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1.  Transduction motif analysis of gastric cancer based on a human signaling network 
To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.
doi:10.1590/1414-431X20143527
PMCID: PMC4075304  PMID: 24838641
Significantly different motifs; Human signaling network; Gastric cancer
2.  Achieving optimum mechanical performance in metallic nanolayered Cu/X (X = Zr, Cr) micropillars 
Scientific Reports  2014;4:4205.
The selection and design of modern high-performance structural engineering materials such as nanostructured metallic multilayers (NMMs) is driven by optimizing combinations of mechanical properties and requirements for predictable and noncatastrophic failure in service. Here, the Cu/X (X = Zr, Cr) nanolayered micropillars with equal layer thickness (h) spanning from 5–125 nm are uniaxially compressed and it is found that these NMMs exhibit a maximum strain hardening capability and simultaneously display a transition from bulk-like to small-volume materials behavior associated with the strength at a critical intrinsic size h ~ 20 nm. We develop a deformation mode-map to bridge the gap between the interface characteristics of NMMs and their failure phenomena, which, as shrinking the intrinsic size, transit from localized interface debonding/extrusion to interface shearing. Our findings demonstrate that the optimum robust performance can be achieved in NMMs and provide guidance for their microstructure sensitive design for performance optimization.
doi:10.1038/srep04205
PMCID: PMC3966053  PMID: 24667702
4.  Microstructural percolation assisted breakthrough of trade-off between strength and ductility in CuZr-based metallic glass composites 
Scientific Reports  2014;4:4167.
As two important mechanical properties, strength and ductility generally tend to be muturally exclusive in conventional engineering materials. The breakthrough of such a trade-off has been potentiated by the recently developed CuZr-based bulk metallic glass (BMG) composites ductilized by a shape memory CuZr(B2) phase. Here the microstructural dependences of tensile properties for the CuZr-based BMG composites were elucidated qualitatively and modeled quantitatively, and the underlying mechanisms were unraveled. Through the microstructural percolation induced by matching the length scales of particle size and interparticle spacing, a notable breakthrough was achieved in the composites that the general conflicts between strength and ductility can be defeated. This study is expected to greatly aid in the microstructural design and tailoring for improved properties of BMG composites. It also has implications for the development of strong and ductile materials in the future.
doi:10.1038/srep04167
PMCID: PMC3933912  PMID: 24566737
5.  Identification and functional analysis of 9p24 amplified genes in human breast cancer 
Oncogene  2011;31(3):10.1038/onc.2011.227.
Previously, our group identified a novel amplicon at chromosome 9p24 in human esophageal and breast cancers, and cloned the novel gene, GASC1 (gene amplified in squamous cell carcinoma 1, also known as JMJD2C/KDM4C), from this amplicon. GASC1 is a histone demethylase involved in the deregulation of histone methylation in cancer cells. In the current study, we aimed to comprehensively characterize the genes in the 9p24 amplicon in human breast cancer. We performed extensive genomic analyses on a panel of cancer cell lines and narrowed the shortest region of overlap to approximately 2 Mb. Based on statistical analysis of copy number increase and overexpression, the 9p24 amplicon contains six candidate oncogenes. Among these, four genes (GASC1 UHRF2, KIAA1432 and C9orf123) are overexpressed only in the context of gene amplification while two genes (ERMP1 and IL33) are overexpressed independent of the copy number increase. We then focused our studies on the UHRF2 gene, which has a potential involvement in both DNA methylation and histone modification. Knocking down UHRF2 expression inhibited the growth of breast cancer cells specifically with 9p24 amplification. Conversely, ectopic overexpression of UHRF2 in non-tumorigenic MCF10A cells promoted cell proliferation. Furthermore, we demonstrated that UHRF2 has the ability to suppress the expression of key cell-cycle inhibitors, such as p16INK4a, p21Waf1/Cip1 and p27Kip1. Taken together, our studies support the notion that the 9p24 amplicon contains multiple oncogenes that may integrate genetic and epigenetic codes and have important roles in human tumorigenesis.
doi:10.1038/onc.2011.227
PMCID: PMC3886828  PMID: 21666724
chromosome 9p24; GASC1; UHRF2; gene amplification
6.  Microalloying Ultrafine Grained Al Alloys with Enhanced Ductility 
Scientific Reports  2014;4:3605.
