign hepatic lesions. The diffusion characteristics of benign lesions that mimic malignant ones have rarely been investigated.
doi:10.3748/wjg.v21.i5.1621
PMCID: PMC4316105  PMID: 25663782
Breath-hold imaging; Diffusion-weighted imaging; Hepatic tumor; Meta-analysis
3.  Early B-cell factor 3 (EBF3) is a novel tumor suppressor gene with promoter hypermethylation in pediatric acute myeloid leukemia 
Background
Pediatric acute myeloid leukemia (AML) comprises up to 20% of all childhood leukemia. Recent research shows that aberrant DNA methylation patterning may play a role in leukemogenesis. The epigenetic silencing of the EBF3 locus is very frequent in glioblastoma. However, the expression profiles and molecular function of EBF3 in pediatric AML is still unclear.
Methods
Twelve human acute leukemia cell lines, 105 pediatric AML samples and 30 normal bone marrow/idiopathic thrombocytopenic purpura (NBM/ITP) control samples were analyzed. Transcriptional level of EBF3 was evaluated by semi-quantitative and real-time PCR. EBF3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS). The molecular mechanism of EBF3 was investigated by apoptosis assays and PCR array analysis.
Results
EBF3 promoter was hypermethylated in 10/12 leukemia cell lines. Aberrant EBF3 methylation was observed in 42.9% (45/105) of the pediatric AML samples using MSP analysis, and the BGS results confirmed promoter methylation. EBF3 expression was decreased in the AML samples compared with control. Methylated samples revealed similar survival outcomes by Kaplan-Meier survival analysis. EBF3 overexpression significantly inhibited cell proliferation and increased apoptosis. Real-time PCR array analysis revealed 93 dysregulated genes possibly implicated in the apoptosis of EBF3-induced AML cells.
Conclusion
In this study, we firstly identified epigenetic inactivation of EBF3 in both AML cell lines and pediatric AML samples for the first time. Our findings also showed for the first time that transcriptional overexpression of EBF3 could inhibit proliferation and induce apoptosis in AML cells. We identified 93 dysregulated apoptosis-related genes in EBF3-overexpressing, including DCC, AIFM2 and DAPK1. Most of these genes have never been related with EBF3 over expression. These results may provide new insights into the molecular mechanism of EBF3-induced apoptosis; however, further research will be required to determine the underlying details.
Our findings suggest that EBF3 may act as a putative tumor suppressor gene in pediatric AML.
doi:10.1186/s13046-014-0118-1
PMCID: PMC4311429  PMID: 25609158
Early B-cell factor 3; Pediatric acute myeloid leukemia; Methylation; Tumor suppressor; Real-time PCR array
4.  siRNA induces gelsolin gene transcription activation in human esophageal cancer cell 
Scientific Reports  2015;5:7901.
Recent studies show that targeting gene promoter or 3′ terminal regions of mRNA with siRNA induces target gene transcription. However, the ability of exon-targeting siRNA to affect transcription has yet to be demonstrated. We designed and synthesized siRNA against various exons in the gelsolin gene (GSN) to knockdown GSN transcript in KYSE150 and KYSE450 cells. Surprisingly, we found that siGSN-2, targeting the GSN twelfth exon, induced GSN gene transcription detected by real time RT-PCR. An siGSN-2 co-precipitation assay was performed and H3 histone, previously shown to correlate with gene transcription, was detected in the siGSN-2 pull-down pellet. However, H3 histone was not detected in an siGSN-1-precipitated pellet, which resulted in GSN knockdown. In addition, siGSN-2 decreased stress fibers, lamellipodia and filopodia, demonstrating that siGSN-2 induced GSN transcription activation and exerted biological function. In conclusion, our finds reveal siRNA, which is derived from target gene exon, can form the complex with H3 histone to be involved in the regulation of gene expression.
doi:10.1038/srep07901
PMCID: PMC4298738  PMID: 25600697
5.  Application of Multiple-Locus Variable Number Tandem Repeat Analysis to Identify Outbreak-Associated Neisseria meningitides Serogroup C Sequence Type 4821 in China 
PLoS ONE  2015;10(1):e0116422.
