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1.  Astrocytic Toll-Like Receptor 3 Is Associated with Ischemic Preconditioning- Induced Protection against Brain Ischemia in Rodents 
PLoS ONE  2014;9(6):e99526.
Background
Cerebral ischemic preconditioning (IPC) protects brain against ischemic injury. Activation of Toll-like receptor 3 (TLR3) signaling can induce neuroprotective mediators, but whether astrocytic TLR3 signaling is involved in IPC-induced ischemic tolerance is not known.
Methods
IPC was modeled in mice with three brief episodes of bilateral carotid occlusion. In vitro, IPC was modeled in astrocytes by 1-h oxygen-glucose deprivation (OGD). Injury and components of the TLR3 signaling pathway were measured after a subsequent protracted ischemic event. A neutralizing antibody against TLR3 was used to evaluate the role of TLR3 signaling in ischemic tolerance.
Results
IPC in vivo reduced brain damage from permanent middle cerebral artery occlusion in mice and increased expression of TLR3 in cortical astrocytes. IPC also reduced damage in isolated astrocytes after 12-h OGD. In astrocytes, IPC or 12-h OGD alone increased TLR3 expression, and 12-h OGD alone increased expression of phosphorylated NFκB (pNFκB). However, IPC or 12-h OGD alone did not alter the expression of Toll/interleukin receptor domain-containing adaptor-inducing IFNβ (TRIF) or phosphorylated interferon regulatory factor 3 (pIRF3). Exposure to IPC before OGD increased TRIF and pIRF3 expression but decreased pNFκB expression. Analysis of cytokines showed that 12-h OGD alone increased IFNβ and IL-6 secretion; 12-h OGD preceded by IPC further increased IFNβ secretion but decreased IL-6 secretion. Preconditioning with TLR3 ligand Poly I:C increased pIRF3 expression and protected astrocytes against ischemic injury; however, cells treated with a neutralizing antibody against TLR3 lacked the IPC- and Poly I:C-induced ischemic protection and augmentation of IFNβ.
Conclusions
The results suggest that IPC-induced ischemic tolerance is mediated by astrocytic TLR3 signaling. This reprogramming of TLR3 signaling by IPC in astrocytes may play an important role in suppression of the post-ischemic inflammatory response and thereby protect against ischemic damage. The mechanism may be via activation of the TLR3/TRIF/IRF3 signaling pathway.
doi:10.1371/journal.pone.0099526
PMCID: PMC4051824  PMID: 24914679
2.  Delivery of the co-expression plasmid pEndo-Si-Stat3 by attenuated Salmonella serovar typhimurium for prostate cancer treatment 
Journal of cancer research and clinical oncology  2013;139(6):10.1007/s00432-013-1398-0.
Objectives
To investigate the therapeutic utility of an attenuated bacterium carrying a plasmid that co-expresses Endostatin, an inhibitor of tumor neovasculogenesis, and a shRNA that targets Stat3 to suppress prostate cancer growth.
Methods
Plasmid pEndo-Si-Stat3 was constructed and introduced into an attenuated strain of Salmonella enterica serovar typhimurium. The resultant recombinant bacterium was used as a vector to deliver the plasmid to tumor cells growing in vivo. Tumor-associated gene and protein expression changes were measured by using RT-PCR and Western blot analyses. Expression of Endostatin in tumor tissue was detected by ELISA. The presence of vector bacteria in tissues was monitored and tumor destruction was assessed by using TUNEL and H&E staining assays.
Results
Bacterially delivered pEndo-Si-Stat3 decreased Stat3 levels and increased Endostatin expression in mouse tumors, resulting in a significant suppression of tumor growth (P < 0.01). Expression of Bcl-2 and PCNA was down-regulated and Caspase3 expression was up-regulated to promote apoptosis of tumor cells.