Bulk ultrafine grained (UFG)/nanocrystal metals possess exceptional strength but normally poor ductility and thermal stability, which hinder their practical applications especially in high-temperature environments. Through microalloying strategy that enables the control of grains and precipitations in nanostructured regime, here we design and successfully produce a highly microstructure-stable UFG Al-Cu-Sc alloy with ~275% increment in ductility and simultaneously ~50% enhancement in yield strength compared with its Sc-free counterpart. Although the precipitations in UFG alloys are usually preferentially occurred at grain boundaries even at room temperature, minor Sc addition into the UFG Al-Cu alloys is found to effectively stabilize the as-processed microstructure, strongly suppress the θ-Al2Cu phase precipitation at grain boundary, and remarkably promote the θ′-Al2Cu nanoparticles dispersed in the grain interior in artificial aging. A similar microalloying strategy is expected to be equally effective for other UFG heat-treatable alloys.
doi:10.1038/srep03605
PMCID: PMC3884224  PMID: 24398915
7.  Volumetric bone mineral density at the spine and hip in Chinese American and White women 
Summary
This study evaluated racial differences in bone size and volumetric density at the spine and hip in pre-and postmenopausal Chinese American and White women. Compared with White women, Chinese American women have greater cortical volumetric bone density (vBMD) at the hip, congruent with the results at the peripheral skeleton.
Introduction
Chinese American women have lower rates of fracture than White women despite lower areal bone density. At the forearm and tibia, however, Chinese American women have higher cortical vBMD as well as greater trabecular and cortical thickness, but smaller bone area as measured by high-resolution peripheral quantitative computed tomography (HR-pQCT) compared with White women. Since HR-pQCT data are obtained at peripheral sites, it is unclear whether these differences are relevant to the clinically important lumbar spine and hip. This study assesses racial differences in bone size and vBMD at the spine and hip in Chinese American and White women.
Methods
QCT of the spine and hip was measured to assess racial differences in bone size, structure, and vBMD in pre-(n=83) and postmenopausal (n=50) Chinese American and White women. Data were adjusted for weight, height, physical activity, total calcium intake, parathyroid hormone, and 25-hydroxyvitamin D levels.
Results
Among premenopausal women, lumbar spine trabecular vBMD was 5.8% greater in Chinese American versus White women (p=0.01). At the hip, cortical vBMD was 3% greater at the femoral neck (p=0.05) and 3.6% greater at the total hip (p=0.01) in premenopausal Chinese American compared with White women. Among postmenopausal women, there was no difference in lumbar spine trabecular vBMD. Cortical vBMD was 4% greater at the total hip (p= 0.02) and tended to be greater at the femoral neck (p=0.058) in Chinese American versus White women.
Conclusions
Consistent with earlier findings in the peripheral skeleton, cortical vBMD is greater at the hip in Chinese American versus White women.
doi:10.1007/s00198-011-1855-z
PMCID: PMC3552556  PMID: 22147209
Central QCT; Chinese American; Race; Volumetric bone density; White
8.  HIV Infection Affects Streptococcus mutans Levels, but Not Genotypes 
Journal of Dental Research  2012;91(9):834-840.
We report a clinical study that examines whether HIV infection affects Streptococcus mutans colonization in the oral cavity. Whole stimulated saliva samples were collected from 46 HIV-seropositive individuals and 69 HIV-seronegative control individuals. The level of S. mutans colonization was determined by conventional culture methods. The genotype of S. mutans was compared between 10 HIV-positive individuals before and after highly active antiretroviral therapy (HAART) and 10 non-HIV-infected control individuals. The results were analyzed against viral load, CD4+ and CD8+ T-cell counts, salivary flow rate, and caries status. We observed that S. mutans levels were higher in HIV-infected individuals than in the non-HIV-infected control individuals (p = 0.013). No significant differences in S. mutans genotypes were found between the two groups over the six-month study period, even after HAART. There was a bivariate linear relationship between S. mutans levels and CD8+ counts (r = 0.412; p = 0.007), but not between S. mutans levels and either CD4+ counts or viral load. Furthermore, compared with non-HIV-infected control individuals, HIV-infected individuals experienced lower salivary secretion (p = 0.009) and a positive trend toward more decayed tooth surfaces (p = 0.027). These findings suggest that HIV infection can have a significant effect on the level of S. mutans, but not genotypes.
doi:10.1177/0022034512454298
PMCID: PMC3420392  PMID: 22821240
HIV infections; Streptococcus mutans; genotype; saliva; CD8+ T-lymphocytes; HAART
9.  A phase I study of the combination of ro4929097 and cediranib in patients with advanced solid tumours (PJC-004/NCI 8503) 
British Journal of Cancer  2013;109(4):943-949.
Background:
The Notch signalling pathway has been implicated in tumour initiation, progression, angiogenesis and development of resistance to vascular endothelial growth factor (VEGF) targeting, providing a rationale for the combination of RO4929097, a γ-secretase inhibitor, and cediranib, a VEGF receptor tyrosine kinase inhibitor.
