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1.  Mutations of Novel Influenza A(H10N8) Virus in Chicken Eggs and MDCK Cells 
Emerging Infectious Diseases  2014;20(9):1541-1543.
The recent emergence of human infection with influenza A(H10N8) virus is an urgent public health concern. Genomic analysis showed that the virus was conserved in chicken eggs but presented substantial adaptive mutations in MDCK cells. Our results provide additional evidence for the avian origin of this influenza virus.
doi:10.3201/eid2009.140257
PMCID: PMC4178415  PMID: 25148105
influenza A virus; mutation; genome; avian-origin; antiviral drug resistance; viruses; A(H10N8)
2.  Non-detection of Epstein-Barr virus and Human Papillomavirus in a region of high gastric cancer risk indicates a lack of a role for these viruses in gastric carcinomas 
Genetics and Molecular Biology  2013;36(2):183-184.
Gastric mucosa tissue was collected from patients with gastroduodenal diseases in a region of norrteastern China showing a high risk of gastric cancer incidence. The presence of EBV and HPV were assayed to investigate the relationship between gastric carcinomas and virus infection. Neither EBV nor HPV DNA was detected in tissue from the patients. The role of EBV and HPV in gastric cancer is not well understood and still needs to be clarified.
doi:10.1590/S1415-47572013005000018
PMCID: PMC3715283  PMID: 23885199
Human papillomavirus; Epstein-Barr virus; polymerase chain reaction; gastric carcinoma
3.  MicroRNA-26 governs profibrillatory inward-rectifier potassium current changes in atrial fibrillation 
The Journal of Clinical Investigation  2013;123(5):1939-1951.
Atrial fibrillation (AF) is a highly prevalent arrhythmia with pronounced morbidity and mortality. Inward-rectifier K+ current (IK1) is believed to be an important regulator of reentrant-spiral dynamics and a major component of AF-related electrical remodeling. MicroRNA-26 (miR-26) is predicted to target the gene encoding KIR2.1, KCNJ2. We found that miR-26 was downregulated in atrial samples from AF animals and patients and this downregulation was accompanied by upregulation of IK1/KIR2.1 protein. miR-26 overexpression suppressed expression of KCNJ2/KIR2.1. In contrast, miR-26 knockdown, inhibition, or binding-site mutation enhanced KCNJ2/KIR2.1 expression, establishing KCNJ2 as a miR-26 target. Knockdown of endogenous miR-26 promoted AF in mice, whereas adenovirus-mediated expression of miR-26 reduced AF vulnerability. Kcnj2-specific miR-masks eliminated miR-26–mediated reductions in Kcnj2, abolishing miR-26’s protective effects, while coinjection of a Kcnj2-specific miR-mimic prevented miR-26 knockdown-associated AF in mice. Nuclear factor of activated T cells (NFAT), a known actor in AF-associated remodeling, was found to negatively regulate miR-26 transcription. Our results demonstrate that miR-26 controls the expression of KCNJ2 and suggest that this downregulation may promote AF.
doi:10.1172/JCI62185
PMCID: PMC3635715  PMID: 23543060
4.  A continued saga of Boc5, the first non-peptidic glucagon-like peptide-1 receptor agonist with in vivo activities 
Acta Pharmacologica Sinica  2012;33(2):148-154.
Glucagon-like peptide-1 (GLP-1)-based therapy presents a promising option for treating type 2 diabetes. However, there are several limitations relative to the peptidic GLP-1 mimetics currently on the market or under development. This concern has led to a continued interest in the search for non-peptidic agonists for GLP-1 receptor (GLP-1R). Here, we briefly review the discovery, characterization and current status of a novel class of cyclobutane-derivative-based non-peptidic agonists for GLP-1R, including Boc5 and its newly discovered analogue WB4–24. Although the oral bioavailability of such compounds still poses great challenges, the progress made so far encourages us to identify a truly 'druggable' small molecule agonist for GLP-1R.
doi:10.1038/aps.2011.169
PMCID: PMC4010345  PMID: 22301855
type 2 diabetes; glucagon-like peptide-1; non-peptidic agonist; Boc5; G-protein coupled receptor
5.  MicroRNA expression profiling of mature ovarian teratomas 
Oncology Letters  2011;3(1):35-38.