Neisseria meningitidis (N. meningitidis) serogroup C sequence type (ST)-4821 caused an outbreak in 2010 in Shandong province of China. Twenty-one non-outbreak-associated strains were isolated, along with twenty-eight N. meningitides serogroup C ST-4821 isolates. Therefore, it’s essential to identify and clarify characterization of the real outbreak-associated strains with a rapid method during an outbreak investigation. In this study, multiple-locus variable number tandem repeat analysis (MLVA) was applied to analyze 84 N. meningitidis strains, among which 58 were recovered from two outbreaks and 26 were sporadic isolates. Three MLVA schemes with different combination of VNTR loci were tested, and two of them were suitable for isolates from China: scheme 2 with six loci was found to separate ST into finer resolution, and scheme 3 with five loci can be used to identify outbreak-associated isolates from the same outbreak that caused by N. meningitidis serogroup C ST-4821.
doi:10.1371/journal.pone.0116422
PMCID: PMC4300189  PMID: 25603352
6.  Detection of Herb-Symptom Associations from Traditional Chinese Medicine Clinical Data 
Background. Traditional Chinese medicine (TCM) is an individualized medicine by observing the symptoms and signs (symptoms in brief) of patients. We aim to extract the meaningful herb-symptom relationships from large scale TCM clinical data. Methods. To investigate the correlations between symptoms and herbs held for patients, we use four clinical data sets collected from TCM outpatient clinical settings and calculate the similarities between patient pairs in terms of the herb constituents of their prescriptions and their manifesting symptoms by cosine measure. To address the large-scale multiple testing problems for the detection of herb-symptom associations and the dependence between herbs involving similar efficacies, we propose a network-based correlation analysis (NetCorrA) method to detect the herb-symptom associations. Results. The results show that there are strong positive correlations between symptom similarity and herb similarity, which indicates that herb-symptom correspondence is a clinical principle adhered to by most TCM physicians. Furthermore, the NetCorrA method obtains meaningful herb-symptom associations and performs better than the chi-square correlation method by filtering the false positive associations. Conclusions. Symptoms play significant roles for the prescriptions of herb treatment. The herb-symptom correspondence principle indicates that clinical phenotypic targets (i.e., symptoms) of herbs exist and would be valuable for further investigations.
doi:10.1155/2015/270450
PMCID: PMC4305614  PMID: 25650023
7.  Gambogic Acid Induces Apoptosis in Imatinib-Resistant Chronic Myeloid Leukemia Cells via Inducing Proteasome Inhibition and Caspase-Dependent Bcr-Abl Downregulation 
Purpose
Chronic myelogenous leukemia (CML) is characterized by the constitutive activation of Bcr-Abl tyrosine kinase. Bcr-Abl-T315I is the predominant mutation that causes resistance to imatinib, cytotoxic drugs, and the second-generation tyrosine kinase inhibitors. The emergence of imatinib resistance in patients with CML leads to searching for novel approaches to the treatment of CML. Gambogic acid, a small molecule derived from Chinese herb gamboges, has been approved for phase II clinical trial for cancer therapy by the Chinese Food and Drug Administration (FDA). In this study, we investigated the effect of gambogic acid on cell survival or apoptosis in CML cells bearing Bcr-Abl-T315I or wild-type Bcr-Abl.
Experimental Design
CML cell lines (KBM5, KBM5-T315I, and K562), primary cells from patients with CML with clinical resistance to imatinib, and normal monocytes from healthy volunteers were treated with gambogic acid, imatinib, or their combination, followed by measuring the effects on cell growth, apoptosis, and signal pathways. The in vivo antitumor activity of gambogic acid and its combination with imatinib was also assessed with nude xenografts.
Results
Gambogic acid induced apoptosis and cell proliferation inhibition in CML cells and inhibited the growth of imatinib-resistant Bcr-Abl-T315I xenografts in nude mice. Our data suggest that GA-induced proteasome inhibition is required for caspase activation in both imatinib-resistant and -sensitive CML cells, and caspase activation is required for gambogic acid–induced Bcr-Abl downregulation and apoptotic cell death.
Conclusions
These findings suggest an alternative strategy to overcome imatinib resistance by enhancing Bcr-Abl downregulation with the medicinal compound gambogic acid, which may have great clinical significance in imatinib-resistant cancer therapy.
doi:10.1158/1078-0432.CCR-13-1063
PMCID: PMC3938960  PMID: 24334603
8.  Molecular Targeting of the Oncoprotein PLK1 in Pediatric Acute Myeloid Leukemia: RO3280, a Novel PLK1 Inhibitor, Induces Apoptosis in Leukemia Cells 
Polo-like kinase 1 (PLK1) is highly expressed in many cancers and therefore a biomarker of transformation and potential target for the development of cancer-specific small molecule drugs. RO3280 was recently identified as a novel PLK1 inhibitor; however its therapeutic effects in leukemia treatment are still unknown. We found that the PLK1 protein was highly expressed in leukemia cell lines as well as 73.3% (11/15) of pediatric acute myeloid leukemia (AML) samples. PLK1 mRNA expression was significantly higher in AML samples compared with control samples (82.95 ± 110.28 vs. 6.36 ± 6.35; p < 0.001). Kaplan-Meier survival analysis revealed that shorter survival time correlated with high tumor PLK1 expression (p = 0.002). The 50% inhibitory concentration (IC50) of RO3280 for acute leukemia cells was between 74 and 797 nM. The IC50 of RO3280 in primary acute lymphocytic leukemia (ALL) and AML cells was between 35.49 and 110.76 nM and 52.80 and 147.50 nM, respectively. RO3280 induced apoptosis and cell cycle disorder in leukemia cells. RO3280 treatment regulated several apoptosis-associated genes. The regulation of DCC, CDKN1A, BTK, and SOCS2 was verified by western blot. These results provide insights into the potential use of RO3280 for AML therapy; however, the underlying mechanisms remain to be determined.