Methods:
Patients received escalating doses of RO4929097 (on a 3 days-on and 4 days-off schedule) in combination with cediranib (once daily). Cycle 1 was 42 days long with RO4929097 given alone for the first 3 weeks followed by the co-administration of both RO4929097 and cediranib starting from day 22. Cycle 2 and onwards were 21 days long. Soluble markers of angiogenesis were measured in plasma samples. Archival tumour specimens were assessed for expression of three different components of Notch signalling pathway and genotyping.
Results:
In total, 20 patients were treated in three dose levels (DLs). The recommended phase II dose was defined as 20 mg for RO4929097 on 3 days-on and 4 days-off schedule and 30 mg daily for cediranib. The most frequent treatment-related adverse events (AEs) were diarrhoea, hypertension, fatigue and nausea. Eleven patients had a best response of stable disease and one patient achieved partial response. We did not detect any correlation between tested biomarkers of angiogenesis or the Notch pathway and treatment effect. There was no correlation between mutational status and time to treatment failure.
Conclusion:
RO4929097 in combination with cediranib is generally well tolerated at the DLs tested. Preliminary evidence of antitumour efficacy with prolonged disease stabilisation in some patients with progressive malignancies warrants further clinical investigation of this treatment strategy.
doi:10.1038/bjc.2013.380
PMCID: PMC3749563  PMID: 23868004
RO4929097; cediranib; phase I; combination study
10.  The PRESTO technique for fMRI 
Neuroimage  2012;62(2):676-681.
In the early days of BOLD fMRI, the acquisition of T2* weighted data was greatly facilitated by rapid scan techniques such as EPI. The latter, however, was only available on a few MRI systems that were equipped with specialized hardware that allowed rapid switching of the imaging gradients. For this reason, soon after the invention of fMRI, the scan technique PRESTO was developed to make rapid T2* weighted scanning available on standard clinical scanning. This method combined echo shifting, which allows for echo times longer than the sequence repetition time, with acquisition of multiple k-space lines per excitation. These two concepts were combined in order to achieve a method fast enough for fMRI, while maintaining a sufficiently long echo time for optimal contrast. PRESTO has been primarily used for 3D scanning, which minimized the contribution of large vessels due to inflow effects. Although PRESTO is still being used today, its appeal has lessened somewhat due to increased gradient performance of modern MRI scanners. Compared to 2D EPI, PRESTO may have somewhat reduced temporal stability, which is a disadvantage for fMRI that may not outweigh the advantage of reduced inflow effects provided by 3D scanning. In this overview, the history of the development of the PRESTO is presented, followed by a qualitative comparison with EPI.
doi:10.1016/j.neuroimage.2012.01.017
PMCID: PMC3389260  PMID: 22245350
Functional magnetic resonance imaging (fMRI); Blood oxygenation level dependent (BOLD) contrast; PRESTO (Principles of Echo-Shifting with a Train of Observation); Echo shifting
11.  Crystallization-aided extraordinary plastic deformation in nanolayered crystalline Cu/amorphous Cu-Zr micropillars 
Scientific Reports  2013;3:2324.
Metallic glasses are lucrative engineering materials owing to their superior mechanical properties such as high strength and great elastic strain. However, the Achilles' heel of metallic amorphous materials — low plasticity caused by instantaneous catastrophic shear banding, significantly undercut their structural applications. Here, the nanolayered crystalline Cu/amorphous Cu-Zr micropillars with equal layer thickness spanning from 20–100 nm are uniaxially compressed and it is found that the Cu/Cu-Zr micropillars exhibit superhigh homogeneous deformation (≥ 30% strain) rather than localized shear banding at room temperature. This extraordinary plasticity is aided by the deformation-induced devitrification via absorption/annihilation of abundant dislocations, triggering the cooperative shearing of shear transformation zones in glassy layers, which simultaneously renders the work-softening. The synthesis of such heterogeneous nanolayered structure not only hampers shear band generation but also provides a viable route to enhance the controllability of plastic deformation in metallic glassy composites via deformation-induced devitrification mechanism.