MicroRNAs (miRNAs) are a class of endogenous, small, non-coding RNAs that regulate gene expression by targeting mRNAs and inhibiting expression via translation repression or RNA degradation. Emerging evidence indicates that miRNAs play a crucial role in the pathogenesis of human diseases, including tumor development. We profiled the miRNA expression between mature ovarian teratoma samples and matched normal tissues using miRNA microarrays, followed by validation with quantitative RT-PCR (qRT-PCR). The most highly expressed miRNAs in mature ovarian teratoma tissues were miRNA-520a-5p, miRNA-26b*, miRNA-421, miRNA-492 and miRNA-555, with a 1.3- to 2.6-fold change, whereas the least expressed miRNAs were miRNA-142-3p, let-7a, miRNA-19a, miRNA-34a, miRNA-620, miRNA-934, miRNA-657, miRNA-720, miRNA-22, miRNA-629 and miRNA-214, with a decreased level of 55–87% compared with normal tissues. The findings of the present study are the first to provide an altered miRNA profile for mature ovarian teratomas and differentially expressed miRNAs, which, if validated in future studies, may be essential in the pathogenesis of mature ovarian teratomas.
doi:10.3892/ol.2011.438
PMCID: PMC3362642  PMID: 22740852
microRNAs; mature ovarian teratomas; microarrays
6.  Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum 
BMC Genomics  2015;16(1):54.
Background
Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive.
Results
The transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. A total of 14305 splice junctions were discovered. Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions (IR, 9369), alternative 5’ splice sites (A5SS, 167), and alternative 3’ splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than those observed in the fungus Aspergillus oryzae using Illumina Solexa technology. This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum. Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms. Moreover, comparative transcriptomics determined that most enzymes related to glycolysis and the citrate cycle and glyoxylate cycle as well as a few carbohydrate-active enzymes are transcriptionally regulated.
Conclusions
This study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum, revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1251-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1251-8
PMCID: PMC4324775  PMID: 25652134
Alternative splicing; Fungi; RNA-Seq; Intron retention; Transcriptome; Trichoderma longibrachiatum
7.  Brazilin inhibits amyloid β-protein fibrillogenesis, remodels amyloid fibrils and reduces amyloid cytotoxicity 
Scientific Reports  2015;5:7992.
Soluble amyloid β-protein (Aβ) oligomers, the main neurotoxic species, are predominantly formed from monomers through a fibril-catalyzed secondary nucleation. Herein, we virtually screened an in-house library of natural compounds and discovered brazilin as a dual functional compound in both Aβ42 fibrillogenesis inhibition and mature fibril remodeling, leading to significant reduction in Aβ42 cytotoxicity. The potent inhibitory effect of brazilin was proven by an IC50 of 1.5 ± 0.3 μM, which was smaller than that of (−)-epigallocatechin gallate in Phase III clinical trials and about one order of magnitude smaller than those of curcumin and resveratrol. Most importantly, it was found that brazilin redirected Aβ42 monomers and its mature fibrils into unstructured Aβ aggregates with some β-sheet structures, which could prevent both the primary nucleation and the fibril-catalyzed secondary nucleation. Molecular simulations demonstrated that brazilin inhibited Aβ42 fibrillogenesis by directly binding to Aβ42 species via hydrophobic interactions and hydrogen bonding and remodeled mature fibrils by disrupting the intermolecular salt bridge Asp23-Lys28 via hydrogen bonding. Both experimental and computational studies revealed a different working mechanism of brazilin from that of known inhibitors. These findings indicate that brazilin is of great potential as a neuroprotective and therapeutic agent for Alzheimer's disease.
doi:10.1038/srep07992
PMCID: PMC4303869  PMID: 25613018
8.  Transcriptome analysis of food habit transition from carnivory to herbivory in a typical vertebrate herbivore, grass carp Ctenopharyngodon idella 
BMC Genomics  2015;16(1):15.
Background
Although feeding behavior and food habit are ecologically and economically important properties, little is known about formation and evolution of herbivory. Grass carp (Ctenopharyngodon idella) is an ecologically appealing model of vertebrate herbivore, widely cultivated in the world as edible fish or as biological control agents for aquatic weeds. Grass carp exhibits food habit transition from carnivory to herbivory during development. However, currently little is known about the genes regulating the unique food habit transition and the formation of herbivory, and how they could achieve higher growth rates on plant materials, which have a relatively poor nutritional quality.
Results
We showed that grass carp fed with duckweed (modeling fish after food habit transition) had significantly higher relative length of gut than fish before food habit transition or those fed with chironomid larvae (fish without transition). Using transcriptome sequencing, we identified 10,184 differentially expressed genes between grass carp before and after transition in brain, liver and gut. By eliminating genes potentially involved in development (via comparing fish with or without food habit transition), we identified changes in expression of genes involved in cell proliferation and differentiation, appetite control, circadian rhythm, and digestion and metabolism between fish before and after food habit transition. Up-regulation of GHRb, Egfr, Fgf, Fgfbp1, Insra, Irs2, Jak, STAT, PKC, PI3K expression in fish fed with duckweed, consistent with faster gut growth, could promote the food habit transition. Grass carp after food habit transition had increased appetite signal in brain. Altered expressions of Per, Cry, Clock, Bmal2, Pdp, Dec and Fbxl3 might reset circadian phase of fish after food habit transition. Expression of genes involved in digestion and metabolism were significantly different between fish before and after the transition.