doi:10.3390/ijms16011266
PMCID: PMC4307303  PMID: 25574601
RO3280; pediatric acute myeloid leukemia (AML); polo-like kinase 1 (PLK1); apoptosis; oncogene target
9.  Reader's Forum 
doi:10.4041/kjod.2015.45.1.1
PMCID: PMC4320312  PMID: 25667911
10.  Abnormal Expression of Serum Soluble E-Cadherin is Correlated with Clinicopathological Features and Prognosis of Breast Cancer 
Background
Increased amounts of soluble E-cadherin (E-cad) have been found in the serum in various cancers, but the role of serum soluble E-cad in the prognosis of breast cancer patients has not been explored in Asian populations.
Material/Method
Blood samples from 111 consecutive patients diagnosed with breast cancer and 55 healthy controls were investigated. Serum soluble E-cad expression levels were measured by enzyme-linked immunosorbent assay (ELISA) with an immunoassay kit according to the manufacturer’s directions. Kaplan-Meier analyses were used to evaluate the association between serum soluble E-cad expression level and survival. All statistical tests were 2-sided.
Results
The serum levels of soluble E-cad in breast cancer patients were significantly higher than those of the control group (2218.9±319.6 ng/ml vs. 742.8±91.7 ng/ml, p<0.001). Serum levels of soluble E-cad correlated significantly with TNM stage (P=0.007), tumor grade (P=0.03), and lymph node metastasis (P<0.001). Kaplan-Meier analysis with the log-rank test indicated that high serum levels of soluble E-cad had a significant impact on overall survival (55.4% vs. 81.4%; P=0.032) and disease-free survival (36.8% vs. 67.8%; P=0.002) in breast cancer. Multivariate analysis revealed that serum levels of soluble E-cad were independently associated with overall survival and disease-free survival in breast cancer patients.
Conclusions
Serum soluble E-cad level is an independent prognostic factor in Asian breast cancer patients.
doi:10.12659/MSM.892049
PMCID: PMC4280058  PMID: 25553984
Biological Markers; Breast Neoplasms; Cadherins; Prognosis
11.  Histone acetyltransferase inhibitor II induces apoptosis in glioma cell lines via the p53 signaling pathway 
Background
Histone acetyltransferase (HAT) inhibitors can inhibit proliferation and induce apoptosis in cancer cell lines. The novel cell-permeable p300/CREB-binding protein (CBP)-selective HAT inhibitor HATi II can reduce histone H3 acetylation and induce chromatin condensation in HeLa cells. Here, we examined the effects and mechanism of action of HATi II in glioma cell lines.
Methods
Cell viability was assessed using the CCK-8 assay. Cell cycle analysis was performed using flow cytometry. Apoptosis was evaluated using Annexin V staining and flow cytometry, Hoechst 33342 staining and the TUNEL assay. Expression and cleavage of caspase-3, caspase-9 and poly ADP-ribose polymerase (PARP) were assessed by Western blotting. Statistical analysis was performed using two-tailed Student’s t-tests. The gene expression profiles of U251 glioma cells treated with HATi II or DMSO were analyzed using the Arraystar Human 8 x 60 K LncRNA/mRNA expression array; data was analyzed using MEV (Multi Experiment View) cluster software. Datasets representing genes with altered expression profiles (≥2-fold) derived from the cluster analyses were subjected to gene ontology and pathway analysis.
Results
HATi II inhibited the proliferation of U251, U87, HS683 and SHG44 cells in a dose-dependent manner. HATi II induced cell cycle arrest at the G2/M phase, and induced significant levels of apoptosis, apoptotic body formation and DNA fragmentation in HATi II-treated U251 and SHG44 cells. HATi II induced cleavage of caspase-3, caspase-9 and PARP in U251 and SHG44 cells. In HATi II-treated U251 cells, 965 genes were upregulated, 984 genes were downregulated and 3492/33327 lncRNAs were differentially expressed. GO analysis showed the differentially expressed genes with known functions are involved in a variety of processes; alcoholism, p53 signaling pathway, cytokine-cytokine receptor interaction and transcriptional mis-regulation in cancer were the four most significant pathways. Upregulation of p53 signaling pathway-related genes in HATi II-treated cells was confirmed by quantitative RT-PCR and Western blotting.