doi:10.1038/srep02324
PMCID: PMC3728591  PMID: 23900595
12.  In vitro proliferation and differentiation of hepatic oval cells and their potential capacity for intrahepatic transplantation 
Hepatic oval cells (HOCs) are recognized as facultative liver progenitor cells that play a role in liver regeneration after acute liver injury. Here, we investigated the in vitro proliferation and differentiation characteristics of HOCs in order to explore their potential capacity for intrahepatic transplantation. Clusters or scattered HOCs were detected in the portal area and interlobular bile duct in the liver of rats subjected to the modified 2-acetylaminofluorene and partial hepatectomy method. Isolated HOCs were positive for c-kit and CD90 staining (99.8% and 88.8%, respectively), and negative for CD34 staining (3.6%) as shown by immunostaining and flow cytometric analysis. In addition, HOCs could be differentiated into hepatocytes and bile duct epithelial cells after leukemia inhibitory factor deprivation. A two-cuff technique was used for orthotopic liver transplantation, and HOCs were subsequently transplanted into recipients. Biochemical indicators of liver function were assessed 4 weeks after transplantation. HOC transplantation significantly prolonged the median survival time and improved the liver function of rats receiving HOCs compared to controls (P=0.003, Student t-test). Administration of HOCs to rats also receiving liver transplantation significantly reduced acute allograft rejection compared to control liver transplant rats 3 weeks following transplantation (rejection activity index score: control=6.3±0.9; HOC=3.5±1.5; P=0.005). These results indicate that HOCs may be useful in therapeutic liver regeneration after orthotopic liver transplantation.
doi:10.1590/1414-431X20132620
PMCID: PMC3854420  PMID: 23903688
Hepatic oval cells; Proliferation; Differentiation; Liver transplantation
13.  Flow Cytometry Total Cell Counts: A Field Study Assessing Microbiological Water Quality and Growth in Unchlorinated Drinking Water Distribution Systems 
BioMed Research International  2013;2013:595872.
The objective of this study was to evaluate the application of flow cytometry total cell counts (TCCs) as a parameter to assess microbial growth in drinking water distribution systems and to determine the relationships between different parameters describing the biostability of treated water. A one-year sampling program was carried out in two distribution systems in The Netherlands. Results demonstrated that, in both systems, the biomass differences measured by ATP were not significant. TCC differences were also not significant in treatment plant 1, but decreased slightly in treatment plant 2. TCC values were found to be higher at temperatures above 15°C than at temperatures below 15°C. The correlation study of parameters describing biostability found no relationship among TCC, heterotrophic plate counts, and Aeromonas. Also no relationship was found between TCC and ATP. Some correlation was found between the subgroup of high nucleic acid content bacteria and ATP (R2 = 0.63). Overall, the results demonstrated that TCC is a valuable parameter to assess the drinking water biological quality and regrowth; it can directly and sensitively quantify biomass, detect small changes, and can be used to determine the subgroup of active HNA bacteria that are related to ATP.
doi:10.1155/2013/595872
PMCID: PMC3684093  PMID: 23819117
14.  Heroin abuse accelerates biological aging: a novel insight from telomerase and brain imaging interaction 
Translational Psychiatry  2013;3(5):e260-.
Heroin abuse and natural aging exert common influences on immunological cell functioning. This observation led to a recent and untested idea that aging may be accelerated in abusers of heroin. We examined this claim by testing whether heroin use is associated with premature aging at both cellular and brain system levels. A group of abstinent heroin users (n=33) and matched healthy controls (n=30) were recruited and measured on various biological indicators of aging. These measures included peripheral blood telomerase activity, which reflects cellular aging, and both structural and functional measures of brain magnetic resonance imaging. We found that heroin users were characterized by significantly low telomerase activity (0.21 vs 1.78; 88% reduction; t(61)=6.96, P<0.001; 95% confidence interval=1.12–2.02), which interacted with heroin use to affect the structural integrity of gray and white matter of the prefrontal cortex (PFC; AlphaSim corrected P<0.05), a key brain region implicated in aging. Using the PFC location identified from the structural analyses as a ‘seed' region, it was further revealed that telomerase activity interacted with heroin use to impact age-sensitive brain functional networks (AlphaSim corrected P<0.05), which correlated with behavioral performance on executive functioning, memory and attentional control (Pearson correlation, all P<0.05). To our knowledge, this study is the first to attempt a direct integration of peripheral molecular, brain system and behavioral measures in the context of substance abuse. The present finding that heroin abuse is associated with accelerated aging at both cellular and brain system levels is novel and forms a unique contribution to our knowledge in how the biological processes of drug abusers may be disrupted.
doi:10.1038/tp.2013.36
PMCID: PMC3669923  PMID: 23695235
addiction; aging; heroin; MRI; prefrontal cortex; resting state; telomerase
15.  NADPH oxidase inhibition prevents beta cell dysfunction induced by prolonged elevation of oleate in rodents 
Diabetologia  2013;56(5):1078-1087.
Aims/hypothesis
The activation of NADPH oxidase has been implicated in NEFA-induced beta cell dysfunction. However, the causal role of this activation in vivo remains unclear. Here, using rodents, we investigated whether pharmacological or genetic inhibition of NADPH oxidase could prevent NEFA-induced beta cell dysfunction in vivo.