Conclusions
We suggest that the food habit transition from carnivory to herbivory in grass carp might be due to enhanced gut growth, increased appetite, resetting of circadian phase and enhanced digestion and metabolism. We also found extensive alternative splicing and novel transcript accompanying food habit transition. These differences together might account for the food habit transition and the formation of herbivory in grass carp.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1217-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1217-x
PMCID: PMC4307112  PMID: 25608568
Food habit transition; Carnivory; Herbivory; Grass carp; Transcriptome sequencing
9.  Bilateral pleural effusion as an initial manifestation of multiple myeloma: A case report and literature review 
Multiple myeloma (MM) is a rare type of malignant hematological neoplasm. Although primarily involving the bone marrow, MM has a significant risk of metastasizing to other organs and may present with various clinical symptoms. However, the involvement of the respiratory system in the course of MM is extremely uncommon, particularly presenting with bilateral pleural effusion as the sole initial manifestation, which may result in a delayed diagnosis of MM. The present study describes the extremely rare case of a patient with MM presenting with myelomatous pleural effusion (MPE). The 78-year-old patient was admitted to the Department of Respiratory Medicine, Taizhou People’s Hospital (Taizhou, China) in March 2014, complaining of persistent dyspnea. Following admission, chest computed tomography scans revealed bilateral pleural effusion and a small amount of pericardial effusion, but no evident mass lesion. Thoracentesis was performed and the resulting pleural effusion was exudative and slightly bloody. In the following cytological examination, myeloma cells were identified in the pleural effusion. The patient was diagnosed definitively with MM following a histopathological study of the bone marrow aspiration. Therefore, the observations of the present case report may promote the consideration of MM in the differential diagnosis of patients with unexplained and refractory pleural effusion. The present study also reviewed the literature with regard to the association between MM and pleural effusion.
doi:10.3892/etm.2015.2184
PMCID: PMC4316953  PMID: 25667674
multiple myeloma; pleural effusion
10.  Sesquiterpene Lactones Inhibit Advanced Oxidation Protein Product-Induced MCP-1 Expression in Podocytes via an IKK/NF-κB-Dependent Mechanism 
Inflammation is a relevant factor in the pathogenesis of diabetes nephropathy (DN). Sesquiterpene lactones (SLs), originally isolated from Tanacetum parthenium, have been reported to exhibit anti-inflammatory effects but few studies have examined their effects on DN. To determine whether advanced oxidation protein products (AOPPs) can induce the expression of chemokine monocyte chemoattractant protein- (MCP-) 1 in cultured mouse podocytes and to explore the mechanisms of the potential renoprotection of SLs, we treated podocytes with AOPPs and SLs (parthenolide and its derivatives micheliolide, compound 1, and compound 2). MCP-1 mRNA and protein expression were tested using quantitative real-time PCR and ELISA, respectively, and the protein levels of IKKβ, phospho-IKKβ, IκBα, NF-κB p65, phospho-NF-κB p65, and tubulin were analyzed by Western blotting. AOPPs activated the expression of MCP-1 mRNA and protein in a dose- and time-dependent manner, activated IKKβ and NF-κB p65, and promoted IκBα degradation. The IKK/NF-κB inhibitor parthenolide decreased AOPP-induced MCP-1 expression. Pretreatment with SLs inhibited MCP-1 mRNA and protein expression and suppressed IKKβ and NF-κB p65 phosphorylation and IκBα degradation. Taken together, these findings provide a novel explanation for the anti-inflammatory effects of SLs that will ultimately benefit DN and potentially other inflammatory and immune renal diseases.
doi:10.1155/2015/934058
PMCID: PMC4309307  PMID: 25664142
11.  Impact of Water Content and Temperature on the Degradation of Cry1Ac Protein in Leaves and Buds of Bt Cotton in the Soil 
PLoS ONE  2015;10(1):e115240.