Conclusions
Successful delivery by attenuated Salmonella of the combination therapeutic plasmid simultaneously knocked down the expression of Stat3 and resulted in over-expression of Endostatin, which synergistically inhibited prostate cancer growth.
doi:10.1007/s00432-013-1398-0
PMCID: PMC3874139  PMID: 23463096
Prostate cancer; Stat3; Endostatin; Attenuated Salmonella typhimurium
4.  The Ets transcription factor GABP is a novel component of the Hippo pathway essential for growth and antioxidant defense 
Cell reports  2013;3(5):10.1016/j.celrep.2013.04.020.
Summary
The transcriptional co-activator YAP plays an important role in organ size control and tumorigenesis. However, how Yap gene expression is regulated remains unknown. This study shows that the Ets family member GABP binds to the Yap promoter and activates YAP transcription. The depletion of GABP downregulates YAP, resulting in a G1/S cell cycle block and increased cell death, both of which are substantially rescued by reconstituting YAP. GABP can be inactivated by oxidative mechanisms, and acetaminophen-induced GSH depletion inhibits GABP transcriptional activity and depletes YAP. In contrast, activating YAP by deleting Mst1/Mst2 strongly protects acetaminophen-induced liver injury. Similar to its effects on YAP, the Hippo signaling inhibits GABP transcriptional activity through several mechanisms. In human liver cancers, enhanced YAP expression is correlated with increased nuclear expression of GABP. Therefore, we conclude that GABP is an activator of Yap gene expression and a potential therapeutic target for cancers driven by YAP.
doi:10.1016/j.celrep.2013.04.020
PMCID: PMC3855275  PMID: 23684612
GABP; Hippo pathway; YAP; Glutathione depletion; Liver injury; liver cancer
5.  Hydrothermal growth of TiO2 nanowire membranes sensitized with CdS quantum dots for the enhancement of photocatalytic performance 
Nanoscale Research Letters  2014;9(1):270.
In this paper, TiO2 nanowires (NWs) on Ti foils were prepared using a simple hydrothermal approach and annealing treatment. CdS quantum dots (QDs) were assembled onto the crystallized TiO2 NWs by sequential chemical bath deposition. Ultraviolet-visible absorption spectra showed that CdS adds bands in the visible to the TiO2 absorption and exhibited a broad absorption band in the visible region, which extended the scope of absorption spectrum and helped improve the photocatalytic degradation efficiency. The results of photocatalytic experiment revealed that CdS-TiO2 NWs possessed higher photocatalytic activities toward methyl orange than pure TiO2 nanowires. The degradation efficiency of 96.32% after ten cycles indicated that the as-prepared CdS-TiO2 composite exhibited excellent long-time recyclable ability and can be reused for the degradation of contaminants.
doi:10.1186/1556-276X-9-270
PMCID: PMC4046152  PMID: 24936164
Hydrothermal; S-CBD; CdS-TiO2 NWs; Photocatalytic activity
6.  miR-106b-25/miR-17-92 clusters: Polycistrons with oncogenic roles in hepatocellular carcinoma 
MicroRNAs are small endogenously expressed RNA molecules which are involved in the process of silencing gene expression through translational regulation. The polycistronic miR-17-92 cluster is the first microRNA cluster shown to play a role in tumorigenesis. It has two other paralogs in the human genome, the miR-106b-25 cluster and the miR-106a-363 cluster. Collectively, the microRNAs encoded by these clusters can be further grouped based on the seed sequences into four families, namely the miR-17, the miR-92, the miR-18 and the miR-19 families. Over-expression of the miR-106b-25 and miR-17-92 clusters has been reported not only during the development of cirrhosis but also subsequently during the development of hepatocellular carcinoma. Members of these clusters have also been shown to affect the replication of hepatitis B and hepatitis C viruses. Various targets of these microRNAs have been identified, and these targets are involved in tumor growth, cell survival and metastasis. In this review, we first describe the regulation of these clusters by c-Myc and E2F1, and how the members of these clusters in turn regulate E2F1 expression forming an auto-regulatory loop. In addition, the roles of the various members of the clusters in affecting relevant target gene expression in the pathogenesis of hepatocellular carcinoma will also be discussed.
doi:10.3748/wjg.v20.i20.5962
PMCID: PMC4033436  PMID: 24876719
miR-106b-25 cluster; miR-17-92 cluster; Hepatocellular carcinoma; Liver cirrhosis; MicroRNAs
7.  Use of lectin microarray to differentiate gastric cancer from gastric ulcer 
AIM: To investigate the feasibility of lectin microarray for differentiating gastric cancer from gastric ulcer.