Methods
Normal rats were infused for 48 h with saline or oleate with or without the NADPH oxidase inhibitor apocynin. In addition, NADPH oxidase subunit p47phox-null mice and wild-type littermate controls were infused with saline or oleate for 48 h. This was followed by measurement of NADPH oxidase activity, reactive oxygen species (ROS) and superoxide imaging and assessment of beta cell function in isolated islets and hyperglycaemic clamps.
Results
Oleate infusion in rats increased NADPH oxidase activity, consistent with increased total but not mitochondrial superoxide in islets and impaired beta cell function in isolated islets and during hyperglycaemic clamps. Co-infusion of apocynin with oleate normalised NADPH oxidase activity and total superoxide levels and prevented beta cell dysfunction. Similarly, 48 h NEFA elevation in wild-type mice increased total but not mitochondrial superoxide and impaired beta cell function in isolated islets. p47phox-null mice were protected against these effects when subjected to 48 h oleate infusion. Finally, oleate increased the levels of total ROS, in both models, whereas inhibition of NADPH oxidase prevented this increase, suggesting that NADPH oxidase is the main source of ROS in this model.
Conclusions/interpretation
These data show that NADPH-oxidase-derived cytosolic superoxide is increased in islets upon oleate infusion in vivo; and whole-body NADPH-oxidase inhibition decreases superoxide in concert with restoration of islet function.
Electronic supplementary material
The online version of this article (doi:10.1007/s00125-013-2858-4) contains peer-reviewed but unedited supplementary material, which is available to authorised users.
doi:10.1007/s00125-013-2858-4
PMCID: PMC3622749  PMID: 23429921
Beta cell dysfunction; In vivo; Lipotoxicity; NADPH oxidase; Oleate; Oxidative stress
16.  Genetic variation in radiation and platinum pathways predicts severe acute radiation toxicity in patients with esophageal adenocarcinoma treated with cisplatin-based preoperative radiochemotherapy: results from the Eastern Cooperative Oncology Group 
Purpose
Germline genetic variations may partly explain the clinical observation that normal tissue tolerance to radiochemotherapy varies by individual. Our objective was to evaluate the association between single-nucleotide polymorphisms (SNPs) in radiation/platinum pathways and serious treatment-related toxicity in subjects with esophageal adenocarcinoma who received cisplatin-based preoperative radiochemotherapy.
Methods
In a multicenter clinical trial (E1201), 81 eligible treatment-naïve subjects with resectable esophageal adenocarcinoma received cisplatin-based chemotherapy concurrent with radiotherapy, with planned subsequent surgical resection. Toxicity endpoints were defined as grade ≥3 radiation-related or myelosuppressive events probably or definitely related to therapy, occurring during or up to 6 weeks following the completion of radiochemotherapy. SNPs were analyzed in 60 subjects in pathways related to nucleotide/base excision- or double stranded break repair, or platinum influx, efflux, or detoxification.
Results
Grade ≥3 radiation-related toxicity (mostly dysphagia) and myelosuppression occurred in 18 and 33% of subjects, respectively. The variant alleles of the XRCC2 5′ flanking SNP (detected in 28% of subjects) and of GST-Pi Ile-105-Val (detected in 65% of subjects) were each associated with higher odds of serious radiation-related toxicity compared to the major allele homozygote (47% vs. 9%, and 31% vs. 0%, respectively; P = 0.005). No SNP was associated with myelosuppression.
Conclusions
This novel finding in a well-characterized cohort with robust endpoint data supports further investigation of XRCC2 and GST-Pi as potential predictors of radiation toxicity.
doi:10.1007/s00280-011-1556-5
PMCID: PMC3563156  PMID: 21286719
Chemoradiation; Esophageal cancer; Radiation toxicity prediction; Single nucleotide polymorphism; Trimodality
17.  Role of ultrasound in the assessment of benignity and malignancy of parotid masses 
Wu, S | Liu, G | Chen, R | Guan, Y
Dentomaxillofacial Radiology  2012;41(2):131-135.
Objectives
This study aimed to investigate the value of ultrasound in the identification of benign and malignant parotid masses.
Methods
Data of 189 patients with parotid gland masses undergoing ultrasound-guided fine-needle aspiration (FNA), core biopsy or surgery were reviewed retrospectively and the presumed sonographic diagnoses were compared with the histopathology. The sensitivity, specificity and accuracy of sonographic diagnoses were assessed and the sonographic characteristics of those lesions, including shape, margin, echogenicity, echotexture and vascularization, were studied.