Determining the influence of soil environmental factors on degradation of Cry1Ac protein from Bt cotton residues is vital for assessing the ecological risks of this commercialized transgenic crop. In this study, the degradation of Cry1Ac protein in leaves and in buds of Bt cotton in soil was evaluated under different soil water content and temperature settings in the laboratory. An exponential model and a shift-log model were used to fit the degradation dynamics of Cry1Ac protein and estimate the DT50 and DT90 values. The results showed that Cry1Ac protein in the leaves and buds underwent rapid degradation in the early stage (before day 48), followed by a slow decline in the later stage under different soil water content and temperature. Cry1Ac protein degraded the most rapidly in the early stage at 35°C with 70% soil water holding capacity. The DT50 values were 12.29 d and 10.17 d and the DT90 values were 41.06 d and 33.96 d in the leaves and buds, respectively. Our findings indicated that the soil temperature was a major factor influencing the degradation of Cry1Ac protein from Bt cotton residues. Additionally, the relative higher temperature (25°C and 35°C) was found to be more conducive to degradation of Cry1Ac protein in the soil and the greater water content (100%WHC) retarded the process. These findings suggested that under appropriate soil temperature and water content, Cry1Ac protein from Bt cotton residues will not persist and accumulate in soil.
doi:10.1371/journal.pone.0115240
PMCID: PMC4283960  PMID: 25559638
12.  Integrated prevention of mother-to-child transmission for human immunodeficiency virus, syphilis and hepatitis B virus in China 
Abstract
Problem
China continues to face challenges in eliminating mother-to-child transmission of human immunodeficiency virus (HIV), syphilis and hepatitis B virus (HBV).
Approach
In 2010, a programme that integrated and standardized prevention of mother-to-child transmission (PMTCT) efforts for HIV, syphilis and HBV was implemented in 1156 counties. At participating antenatal care clinics, pregnant women were offered all three tests concurrently and free of charge. Further interventions such as free treatment, prophylaxis and testing for mothers and their children were provided for HIV and syphilis.
Local setting
China’s national PMTCT HIV programme started in 2003, at which time there were no national programmes for perinatal syphilis and HBV. In 2009, the rate of maternal-to-child transmission of HIV was 8.1% (57/702). Reported congenital syphilis was 60.8 per 100 000 live births. HBV infection was 7.2% of the overall population infected.
Relevant changes
Between 2010 and 2013 the number of pregnant women attending antenatal care clinics with integrated PMTCT services increased from 5.5 million to 13.1 million. In 2013, 12.7 million pregnant women were tested for HIV, 12.6 million for syphilis and 12.7 million for HBV. Mother-to-child transmission of HIV fell to 6.7% in 2013. Data on syphilis transmission are not yet available.
Lessons learnt
Integrated PMTCT services proved to be feasible and effective, and they are now part of the routine maternal and child health services provided to infected women. The services are provided through a collaboration between maternal and child health clinics, the national and local Centers for Disease Control and Prevention, and general hospitals.
doi:10.2471/BLT.14.139626
PMCID: PMC4271682  PMID: 25558108
13.  Acoustic Radiation Force Impulse Imaging for Non-Invasive Assessment of Renal Histopathology in Chronic Kidney Disease 
PLoS ONE  2014;9(12):e115051.
Objective
To investigate the stiffness values obtained by acoustic radiation force impulse (ARFI) quantification in assessing renal histological fibrosis of chronic kidney disease (CKD).
Methods
163 patients with CKD and 32 healthy volunteers were enrolled between June 2013 and April 2014. ARFI quantification, given as shear wave velocity (SWV), was performed to measure renal parenchyma stiffness. Diagnostic performance of ARFI imaging and conventional ultrasound (US) were compared with histologic scores at renal biopsy. Intra- and inter-observer reliability of SWV measurement was analyzed.
Results
In CKD patients, SWV measurements correlated significantly with pathological parameters (r = −0.422–−0.511, P<0.001), serum creatinine (r = −0.503, P<0.001), and glomerular filtration rate (r = 0.587, P<0.001). The mean SWV in kidneys with severely impaired (histologic score: ≥19 points) was significant lower than that mildly impaired (histologic score: ≤9 points), moderately impaired (histologic score: 10–18 points), and control groups (all P<0.001). Receiver operating characteristic (ROC) curves analyses indicated that the area under the ROC curve for the diagnosis of renal histological fibrosis using ARFI imaging was superior to these conventional US parameters. Using the optimal cut-off value of 2.65 m/s for the diagnosis of mildly impaired kidneys, 2.50 m/s for moderately impaired kidneys, and 2.33 m/s for severely impaired kidneys, the corresponding area under the ROC curves were 0.735, 0.744, and 0.895, respectively. Intra- and intre-observer agreement of SWV measurements were 0.709 (95% CI: 0.390–0.859, P<0.001) and 0.627 (95% CI: 0.233–0.818, P = 0.004), respectively.
Conclusions
ARFI may be an effective tool for evaluating renal histological fibrosis in CKD patients.
doi:10.1371/journal.pone.0115051
PMCID: PMC4278890  PMID: 25546304
14.  Changes in Birth Weight between 2002 and 2012 in Guangzhou, China 
PLoS ONE  2014;9(12):e115703.