METHODS: Twenty cases of human gastric cancer tissue and 20 cases of human gastric ulcer tissue were collected and processed. Protein was extracted from the frozen tissues and stored. The lectins were dissolved in buffer, and the sugar-binding specificities of lectins and the layout of the lectin microarray were summarized. The median of the effective data points for each lectin was globally normalized to the sum of medians of all effective data points for each lectin in one block. Formalin-fixed paraffin-embedded gastric cancer tissues and their corresponding gastric ulcer tissues were subjected to Ag retrieval. Biotinylated lectin was used as the primary antibody and HRP-streptavidin as the secondary antibody. The glycopatterns of glycoprotein in gastric cancer and gastric ulcer specimens were determined by lectin microarray, and then validated by lectin histochemistry. Data are presented as mean ± SD for the indicated number of independent experiments.
RESULTS: The glycosylation level of gastric cancer was significantly higher than that in ulcer. In gastric cancer, most of the lectin binders showed positive signals and the intensity of the signals was stronger, whereas the opposite was the case for ulcers. Significant differences in the pathological score of the two lectins were apparent between ulcer and gastric cancer tissues using the same lectin. For MPL and VVA, all types of gastric cancer detected showed stronger staining and a higher positive rate in comparison with ulcer, especially in the case of signet ring cell carcinoma and intra-mucosal carcinoma. GalNAc bound to MPL showed a significant increase. A statistically significant association between MPL and gastric cancer was observed. As with MPL, there were significant differences in VVA staining between gastric cancer and ulcer.
CONCLUSION: Lectin microarray can differentiate the different glycopatterns in gastric cancer and gastric ulcer, and the lectins MPL and VVA can be used as biomarkers.
doi:10.3748/wjg.v20.i18.5474
PMCID: PMC4017062  PMID: 24833877
Gastric cancer; Gastric ulcer; Lectin microarray; Lectin histochemistry; Differentiate
8.  Impact of renal dysfunction on long-term outcomes of elderly patients with acute coronary syndrome: a longitudinal, prospective observational study 
BMC Nephrology  2014;15:78.
Background
This study investigated the impact of renal dysfunction (RD) on long-term outcomes in elderly patients with acute coronary syndrome (ACS), and evaluated prognostic factors in elderly patients with ACS and RD.
Methods
This longitudinal prospective study included 184 consecutive patients who were admitted with ACS between January 2009 and January 2010 and also had RD. Patients were divided into five groups according to their estimated glomerular filtration rate (eGFR): 1) eGFR ≥ 90 mL/min/1.73 m2 with evidence of kidney damage, 2) 60 ≤ eGFR < 90 mL/min/1.73 m2, 3) 30 ≤ eGFR < 60 mL/min/1.73 m2, 4) 15 ≤ eGFR < 30 mL/min/1.73 m2, and 5) eGFR < 15 mL/min/1.73 m2. The primary endpoints were death and complications during hospitalization. The secondary endpoint was any major adverse cardiac event (MACE) during follow-up.
Results
The mean follow-up period was 502.2 ± 203.6 days. The mean patient age was 73.7 ± 9.4 years, and 61.4% of the patients were men. Severe RD (eGFR < 30 mL/min/1.73 m2) was an independent predictor of MACE. Severe RD was associated with a low hemoglobin level, low left ventricular ejection fraction, and high levels of high-sensitivity C-reactive protein, N-terminal pro-B-type natriuretic peptide, and cystatin C. Survival was significantly poorer in patients with severe RD than in patients with mild RD.