Results
Of the 189 patients, the final pathological diagnosis included 18 malignant tumours and 171 benign masses; the presumed sonographic diagnoses showed 165 cases as benign and probably benign masses (11 cases were confirmed malignant, 154 cases benign) and 24 cases were diagnosed as probably malignant and malignant masses (7 cases were confirmed malignant, 17 cases benign). The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of ultrasound for the diagnosis of parotid gland masses were 38.9%, 90.1%, 29.2%, 93.3% and 85.2%, respectively, and accuracy for malignant masses was 20%. The sonographic characteristics of parotid masses between benign and malignant lesions had no significant differences. The parotid gland masses in this study included pleomorphic adenoma, Warthin's tumour, retention cyst, haemangiomas, chronic granuloma, lymphoma, fibrolipoma, abscess, basal cell adenoma, oncocytoma, lymphatic tuberculosis, myoepithelioma, neurilemmoma, mucoepidermoid carcinoma, adenoid cystic carcinoma, alveolar soft part sarcoma and retinal blastoma (metastasis).
Conclusions
It is challenging to use sonography for differentiating between benign and malignant parotid gland masses. To make a definite diagnosis, ultrasound-guided FNA or core biopsy is advocated.
doi:10.1259/dmfr/60907848
PMCID: PMC3520365  PMID: 22116132
parotid gland; mass; benign; malignant; ultrasound
18.  The QKI-PLP pathway controls SIRT2 abundance in CNS myelin 
Glia  2011;60(1):69-82.
Sirtuin 2 (SIRT2), a NAD-dependent deacetylase expressed by oligodendrocytes (OLs), the myelin-producing cells of the central nervous system (CNS), is markedly up-regulated during active myelination (Li et al. 2007; Southwood et al. 2007; Werner et al. 2007). SIRT2 is a component of the myelin proteome and is severely reduced in the Plp1 knockout mouse brain, in which both PLP and DM20 are absent (Werner et al. 2007). The mechanisms that regulate SIRT2 expression in OLs and myelin remain to be investigated. We report for the first time that the expression of SIRT2 is regulated by the QKI-dependent pathway and this effect is mediated through selective regulation of PLP. In the homozygous quakingviable (qkv/qkv) mutant mouse that harbors QKI deficiency in OLs (Bockbrader and Feng 2008; Ebersole et al. 1996; Hardy et al. 1996), PLP, but not DM20 mRNA, was selectively down-regulated and SIRT2 protein was severely reduced while SIRT2 mRNA expression was unaffected. Expression of the cytoplasmic isoform QKI6 in OLs (Zhao et al. 2006) rescued SIRT2 expression in the qkv/qkv mutant concomitantly with restoration of PLP expression. Moreover, SIRT2 protein is diminished in myelin tracts and compact myelin of the PLP-ISEdel mutant brain, in which PLP protein but not DM20 is selectively reduced (Wang et al. 2008). In contrast, SIRT2 expression and its cellular function in regulating process complexity are not affected by the absence of PLP in PLP-ISEdel non-myelinating oligodendrocytes. Collectively, our results indicate that the abundance of SIRT2 in myelin is dependent on PLP, but not DM20.
doi:10.1002/glia.21248
PMCID: PMC3217119  PMID: 21948283
oligodendrocytes; Sirtuin2; PLP; myelin; development; quaking
19.  Switching cell fate, ncRNAs coming to play 
Cell Death & Disease  2013;4(1):e464-.
Cell fate decision is a critical step during physiological development when embryonic stem cells commit to either becoming adult stem cells or somatic cells. Recent advances in reprogramming demonstrate that a similar set of transcription factors (TFs), which are important for maintaining the pluripotent state of stem cells, can also reprogram somatic cells to induced pluripotent stem cells (iPSCs). In addition, trans-differentiation, which entails the use of different sets of defined factors, whereby one type of somatic cell can be directly converted into another and even to cell types from different germ layers has become a parallel widely used approach for switching cell fate. All these progresses have provided powerful tools to manipulate cells for basic science and therapeutic purposes. Besides protein-based factors, non-coding RNAs (ncRNAs), particularly microRNAs and long ncRNAs, are also involved in cell fate determination, including maintaining self-renewal of pluripotent stem cells and directing cell lineage. Targeting specific ncRNAs represents an alternative promising approach to optimize cell-based disease modeling and regenerative therapy. Here we focus on recent advances of ncRNAs in cell fate decision, including ncRNA-induced iPSCs and lineage conversion. We also discuss some underlying mechanisms and implications in molecular pathogenesis of human diseases.