Conclusions
HATi II inhibits proliferation and induces apoptosis via the caspase-dependent pathway in human glioma cell lines, possibly by activating the p53 signaling pathway. HATi II deserves further investigation as a novel treatment for glioma.
Electronic supplementary material
The online version of this article (doi:10.1186/s13046-014-0108-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13046-014-0108-3
PMCID: PMC4321714  PMID: 25523932
HATi II; Glioma; Apoptosis; LncRNA/mRNA; p53 signaling pathway
12.  Rab27b Is a Potential Predictor for Metastasis and Prognosis in Colorectal Cancer 
Objective. Rab27b is reported to correlate with cancer development and progression. However, the association between Rab27b expression and the clinical characteristics of colorectal cancer (CRC) is barely investigated. Methods. One-step quantitative reverse transcription-polymerase chain reaction (qPCR) test with 18 fresh-frozen CRC samples and immunohistochemistry (IHC) analysis in 113 CRC cases were performed to explore the relationship between Rab27b expression and the clinicopathological features of CRC. Cox regression and Kaplan-Meier survival analyses were executed to evaluate the prognosis of CRC. Results. The results demonstrated that the expression levels of Rab27b mRNA and protein were significantly higher in CRC tissues than that in matched noncancerous tissues (P < 0.05). Rab27b protein expression in CRC was statistically correlated with serum CEA level (P = 0.004), lymph node metastasis (P = 0.001), distant metastasis (P = 0.009), and TNM stage (P = 0.001). Cox multifactor analysis and Kaplan-Meier method suggested that higher Rab27b protein expression (P = 0.041) and tumor differentiation (P = 0.001) were significantly associated with the overall survival of CRC patients. Conclusions. The data indicated that higher expression of Rab27b was observed in CRC tissues and Rab27b may be identified as a useful predictor of metastasis and prognosis for CRC.
doi:10.1155/2014/913106
PMCID: PMC4279273  PMID: 25580113
13.  Two cases of paraneoplastic limbic encephalitis associated with small cell lung cancer and a literature review 
In the present study, two cases of paraneoplastic limbic encephalitis (PLE) associated with small cell lung cancer were reported. Using avidin-biotin immunoperoxidase methods, purified recombinant HuD western blotting and Euroline Neuronal Antigens Profile 2 immunoglobulin G western blotting, it was found that the well-characterized anti-Hu and anti-amphiphysin onconeuronal antibodies were present in the serum/cerebrospinal fluid of the patients. With a review of the literature, it was found that patients with PLE of Chinese Han nationality had two types of clinical manifestations, simple and complex, and that the lesions could also be divided into focal and scalable lesions. Furthermore, the clinical manifestations and lesion scopes were associated with certain types of cancer and antibodies. In addition, it was found that the prognosis for patients with PLE with autoantibodies targeting membrane antigens is improved compared with that for patients with PLE with autoantibodies targeting intracellular antigens, due to an increased sensitivity to immunomodulatory treatments and anti-cancer therapy.
doi:10.3892/etm.2014.2142
PMCID: PMC4280946  PMID: 25574194
paraneoplastic limbic encephalitis; anti-Hu antibodies; immunohistochemistry; western blotting
14.  Purification, Cloning, Characterization, and N-Glycosylation Analysis of a Novel β-Fructosidase from Aspergillus oryzae FS4 Synthesizing Levan- and Neolevan-Type Fructooligosaccharides 
PLoS ONE  2014;9(12):e114793.
β-Fructosidases are a widespread group of enzymes that catalyze the hydrolysis of terminal fructosyl units from various substrates. These enzymes also exhibit transglycosylation activity when they function with high concentrations of sucrose, which is used to synthesize fructooligosaccharides (FOS) in the food industry. A β-fructosidase (BfrA) with high transglycosylation activity was purified from Aspergillus oryzae FS4 as a monomeric glycoprotein. Compared with the most extensively studied Aspergillus spp. fructosidases that synthesize inulin-type β-(2-1)-linked FOS, BfrA has unique transfructosylating property of synthesizing levan- and neolevan-type β-(2-6)-linked FOS. The coding sequence (bfrAFS4, 1.86 kb) of BfrA was amplified and expressed in Escherichia coli and Pichia pastoris. Both native and recombinant proteins showed transfructosylation and hydrolyzation activities with broad substrate specificity. These proteins could hydrolyze the following linkages: Glc α-1, 2-β Fru; Glc α-1, 3-α Fru; and Glc α-1, 5-β Fru. Compared with the unglycosylated E. coli-expressed BfrA (E.BfrA), the N-glycosylated native (N.BfrA) and the P. pastoris-expressed BfrA (P.BfrA) were highly stable at a wide pH range (pH 4 to 11), and significantly more thermostable at temperatures up to 50°C with a maximum activity at 55°C. Using sucrose as substrate, the Km and kcat values for total activity were 37.19±5.28 mM and 1.0016±0.039×104 s−1 for N.BfrA. Moreover, 10 of 13 putative N-glycosylation sites were glycosylated on N.BfrA, and N-glycosylation was essential for enzyme thermal stability and optima activity. Thus, BfrA has demonstrated as a well-characterized A. oryzae fructosidase with unique transfructosylating capability of synthesizing levan- and neolevan-type FOS.