Background
Recent surveillance data suggest that mean birth weight has begun to decline in several developed countries. The aim of this study is to examine the changes in birth weight among singleton live births from 2002 to 2012 in Guangzhou, one of the most rapidly developed cities in China.
Methods
We used data from the Guangzhou Perinatal Health Care and Delivery Surveillance System for 34108 and 54575 singleton live births with 28–41 weeks of gestation, who were born to local mothers, in 2002 and 2012, respectively. The trends in birth weight, small (SGA) and large (LGA) for gestational age and gestational length were explored in the overall population and gestational age subgroups.
Results
The mean birth weight decreased from 3162 g in 2002 to 3137 g in 2012 (crude mean difference, −25 g; 95% CI, −30 to −19). The adjusted change in mean birth weight appeared to be slight (−6 g from 2002 to 2012) after controlling for maternal age, gestational age, educational level, parity, newborn's gender and delivery mode. The percentages of SGA and LGA in 2012 were 0.6% and 1.5% lower than those in 2002, respectively. The mean gestational age dropped from 39.2 weeks in 2002 to 38.9 weeks in 2012. In the stratified analysis, we observed the changes in birth weight differed among gestational age groups. The mean birth weight decreased among very preterm births (28–31 weeks), while remained relatively stable among other gestational age subcategories.
Conclusions
Among local population in Guangzhou from 2002 to 2012, birth weight appeared to slightly decrease. The percentage of SGA and LGA also simultaneously dropped, indicating that newborns might gain a healthier weight for gestational age.
doi:10.1371/journal.pone.0115703
PMCID: PMC4274089  PMID: 25531295
15.  Dendritic cells derived from preeclampsia patients influence Th1/Th17 cell differentiation in vitro 
Immune regulation plays important but as-yet-unclear roles in the development of preeclampsia. This study explored potential contributions to immune regulation by dendritic cells (DCs) derived from peripheral blood of preeclampsia patients on the differentiation of Th1 and Th17 cells. Pregnant women with preeclampsia (n = 73) and healthy pregnant women (n = 80) were included in the study. Peripheral blood samples were collected from each participant, and DCs were derived from peripheral blood mononuclear cells in vitro. The phenotypes of DCs, identified by CD14, CD80, CD83, and CD86 expression, were detected by flow cytometry, and secretion of interleukin-23 (IL-23) into the culture medium by DCs was measured by ELISA. CD4 + T cells were separated by the magnetic beads and subjected to flow cytometry to determine their ability to differentiate to Th1 or Th17 cells. Compared with DCs derived from healthy pregnant women, DCs derived from preeclampsia patients expressed higher levels of CD83, CD80, and CD86 (P < 0.05). Additionally, secretion of IL-23 was higher in DCs derived from the preeclampsia group than from the control group (P < 0.001). DCs derived from preeclampsia patients also had a stronger ability to promote the differentiation of CD4 + T cells into Th1/Th17 cells when cultured with different cytokines (P < 0.01). Thus, altered phenotypes and functions of DCs may promote the abnormal balance of Th1 and Th17 in the development of preeclampsia.
PMCID: PMC4307482  PMID: 25664035
Preeclampsia; dendritic cell; Th1 cell; Th17 cell
16.  Huachansu injection inhibits metastasis of pancreatic cancer in mice model of human tumor xenograft 
Background
Huachansu injection (HCS) is a water-soluble preparation made from Bufo gargarizans’s skin, which has been widely used in clinics for tumor therapy in China. Though the anti-cancer activity of HCS has been verified through studies in vitro and in vivo, there is little research about its potential anti-metastasis effect. The primary objective of this study was to assess the effects of HCS on both the invasion of pancreatic cancer cells in vitro and on the progression of liver metastasis in vivo in this study.
Methods
HCS anti-metastasis potential was accessed using both assay of Cell viability and invasion in vitro, and then further Establishing xenograft model in nude mice. In the cell-based assay, mRNA and protein expression of MMP-2, MMP-9 and VEGF was detected by semi-quantitative RT-PCR and western blotting. In animal experiment, liver metastasis nodules and change of liver-body ratio was observed. Meanwhile, correlation of the CA19-9 and CEA content in serum with the progression of liver metastasis was analyzed.
Result
We observed that HCS prevented the invasion of cancer cells, with inhibiting the expressions of MMP-2 and MMP-9, and reduced not only the number of metastasis nodules but the ratio of liver-body weight as well. Furthermore, HCS decreased the expression of MMP-2, MMP-9 and VEGF in liver metastasis, while also reducing CA19-9 contents in serum. In addition, correlation analysis indicated that the level of CA19-9 in serum was closely related to the number of liver metastasis nodules.