doi:10.1038/cddis.2012.196
PMCID: PMC3563984  PMID: 23328671
ncRNAs; lncRNAs; microRNAs; reprogramming; trans-differentiation
20.  Multi-walled carbon nanotube-supported metal-doped ZnO nanoparticles and their photocatalytic property 
A simple and versatile approach has been developed to synthesize multi-walled carbon nanotubes/metal-doped ZnO nanohybrid materials (MWNT/M-doped ZnO) by means of the co-deposition method. The experimental results illuminate that MWNTs can be modified by metal-doped ZnO nanoparticles at 450 °C, such as Mn, Mg, and Co elements. Furthermore, the MWNT/Mg-doped ZnO hybrids have been proven to have a high photocatalytic ability for methyl orange (MO), in which the degraded rate for MO reaches 100 % in 60 min. The enhancement in photocatalytic activity is attributed to the excellent electriconal property of MWNTs and Mg-doping. The resultant MWNT/Mg-doped ZnO nanohybrids have potential applications in photocatalysis and environmental protection.
doi:10.1007/s11051-012-1295-5
PMCID: PMC3568477  PMID: 23420492
Carbon nanotube; Metal-doped ZnO; Oxide hybrid; Photocatalytic property
21.  Pharmacologic reversal of epigenetic silencing of the anticancer protein BRM: a novel targeted treatment strategy 
Oncogene  2011;30(29):3289-3294.
Tumor suppressor genes and oncogenes are both commonly altered during carcinogenesis. For oncogenes and other genes that drive growth, targeting mutated or activated forms (such as the EGFR-Her2/Nneu pathway) has been shown to be an effective anti-cancer approach. Pharmacologically targeting tumor suppressor genes has not been as fruitful, as many tumor suppressor genes are irreversibly silenced through somatic mutation or entirely deleted during carcinogenesis, thereby making it difficult to restore gene function. BRM, a key SWI/SNF complex subunit and a putative tumor suppressor gene, is inactivated in 15–20% of many solid tumor types. Unlike other tumor suppressor genes, the loss of BRM has been shown to be a reversible epigenetic change, rather than an irreversible genetic alteration. Using a high throughput drug screen, we identified a number of compounds that could effectively restore BRM expression and function. Two of these compounds, RH (RH02032) and GK (GK0037), were found to be such reactivating agents. Both compounds led to robust re-expression of BRM, induced downstream expression of BRM-dependent genes and inhibited BRM-dependent growth across a wide range of BRM-deficient cancer cell lines of different origins. We therefore show, for the first time, that pharmacologic reversal of epigenetic changes of the SWI/SNF chromatic remodeling complex subunit, BRM, is a potentially viable and novel therapeutic approach.
doi:10.1038/onc.2011.80
PMCID: PMC3402205  PMID: 21478905
SWI/SNF; epigenetic; tumor suppressor; target therapy; chromatin remodeling; cancer therapy
22.  Two novel BRM insertion promoter sequence variants are associated with loss of BRM expression and lung cancer risk 
Oncogene  2011;30(29):3295-3304.
SWI/SNF (SWItch/sucrose non-fermentable) complexes are ATP-dependent chromatin remodeling enzymes critically involved in the regulation of multiple functions, including gene expression, differentiation, development, DNA repair, cell adhesion and cell cycle control. BRM, a key SWI/SNF complex subunit, is silenced in 15–20% of many solid tumors. As BRM-deficient mice develop 10-fold more tumors when exposed to carcinogens, BRM is a strong candidate for a cancer susceptibility gene. In this paper, we show that BRM is regulated by transcription, thus demonstrating that the promoter region is important for BRM expression. We sequenced the BRM promoter region, finding two novel promoter indel polymorphisms, BRM −741 and BRM −1321, that are in linkage disequilibrium (D′ ≥0.83). The variant insertion alleles of both polymorphisms produce sequence variants that are highly homologous to myocyte enhancer factor-2 (MEF2) transcription factor-binding sites; MEF2 is known to recruit histone deacetylases that silence BRM expression. Each polymorphic BRM insertion variant is found in ~20% of Caucasians, and each correlates strongly with the loss of protein expression of BRM, both in cancer cell lines (P=0.009) and in primary human lung tumor specimens (P=0.015). With such strong functional evidence, we conducted a case–control study of 1199 smokers. We found an increased risk of lung cancer when both BRM homozygous promoter insertion variants were present: adjusted odds ratio of 2.19 (95% confidence interval, 1.40–3.43). Thus, we here demonstrate a strong functional association between these polymorphisms and loss of BRM expression. These polymorphisms thus have the potential to identify a sub-population of smokers at greater lung cancer risk, wherein this risk could be driven by an aberrant SWI/SNF chromatin-remodeling pathway.
doi:10.1038/onc.2011.81
PMCID: PMC3400140  PMID: 21478907
genetic polymorphism; BRG1; SWI/SNF; chromatin remodeling; lung cancer
23.  CSF opening pressure in children with optic nerve head edema 
Neurology  2011;76(19):1658-1661.