doi:10.1371/journal.pone.0114793
PMCID: PMC4264766  PMID: 25501957
15.  Left Atrial Myxoma with versus without Cerebral Embolism: Length of Symptoms, Morphologic Characteristics, and Outcomes 
Texas Heart Institute Journal  2014;41(6):592-595.
The aim of this study was to evaluate the embolic sequelae of left atrial myxomas and their influence on diagnosis, treatment, and prognosis.
Seventy-eight patients were retrospectively investigated. According to their symptoms and neurologic-imaging findings, these patients were classified into 2 groups: embolism (15 patients, 19%) and nonembolism (63 patients, 81%). The time from the first onset of symptoms to diagnosis (that is, the duration of symptoms) was significantly longer in the embolism group than in the nonembolism group (105 ± 190 vs 23 ± 18 d; P <0.01). The myxomas were divided into 2 types on the basis of clinicopathologic findings: type 1, with an irregular or villous surface and a soft consistency, and type 2, with a smooth surface and a compact consistency. There were 42 patients with type 1 myxoma and 36 with type 2. Type 1 myxoma was more frequently found in the embolism group (12 patients, 29%) than was type 2 myxoma (3 patients, 8%). The difference was significant (P=0.04). There were 2 perioperative deaths in the nonembolism group. No recurrence of cardiac myxoma or death was recorded in either group during follow-up. In the embolism group, neurologic symptoms were relieved by surgery, and no subsequent neurologic event was reported.
Because surgical resection is highly effective in left atrial myxoma, we should strive for early diagnosis in order to shorten the duration of symptoms and to avoid worse neurologic damage in patients in whom an embolic event is the initial manifestation.
doi:10.14503/THIJ-13-3862
PMCID: PMC4251328  PMID: 25593521
Cerebral infarction; heart neoplasms/complications; intracranial embolism/etiology; ischemic attack, transient; myxoma, left atrial/pathology; outcomes; retrospective studies
16.  Identification of Sumoylated Proteins in the Silkworm Bombyx mori 
Small ubiquitin-like modifier (SUMO) modification (SUMOylation) is an important and widely used reversible modification system in eukaryotic cells. It regulates various cell processes, including protein targeting, transcriptional regulation, signal transduction, and cell division. To understand its role in the model lepidoptera insect Bombyx mori, a recombinant baculovirus was constructed to express an enhanced green fluorescent protein (eGFP)-SUMO fusion protein along with ubiquitin carrier protein 9 of Bombyx mori (BmUBC9). SUMOylation substrates from Bombyx mori cells infected with this baculovirus were isolated by immunoprecipitation and identified by LC–ESI-MS/MS. A total of 68 candidate SUMOylated proteins were identified, of which 59 proteins were functionally categorized to gene ontology (GO) terms. Analysis of kyoto encyclopedia of genes and genomes (KEGG) pathways showed that 46 of the identified proteins were involved in 76 pathways that mainly play a role in metabolism, spliceosome and ribosome functions, and in RNA transport. Furthermore, SUMOylation of four candidates (polyubiquitin-C-like isoform X1, 3-hydroxyacyl-CoA dehydrogenase, cyclin-related protein FAM58A-like and GTP-binding nuclear protein Ran) were verified by co-immunoprecipitation in Drosophila schneide 2 cells. In addition, 74% of the identified proteins were predicted to have at least one SUMOylation site. The data presented here shed light on the crucial process of protein sumoylation in Bombyx mori.
doi:10.3390/ijms151222011
PMCID: PMC4284691  PMID: 25470021
SUMO; SUMOylation; Bombyx mori; LC–ESI-MS/MS; baculovirus
17.  Breakthrough cancer medicine and its impact on novel drug development in China: report of the US Chinese Anti-Cancer Association (USCACA) and Chinese Society of Clinical Oncology (CSCO) Joint Session at the 17th CSCO Annual Meeting 
Chinese Journal of Cancer  2014;33(12):620-624.
The US Chinese Anti-Cancer Association (USCACA) teamed up with Chinese Society of Clinical Oncology (CSCO) to host a joint session at the17th CSCO Annual Meeting on September 20th, 2014 in Xiamen, China. With a focus on breakthrough cancer medicines, the session featured innovative approaches to evaluate breakthrough agents and established a platform to interactively share successful experiences from case studies of 6 novel agents from both the United States and China. The goal of the session is to inspire scientific and practical considerations for clinical trial design and strategy to expedite cancer drug development in China. A panel discussion further provided in-depth advice on advancing both early and full development of novel cancer medicines in China.
doi:10.5732/cjc.014.10246
PMCID: PMC4308658  PMID: 25418191
Breakthrough; clinical trial; cancer medicine
18.  Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway 
Nature Communications  2014;5:5372.