Conclusion
Our experimental results suggest that HCS has some anti-metastasis potential to suppress the growth of liver metastasis by decreasing the expression of MMP-2 and MMP-9 as well as VEGF.
Electronic supplementary material
The online version of this article (doi:10.1186/1472-6882-14-483) contains supplementary material, which is available to authorized users.
doi:10.1186/1472-6882-14-483
PMCID: PMC4320457  PMID: 25496480
Huachansu; Pancreatic cancer; Liver metastasis; VEGF; MMPs; CA19-9
17.  Copy number variation analysis based on AluScan sequences 
Background
AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing.
Results
In this study, an AluScanCNV package has been assembled for efficient CNV calling from AluScan sequencing data employing a Geary-Hinkley transformation (GHT) of read-depth ratios between either paired test-control samples, or between test samples and a reference template constructed from reference samples, to call the localized CNVs, followed by use of a GISTIC-like algorithm to identify recurrent CNVs and circular binary segmentation (CBS) to reveal large extended CNVs. To evaluate the utility of CNVs called from AluScan data, the AluScans from 23 non-cancer and 38 cancer genomes were analyzed in this study. The glioma samples analyzed yielded the familiar extended copy-number losses on chromosomes 1p and 9. Also, the recurrent somatic CNVs identified from liver cancer samples were similar to those reported for liver cancer WGS with respect to a striking enrichment of copy-number gains in chromosomes 1q and 8q. When localized or recurrent CNV-features capable of distinguishing between liver and non-liver cancer samples were selected by correlation-based machine learning, a highly accurate separation of the liver and non-liver cancer classes was attained.
Conclusions
The results obtained from non-cancer and cancerous tissues indicated that the AluScanCNV package can be employed to call localized, recurrent and extended CNVs from AluScan sequences. Moreover, both the localized and recurrent CNVs identified by this method could be subjected to machine-learning selection to yield distinguishing CNV-features that were capable of separating between liver cancers and other types of cancers. Since the method is applicable to any human DNA sample with or without the availability of a paired control, it can also be employed to analyze the constitutional CNVs of individuals.
Electronic supplementary material
The online version of this article (doi:10.1186/s13336-014-0015-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s13336-014-0015-z
PMCID: PMC4273479  PMID: 25558350
AluScan sequencing; CNV calling; Cancer classification; Machine learning
18.  A Snail1/Notch1 Signaling Axis Controls Embryonic Vascular Development 
Nature communications  2014;5:3998.
Notch1-Delta-like 4 (Dll4) signaling controls vascular development by regulating endothelial cell (EC) targets that modulate vessel wall remodeling and arterial-venous specification. The molecular effectors that modulate Notch signaling during vascular development remain largely undefined. Here we demonstrate that the transcriptional repressor, Snail1, acts as a VEGF-induced regulator of Notch1 signaling and Dll4 expression. EC-specific Snail1 loss-of-function conditional knockout mice die in utero with defects in vessel wall remodeling in association with losses in mural cell investment and disruptions in arterial-venous specification. Snail1 loss-of-function conditional knockout embryos further display up-regulated Notch1 signaling and Dll4 expression that is partially reversed by inhibiting Ɣ-secretase activity in vivo with Dll4 identified as a direct target of Snail1-mediated transcriptional repression. These results document a Snail1-Dll4/Notch1 axis that controls embryonic vascular development.
doi:10.1038/ncomms4998
PMCID: PMC4052376  PMID: 24894949
20.  Radiofrequency Ablation Before Intratumoral Injection of 131I-chTNT Improves the Tumor-to-Normal Tissue Ratio in Solid VX2 Tumor 
Abstract
Purpose
This study was aimed to investigate whether the tumor necrosis induced by radiofrequency ablation (RFA) can improve the ratio of tumor-to-normal tissue (T/NT) after intratumoral injection of 131I-chTNT.
Materials and Method
Eighteen New Zealand rabbits bearing VX2 tumor on the thigh were randomly divided into two treatment groups (control group: intratumoral injection of 131I-chTNT alone; RFA group: RFA + intratumoral injection of 131I-chTNT 3 days after RFA) and each group was further divided into three subgroups I, II, and III (1–2 cm, 2–3 cm, and 3–4 cm in maximum diameter, respectively), by the tumor size. SPECT was performed to evaluate the T/NT on days 1, 8, and 15 after 131I-chTNT injection.
Results
After treatment, all rabbits underwent the SPECT whole-body scan and the T/NT was analyzed. The results showed that T/NT in the RFA group (55.45±41.83) was significantly higher compared with the control group (7.23±5.61) (F=18.89, p=0.001). Meanwhile, a linear ascending trend was found for T/NT in the RFA group along with the follow-up time (r=0.47, p=0.01). The tumor size or the dose of 131I-TNT injection had no significant effect on the variation of T/NT in both groups (p>0.05).