Conclusions
Among patients with ACS, severe RD was associated with advanced age, diabetes, hypertension, and cardiac dysfunction. Severe RD was an independent risk factor for MACE, and was associated with poor prognosis.
doi:10.1186/1471-2369-15-78
PMCID: PMC4047003  PMID: 24884483
Acute coronary syndrome; Glomerular filtration rate; Renal dysfunction; MACE; Elderly
9.  Effect of Amifostine in Head and Neck Cancer Patients Treated with Radiotherapy: A Systematic Review and Meta-Analysis Based on Randomized Controlled Trials 
PLoS ONE  2014;9(5):e95968.
Background
Amifostine is the most clinical used chemical radioprotector, but its effect in patients treated with radiation is not consistent.
Methods
By searching Medline, CENTRAL, EMBASE, ASCO, ESMO, and CNKI databases, the published randomized controlled trials (RCTs) about the efficacy of amifostine in HNSCC patients treated with radiotherapy were collected. The pooled efficacy and side effects of this drug were calculated by RevMan software.
Results
Seventeen trials including a total of 1167 patients (604 and 563 each arm) were analyzed in the meta-analysis. The pooled data showed that the use of amifostine significantly reduce the risk of developing Grade3–4 mucositis (relative risk [RR],0.72; 95% confidence interval [CI],0.54–0.95; p<0.00001), Grade 2–4 acute xerostomia (RR,0.70; 95%CI,0.52–0.96; p = 0.02), or late xerostomia (RR,0.60; 95%CI,0.49–0.74; p<0.00001) and Grade 3–4 dysphagia (RR,0.39; 95%CI,0.17–0.92; p = 0.03). However, subgroup analysis demonstrated that no statistically significant reduction of Grade3–4 mucositis (RR,0.97; 95% CI,0.74–1.26; p = 0.80), Grade 2–4 acute xerostomia (RR,0.35; 95%CI,0.02–5.44; p = 0.45), or late xerostomia (RR,0.40; 95%CI,0.13–1.24; p = 0.11) and Grade 3–4 dysphagia (RR,0.23; 95%CI,0.01–4.78; p = 0.35) was observed in patients treated with concomitant chemoradiotherapy. Compared with placebo or observation, amifostine does not show tumor protective effect in complete response (RR,1.02; 95%CI,0.89–1.17; p = 0.76) and partial response (RR,0.90; 95%CI, 0.56–1.44; p = 0.66). For the hematologic side effect, no statistical difference of Grade 3–4 leucopenia (RR,0.60; 95%CI,0.35–1.05; p = 0.07), anemia (RR,0.80; 95%CI, 0.42–1.53; p = 0.50) and thrombocytopenia (RR,0.43; 95%CI,0.16–1.15; p = 0.09) were found between amifostine and control groups. The most common amifostine related side effects were nausea, emesis, hypotension and allergic with an average incidence rate (Grade 3–4) of 5%, 6%, 4% and 4% respectively.
Conclusion
This systematic review showed that amifostine significantly reduce the serious mucositis, acute/late xerastomia and dysphagia without protection of the tumor in HNSCC patients treated with radiotherapy. And the toxicities of amifostine were generally acceptable.
doi:10.1371/journal.pone.0095968
PMCID: PMC4008569  PMID: 24788761
10.  Spread of Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 in Asia and AbaR-Type Resistance Islands 
Antimicrobial Agents and Chemotherapy  2013;57(11):5239-5246.
In this surveillance study, we identified the genotypes, carbapenem resistance determinants, and structural variations of AbaR-type resistance islands among carbapenem-resistant Acinetobacter baumannii (CRAB) isolates from nine Asian locales. Clonal complex 92 (CC92), corresponding to global clone 2 (GC2), was the most prevalent in most Asian locales (83/108 isolates; 76.9%). CC108, or GC1, was a predominant clone in India. OXA-23 oxacillinase was detected in CRAB isolates from most Asian locales except Taiwan. blaOXA-24 was found in CRAB isolates from Taiwan. AbaR4-type resistance islands, which were divided into six subtypes, were identified in most CRAB isolates investigated. Five isolates from India, Malaysia, Singapore, and Hong Kong contained AbaR3-type resistance islands. Of these, three isolates harbored both AbaR3- and AbaR4-type resistance islands simultaneously. In this study, GC2 was revealed as a prevalent clone in most Asian locales, with the AbaR4-type resistance island predominant, with diverse variants. The significance of this study lies in identifying the spread of global clones of carbapenem-resistant A. baumannii in Asia.
doi:10.1128/AAC.00633-13
PMCID: PMC3811275  PMID: 23939892
11.  Up-Regulating CYP3A4 Expression in C3A Cells by Transfection with a Novel Chimeric Regulator of hPXR-p53-AD 
PLoS ONE  2014;9(5):e95752.