Plant oxylipins are derived from unsaturated fatty acids and play roles in plant growth and development as well as defence. Although recent studies have revealed that fatty acid metabolism is involved in systemic acquired resistance, the precise function of oxylipins in plant defence remains unknown. Here we report a cotton P450 gene SILENCE-INDUCED STEM NECROSIS (SSN), RNAi suppression of which causes a lesion mimic phenotype. SSN is also involved in jasmonate metabolism and the response to wounding. Fatty acid and oxylipin metabolite analysis showed that SSN overexpression causes hyperaccumulation of hydroxide and ketodiene fatty acids and reduced levels of 18:2 fatty acids, whereas silencing causes an imbalance in LOX (lipoxygenase) expression and excessive hydroperoxide fatty acid accumulation. We also show that an unknown oxylipin-derived factor is a putative mobile signal required for systemic cell death and hypothesize that SSN acts as a valve to regulate HR on pathogen infection.
Oxylipin signalling is known to play important roles in plant growth, development and defence against pathogens. Here Sun et al. identify a novel cytochrome P450 in cotton and show that its suppression leads to activation of plant defence responses and alteration of oxylipin metabolism.
doi:10.1038/ncomms6372
PMCID: PMC4241986  PMID: 25371113
19.  Computed tomography-guided cutting needle pleural biopsy: Accuracy and complications 
In cases of pleural lesion, tissue samples can be obtained through thoracoscopy or closed needle biopsy for histopathological analysis. Cutting needle biopsy is a relatively recent addition to these techniques. The aim of this study was to evaluate the diagnostic accuracy and safety of computed tomography-guided cutting needle pleural biopsy (CT-CNPB), as well as the associated complications, in patients with pleural lesion. This study was a retrospective analysis of 92 percutaneous CT-CNPBs on 90 patients between March 2008 and May 2013. For group comparisons, χ2 tests were used to detect the risk factors for diagnostic accuracy (false-negative rate). Of the 92 CT-CNPBs, malignant lesions were diagnosed in 55 cases (mesothelioma in 12, metastatic pleural disease in 36, synoviosarcoma in one, indeterminate-origin disease in one and false-negative lesion in five) and benign pleural disease was diagnosed in 37 cases (inflammation in 15, tuberculosis in 10, granuloma in three, solitary fibrous tumor in two, hematoma in one, fungus in one and indeterminate-origin disease in five). The sensitivity of diagnostic malignant lesion was 90.9%, and the specificity and positive and negative predictive values were 100, 100 and 88.1%, respectively. The overall diagnostic accuracy was 94.6%. A specific diagnosis was achieved in 89.1% of malignant lesions and 86.4% of benign lesions. Univariate analysis of the risk factors affecting accuracy (false-negative rate) did not reveal any significant differences (all P>0.05). The complication rates were 6.5% for pneumothorax, 8.7% for hemorrhage and 1.1% for hemothorax. In conclusion, CT-CNPB is a safe and accurate diagnostic technique that can be recommended as the primary method of diagnosis in patients with pleural thickening or lesions observed by CT scan.
doi:10.3892/etm.2014.2078
PMCID: PMC4247294  PMID: 25452813
pleural biopsy; pleural disease; cutting needle; computed tomography-guided
20.  Expression of the p53 Target Wig-1 Is Associated with HPV Status and Patient Survival in Cervical Carcinoma 
PLoS ONE  2014;9(11):e111125.
The p53 target gene WIG-1 (ZMAT3) is located in chromosomal region 3q26, that is frequently amplified in human tumors, including cervical cancer. We have examined the status of WIG-1 and the encoded Wig-1 protein in cervical carcinoma cell lines and tumor tissue samples. Our analysis of eight cervical cancer lines (Ca Ski, ME-180, MS751, SiHa, SW756, C-4I, C-33A, and HT-3) by spectral karyotype, comparative genomic hybridization and Southern blotting revealed WIG-1 is not the primary target for chromosome 3 gains. However, WIG-1/Wig-1 were readily expressed and WIG-1 mRNA expression was higher in the two HPV-negative cervical cell lines (C33-A, HT-3) than in HPV-positive lines. We then assessed Wig-1 expression by immunohistochemistry in 38 cervical tumor samples. We found higher nuclear Wig-1 expression levels in HPV-negative compared to HPV positive cases (p = 0.002) and in adenocarcinomas as compared to squamous cell lesions (p<0.0001). Cases with moderate nuclear Wig-1 staining and positive cytoplasmic Wig-1 staining showed longer survival than patients with strong nuclear and negative cytoplasmic staining (p = 0.042). Nuclear Wig-1 expression levels were positively associated with age at diagnosis (p = 0.023) and histologic grade (p = 0.034). These results are consistent with a growth-promoting and/or anti-cell death function of nuclear Wig-1 and suggest that Wig-1 expression can serve as a prognostic marker in cervical carcinoma.