Conclusion
RFA before intratumoral injection of 131I-chTNT can dramatically improve T/NT, demonstrating the potential application of this combination therapy.
doi:10.1089/cbr.2012.1418
PMCID: PMC3833304  PMID: 23964639
radioimmunotherapy; radiofrequency ablation; ratio of tumor to normal tissue; tumor necrosis therapy
21.  Hepatitis C Virus NS5A Hijacks ARFGAP1 To Maintain a Phosphatidylinositol 4-Phosphate-Enriched Microenvironment 
Journal of Virology  2014;88(11):5956-5966.
ABSTRACT
Phosphatidylinositol 4-phosphate (PI4P) is well known to be upregulated during hepatitis C virus (HCV) replication. The role of PI4 kinases in HCV has been extensively investigated. Whether the PI4P phosphatase Sac1 is altered by HCV remains unclear. Here, we identified ARFGAP1 to be a novel host factor for HCV replication. We further show that Sac1 interacts with ARFGAP1 and inhibits HCV replication. The elevation of PI4P induced by HCV NS5A is abrogated when the coatomer protein I (COPI) pathway is inhibited. We also found an interaction between NS5A and ARFGAP1. Furthermore, we identified a conserved cluster of positively charged amino acids in NS5A critical for interaction between NS5A and ARFGAP1, induction of PI4P, and HCV replication. Our data demonstrate that ARFGAP1 is a host factor for HCV RNA replication. ARFGAP1 is hijacked by HCV NS5A to remove COPI cargo Sac1 from the site of HCV replication to maintain high levels of PI4P. Our findings provide an additional mechanism by which HCV enhances formation of a PI4P-rich environment.
IMPORTANCE PI4P is enriched in the replication area of HCV; however, whether PI4P phosphatase Sac1 is subverted by HCV is not established. The detailed mechanism of how COPI contributes to viral replication remains unknown, though COPI components were hijacked by HCV. We demonstrate that ARFGAP1 is hijacked by HCV NS5A to remove COPI cargo Sac1 from the HCV replication area to maintain high-level PI4P generated by NS5A. Furthermore, we identify a conserved cluster of positively charged amino acids in NS5A, which are critical for interaction between NS5A and ARFGAP1, induction of PI4P, and HCV replication. This study will shed mechanistic insight on how other RNA viruses hijack COPI and Sac1.
doi:10.1128/JVI.03738-13
PMCID: PMC4093857  PMID: 24623438
22.  Comparison of the Release Profile and Pharmacokinetics of Intact and Fragmented Dexamethasone Intravitreal Implants in Rabbit Eyes 
Abstract
Purpose: Dexamethasone intravitreal implant (DEX implant, Ozurdex®; Allergan, Inc.) is used to treat noninfectious posterior uveitis and macular edema associated with retinal vein occlusion and diabetic retinopathy. Two recently published reports of DEX implant fragmentation shortly after injection have raised concerns about the potential for faster implant dissolution and elevated ocular dexamethasone concentrations. This study compared the in vivo release profile and pharmacokinetic behavior of intact and fragmented DEX implants.
Methods: DEX implant was surgically implanted as a single unit or fragmented into 3 pieces in the posterior segment of opposing eyes of 36 New Zealand white rabbits. The release of dexamethasone over time from 1-piece and 3-piece fragmented implants dissolved in solution in vitro was compared with that from the 1-piece and 3-piece fragmented implants placed in the rabbit eyes. In addition, dexamethasone concentrations in the vitreous and aqueous humors of each eye were measured at 3 h and days 1, 7, 14, 21, and 28. High-performance liquid chromatography and liquid chromatography–tandem mass spectrometry were used for assays.
Results: Dexamethasone release from the 1-piece and 3-piece DEX implants in vivo was not different and was consistent with the in vitro release pattern. Moreover, the concentration profile of dexamethasone in the vitreous and aqueous humors was similar for the 1-piece and 3-piece DEX implants at each time point measured.
Conclusions: DEX implant fragmentation neither accelerated its dissolution nor increased the dexamethasone concentration delivered at a given time. Accordingly, DEX implant fragmentation is unlikely to have clinically significant effects in patients.
doi:10.1089/jop.2014.0082
PMCID: PMC4259187  PMID: 25411827
23.  Adrenergic regulation of the rapid component of delayed rectifier K+ currents in guinea pig cardiomyocytes 
Journal of Thoracic Disease  2014;6(12):1778-1784.
Background
Guinea pig ventricular cardiomyocytes display the rapid component of the delayed rectifier potassium current (Ikr) that contributes to ventricular repolarization and promotes stress-induced arrhythmias. Adrenergic stimulation favors ventricular arrhythmogenesis but its effects on Ikr are poorly understood.