Background:
We previously reported that an abnormal CSF opening pressure (OP) in children was greater than 28 cm H2O. Since elevated intracranial pressure can cause optic nerve head edema (ONHE), we would expect that most patients with ONHE would have an OP greater than 28 cm H2O. This study describes the range of OP for children with ONHE and compared them to age-matched controls without ONHE.
Methods:
Case subjects were children (1–18 years of age) enrolled in a prospective study of CSF OP that demonstrated ONHE at time of lumbar puncture and that the ONHE later resolved. Patients with ONHE secondary to infectious, inflammatory, or ischemic conditions were excluded. Control subjects from the same study, but without ONHE, were matched to cases.
Results:
Of the 472 subjects enrolled in the study, 41 OP measurements were obtained from 33 patients with ONHE who did not have any exclusionary criteria and matched to 41 control subjects without ONHE. Case subjects had a significantly higher OP (mean, 41.4 cm H20; range, 22–56) than control subjects (mean, 18.9 cm H2O; range, 9–29; p < 0.01). Forty of 41 (97.6%) case subjects and 2 of 41 (4.8%) control subjects had OP measures >28 cm H2O.
Conclusions:
Children with ONHE not related to infectious, inflammatory, or ischemic causes typically have an OP >28 cm H2O, significantly higher than age-matched controls without ONHE. This study provides further support to our previously published findings that suggests an abnormal OP in children is typically above 28 cm H2O.
doi:10.1212/WNL.0b013e318219fb80
PMCID: PMC3100091  PMID: 21555733
24.  Multi-walled carbon nanotubes supported Cu-doped ZnO nanoparticles and their optical property 
Multi-walled carbon nanotubes (MWNTs)/Cu-doped ZnO composite powders were prepared by co-precipitation method, and were characterized by X-ray diffraction, electron microscopy, fluorescence spectrum, and ultraviolet spectrum. Experimental results show that the MWNTs can be modified by Cu-doped ZnO nanoparticles with hexagonal wurtzite structure after annealed at 450 °C, and the nanoparticle size is about 15 nm. Two ultraviolet (UV) peaks and a green band centered at about 510 nm are observed in the fluorescence spectrum of MWNTs/Cu-doped ZnO composite powder annealed at 450 °C. Furthermore, MWNTs and Cu doping significantly improve the UV absorption ability of ZnO.
doi:10.1007/s11051-012-0817-5
PMCID: PMC3394237  PMID: 22798725
Carbon nanotube; Cu-doped ZnO; Composite powder; Optical property; Synthesis
25.  The circadian mutation PER2S662G is linked to cell cycle progression and tumorigenesis 
Gu, X | Xing, L | Shi, G | Liu, Z | Wang, X | Qu, Z | Wu, X | Dong, Z | Gao, X | Liu, G | Yang, L | Xu, Y
Cell Death and Differentiation  2011;19(3):397-405.
Circadian oscillation and cell cycle progression are the two most essential rhythmic events present in almost all organisms. Circadian rhythms keep track of time and provide temporal regulation with a period of about 24 h. The cell cycle is optimized for growth and division, but not for time keeping. Circadian gated cell divisions are observed in nearly all organisms. However, the implications of this coupling to the physiology of mammals are unknown. A mutation (S662G) in the clock protein PERIOD2 (PER2) is responsible for familial advanced sleep phase syndrome in which sleep onset occurs in the early evening and wakefulness occurs in the early morning. Here, we provide evidence that the PER2S662 mutation leads to enhanced resistance to X-ray-induced apoptosis and increased E1A- and RAS-mediated oncogenic transformation. Accordingly, the PER2S662 mutation affects tumorigenesis in cancer-sensitized p53R172H/+ mice. Finally, analyzing the clock-controlled cell cycle genes p21, c-Myc, Cyclin D1 and p27, we found that the relative phases between p21 and Cyclin D expression profiles have been changed significantly in these Per2 allele mutant mouse embryonic fibroblasts. This key role of the Per2-mediated phase alteration of p21 provides what we believe to be a novel mechanism in understanding cell cycle progression, its plasticity and its resistance to interference.
doi:10.1038/cdd.2011.103
PMCID: PMC3278723  PMID: 21818120
PER2; circadian rhythms; cell cycle; tumorigenesis; FASPS

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