doi:10.1371/journal.pone.0111125
PMCID: PMC4224373  PMID: 25379706
21.  Genetic Diversity of Neisseria meningitidis Serogroup C ST-4821 in China Based on Multiple-Locus Variable Number Tandem Repeat Analysis 
PLoS ONE  2014;9(11):e111866.
Neisseria meningitidis sequence type (ST)-4821 was first reported in China in 2003, and a new hyper-virulent lineage has been designated as the ST-4821 complex. A large number of N. meningitidis ST-4821 strains have been identified in China since 2003; however, the microevolution characteristics of this complex are unclear. Different combinations of variable number of tandem repeats (VNTR) loci were used in multiple-locus VNTR analysis (MLVA) to analyze 118 N. meningitidis serogroup C ST-4821 strains isolated from seventeen provinces between 2003 and 2012. Additionally, MLVA with five VNTR loci was performed due to its high discriminatory power. One hundred and eighteen isolates were found to comprise 112 subtypes based on MLVA, and 16 outbreak-associated strains were clustered into one group. These data indicate a high level of diversity for N. meningitidis ST-4821 due to microevolution in the last decade. In addition, the results revealed high similarity between isolates from the same geographic origins, which is helpful when monitoring the spread of N. meningitidis serogroup C ST-4821 and will provide valuable information for the control and prevention of bacterial meningitis in China.
doi:10.1371/journal.pone.0111866
PMCID: PMC4222954  PMID: 25375168
22.  Accuracy of Pupil Assessment for the Detection of Glaucoma 
Ophthalmology  2013;120(11):10.1016/j.ophtha.2013.04.012.
Objective
To assess the accuracy of using pupillary light reflex (PLR) in detecting glaucoma.
Clinical Relevance
Glaucoma is a specific disease of the optic nerve and is often more severe in 1 eye. When large enough, this asymmetry in disease severity can cause a relative afferent pupillary defect (RAPD). Better detection of RAPDs may be one way to identify persons with glaucoma.
Methods
We searched Medline and Embase through June 2012 and searched bibliographies for relevant studies for additional references. Two authors independently reviewed all articles and selected studies that assessed PLRs in patients with glaucoma. We analyzed data using mixed-effect bivariate summary receiver operating characteristic meta-analysis models.
Results
A total of 30 studies were included in this review. An RAPD was observed in 9% to 82% of patients with glaucoma. Eleven studies with a total of 7271 participants were included in the analysis, and the pooled estimate corresponded to a sensitivity of 0.63 (95% confidence interval [CI], 0.43–0.80) and a specificity of 0.93 (95% CI, 0.85–0.97). After excluding 2 studies that used the swinging flashlight test, the sensitivity increased to 0.74 (95% CI, 0.59–0.85) with a specificity of 0.85 (95% CI, 0.77–0.90). Study designs and different pupil measurement techniques explained part of the heterogeneity between studies.
Conclusions
Patients with glaucoma frequently have an abnormal PLR and comparing the responses between the 2 eyes can in part distinguish between those with glaucoma and those without the disease. Newer instruments and analytic approaches to assess pupil function may improve the performance of pupil screening.
doi:10.1016/j.ophtha.2013.04.012
PMCID: PMC3818414  PMID: 23809274
23.  Multiple NUCLEAR FACTOR Y Transcription Factors Respond to Abiotic Stress in Brassica napus L 
PLoS ONE  2014;9(10):e111354.