Methods
Adrenergic modulation of Ikr was studied in isolated guinea pig ventricular cardiomyocytes using whole-cell patch clamping.
Results
We found that the Ikr amplitude was reduced to 0.66±0.02 and 0.62±0.03 in response to 0.1 µM phenylephrine (PE), an α1AR agonist, and 10 µM isoproterenol (ISO), a βAR agonist, respectively. The effect of PE can be blocked by the selective α1A-adrenoceptor antagonist 5-methylurapidil, but not by the α1B-adrenoceptor antagonist chloroethylclonidine or α1D-adrenoceptor antagonist BMY7378. Additionally, the effect of ISO can be blocked by the β1-selective AR antagonist CGP-20712A, but not by the β2-selective AR antagonist ICI-118551. Although PE and ISO was continuously added to cells, ISO did not decrease the current to a greater extent when cells were first given PE. In addition, PE’s effect on Ikr was suppressed by β1AR stimulation.
Conclusions
Ikr can by regulated by both the α1 and β ARs system, and that in addition to direct regulation by each receptor system, crosstalk may exist between the two systems.
doi:10.3978/j.issn.2072-1439.2014.12.27
PMCID: PMC4283310  PMID: 25589973
Adrenergic receptors (ARs); potassium current; crosstalk; cardiomyocytes
24.  T-Cell Prolymphocytic Leukemia with Extensive Cardiovascular Infiltrate Leading to Multiple Myocardial Infarctions and Cardiac Death 
Texas Heart Institute Journal  2014;41(6):626-630.
Lymphocytic neoplasm involving the heart is not common and usually presents with pericardial effusion or focal myocardial infiltration. Myocardial infarctions due to leukemic infiltration of the coronary arteries are rarely reported. We present the case of a 52-year-old Guatemalan man with a one-year history of untreated T-cell prolymphocytic leukemia. He was admitted to our hospital for chemotherapy and evaluation of a pulmonary cavitary lesion by wedge resection. During sedation, the patient experienced acute respiratory failure and hypovolemic shock, from which he could not be resuscitated.
Autopsy revealed that leukemic cells extensively infiltrated the aorta, myocardium, and coronary arteries. The lumina of the 3 major coronary artery branches showed 70% to 95% stenosis, with multifocal remote myocardial infarctions. Tumor cells were also detected in the lungs and other organs. The acute cardiorespiratory insufficiency secondary to leukemia—particularly the extensive infiltration of the coronary arteries and myocardium, and the multiple myocardial infarctions—eventually resulted in cardiac death.
doi:10.14503/THIJ-13-3581
PMCID: PMC4251335  PMID: 25593528
Aorta; autopsy; coronary arteries; heart neoplasms/secondary/etiology; leukemia, lymphoid/pathology; leukemia, T-cell prolymphocytic; myocardial infarction
25.  Synchronous poorly-differentiated neuroendocrine carcinoma and gastrointestinal stromal tumor of the stomach: a case report with immunohistochemical and molecular genetic analyses of KIT and PDGFRA 
Although the stomach is the most common location for gastrointestinal stromal tumor (GIST) with co-primary tumors, the synchronous appearance of a poorly differentiated neuroendocrine carcinoma (NEC) and GIST in the stomach is extremely rare. To the best of our knowledge, this is the first case of gastric GIST coexisting with gastric NEC to be reported in the literature. The current study reports the case of a 71-year-old male with gastric poorly differentiated NEC and GIST discovered incidentally during surgical treatment of the NEC. Immunohistochemistry analysis showed that the NEC tumor cells were positive for CK (cytokeratin), CD57, synaptophysin, chromogranin, CD117 (KIT protein), Dog-1 (discovered on GIST-1 protein) and CD34. The synchronous GIST immunophenotype showed positivity for CD117, Dog-1 and CD34 (100%), whereas staining for CK, SMA, desmin and S100 was negative. Ki-67 labeling of proliferating cells was 90% in NEC and 1% in GIST. An accurate diagnosis was confirmed by immunohistochemical findings. Furthermore, genetic analysis using PCR direct sequencing identified no mutations in the KIT (exons 9, 11, 13 and 17) and PDGFRA (exons 12 and 18) genes. The patient developed lymph node metastases and underwent cisplatin-based chemotherapy after the operation. This is the first documented case of synchronous gastric GIST and NEC with the examination of protein expression and gene mutations in KIT and PDGFRA, which will help to further understand the etiology and pathogenesis of NEC coexisting with GIST in a gastric location.
PMCID: PMC4313951
Snchronous tumor; neuroendocrine; carcinoma; GIST; gastric

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