Members of the plant NUCLEAR FACTOR Y (NF-Y) family are composed of the NF-YA, NF-YB, and NF-YC subunits. In Brassica napus (canola), each of these subunits forms a multimember subfamily. Plant NF-Ys were reported to be involved in several abiotic stresses. In this study, we demonstrated that multiple members of thirty three BnNF-Ys responded rapidly to salinity, drought, or ABA treatments. Transcripts of five BnNF-YAs, seven BnNF-YBs, and two BnNF-YCs were up-regulated by salinity stress, whereas the expression of thirteen BnNF-YAs, ten BnNF-YBs, and four BnNF-YCs were induced by drought stress. Under NaCl treatments, the expression of one BnNF-YA10 and four NF-YBs (BnNF-YB3, BnNF-YB7, BnNF-YB10, and BnNF-YB14) were greatly increased. Under PEG treatments, the expression levels of four NF-YAs (BnNF-YA9, BnNF-YA10, BnNF-YA11, and BnNF-YA12) and five NF-YBs (BnNF-YB1, BnNF-YB8, BnNF-YB10, BnNF-YB13, and BnNF-YB14) were greatly induced. The expression profiles of 20 of the 27 salinity- or drought-induced BnNF-Ys were also affected by ABA treatment. The expression levels of six NF-YAs (BnNF-YA1, BnNF-YA7, BnNF-YA8, BnNF-YA9, BnNF-YA10, and BnNF-YA12) and seven BnNF-YB members (BnNF-YB2, BnNF-YB3, BnNF-YB7, BnNF-YB10, BnNF-YB11, BnNF-YB13, and BnNF-YB14) and two NF-YC members (BnNF-YC2 and BnNF-YC3) were greatly up-regulated by ABA treatments. Only a few BnNF-Ys were inhibited by the above three treatments. Several NF-Y subfamily members exhibited collinear expression patterns. The promoters of all stress-responsive BnNF-Ys harbored at least two types of stress-related cis-elements, such as ABRE, DRE, MYB, or MYC. The cis-element organization of BnNF-Ys was similar to that of Arabidopsis thaliana, and the promoter regions exhibited higher levels of nucleotide sequence identity with Brassica rapa than with Brassica oleracea. This work represents an entry point for investigating the roles of canola NF-Y proteins during abiotic stress responses and provides insight into the genetic evolution of Brassica NF-Ys.
doi:10.1371/journal.pone.0111354
PMCID: PMC4214726  PMID: 25356551
24.  Application of Prussian blue staining in the diagnosis of ocular siderosis 
AIM
To explore the value of Prussian blue staining in the diagnosis of ocular siderosis.
METHODS
Between January 2012 and January 2013, the Prussian blue stain used in anterior lens capsule and vitreous liquid after centrifugation from patients with definitive diagnosis and suspicious diagnosed of ocular siderosis. At the same time, give a negative control.
RESULTS
Anterior lens capsule membrane and liquid of vitreous cavity from patients with definitive diagnosis and suspicious diagnosed of ocular siderosis revealed ferric ions that stained positively with Prussian blue. In the control group, there is no positive reaction.
CONCLUSION
Prussian blue staining in the diagnosis of ocular siderosis has a very significant worth, suspected cases can be definitive diagnosed.
doi:10.3980/j.issn.2222-3959.2014.05.09
PMCID: PMC4206882  PMID: 25349794
intraocular foreign bodies; ocular siderosis; Prussian blue staining
25.  Zinc finger protein 382 is downregulated by promoter hypermethylation in pediatric acute myeloid leukemia patients 
Acute myeloid leukemia (AML) is the second-most common form of leukemia in children. Aberrant DNA methylation patterns are characteristic of AML. Zinc finger protein 382 (ZNF382) has been suggested to be a tumor suppressor gene possibly regulated by promoter hypermethylation in various types of human cancer. However, ZNF382 expression and methylation status in pediatric AML is unknown. In the present study, ZNF382 transcription levels were evaluated by quantitative reverse-transcription PCR. Methylation status was investigated by methylation-specific (MSP) PCR and bisulfate genomic sequencing (BGS). The prognostic significance of ZNF382 expression and promoter methylation was assessed in 105 cases of pediatric AML. The array data suggested that the ZNF382 promoter was hypermethylated in the AML cases examined. MSP PCR and BGS analysis revealed that ZNF382 was hypermethylated in leukemia cell lines. Furthermore, treatment with 5-aza-2′-deoxycytidine (5-Aza) upregulated ZNF382 expression in the selected leukemia cell lines. The aberrant methylation of ZNF382 was observed in 10% (2/20) of the control samples compared with 26.7% (28/105) of the AML samples. ZNF382 expression was significantly decreased in the 105 AML patients compared with the controls. Patients with ZNF382 methylation showed lower ZNF382 transcript levels compared with patients exhibiting no methylation. There were no significant differences in clinical characteristics or cytogenetic analysis between the patients with or without ZNF382 methylation. ZNF382 methylation correlated with minimal residual disease (MRD). Kaplan-Meier survival analysis revealed similar survival times in the samples with ZNF382 methylation, and multivariate analysis revealed that ZNF382 methylation was not an independent prognostic factor in pediatric AML. The epigenetic inactivation of ZNF382 by promoter hypermethylation can be observed in AML cell lines and pediatric AML samples. Therefore, our study suggests that ZNF382 may be considered a putative tumor suppressor gene in pediatric AML. However, further studies focusing on the mechanisms responsible for ZNF382 downregulation in pediatric leukemia are required.
doi:10.3892/ijmm.2014.1966
PMCID: PMC4214337  PMID: 25319049
zinc finger protein 382; pediatric acute myeloid leukemia; methylation; tumor suppressor

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