Most hepatoma cell lines lack proper expression and induction of CYP3A4 enzyme, which limits their use for predicting drug metabolism and toxicity. Nuclear receptor pregnane X receptor (PXR) has been well recognized for its critical role in regulating expression of CYP3A4 gene. However, its physiological activity of binding to the particular site of promoter is significantly weakened in hepatic cell lines. To address this problem, we created “chimeric PXR” constructs by appending a strong activation domain (AD) from p53 subunit to either N- or C- termini of the human PXR (hPXR), that is, hPXR-p53 and p53-hPXR. C3A, a hepatoma cell line, was used as the cell model to test the regulation effect of chimeric hPXR over wild type (WT) hPXR on CYP3A4 expression at gene, protein, and metabolism levels, respectively. Compared with C3A cells transiently transfected with WT hPXR, the activity of CYP3A4.XREM.luc reporter gene in C3A cells transfected with hPXR-p53 or p53-hPXR increased 5- and 9-fold respectively, and the levels of CYP3A4 mRNA expression increased 3.5- and 2.6-fold, respectively. C3A cells stably transfected with hPXR-p53-AD exhibited an improved expression of CYP3A4 at both gene (2-fold) and protein (1.5-fold) levels compared to WT C3A cells. Testosterone, a CYP3A4-specific substrate, was used for detecting the metabolism activity of CYP3A4. No testosterone metabolite could be detected in microsomes from WT C3A cells and WT C3A cells-based array, while the formation of 6β-hydroxytestosterone metabolite in the transfected cells was 714 and 55 pmol/mg protein/min, respectively. In addition, all the above expression levels in the transfected cell models could be further induced with additional treatment of Rifampicin, a specific inducer for CYP3A4. In conclusion, our study established a proof-of-principle example that genetic modification with chimeric hPXR-p53-AD could improve CYP3A4 metabolism ability in hepatic cell line.
doi:10.1371/journal.pone.0095752
PMCID: PMC4006776  PMID: 24788541
12.  MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria 
Journal of Thoracic Disease  2014;6(5):517-523.
Background
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates.
Methods
Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification.
Results
Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification.
Conclusions
Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.
doi:10.3978/j.issn.2072-1439.2014.02.15
PMCID: PMC4015004  PMID: 24822113
Anaerobe; matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS); Vitek 2 anaerobe and Corynebacterium card (Vitek 2 ANC card); identification
13.  Necrotizing pneumonia and empyema caused by Neisseria flavescens infection 
Journal of Thoracic Disease  2014;6(5):553-557.
Neisseria flavescens is an uncommon pathogen of human infection, pneumonia and empyema caused by N. flavescens is rarely reported. Herein, we report a 56-year-old diabetic patient presenting necrotising pneumonia and empyema due to N. flavescens infection. The main clinical manifestation of this patient was high fever, sticky pus and gradually aggravating dyspnea. The chest computed tomography (CT) scan showed there are mass of high density areas around hilus of the left lung, hollow sign with inflammation also appeared. A biopsy specimen was taken from the left principal bronchus by lung puncture biopsy and showed necrosis and inflammation. Microscopic examination of direct smear and culture of sticky pus, much more gram-negative diplococcus was present, pathogen was further identified by Vitek NH card, Vitek MS and confirmed as N. flavescens by 16S rRNA gene sequencing finally. Anti-infection therapy following the antimicrobial susceptibility test results was effectively. To our knowledge, this is the first report of pulmonary infection caused by N. flavescens.
doi:10.3978/j.issn.2072-1439.2014.02.16
PMCID: PMC4015020  PMID: 24822118
Neisseria flavescens; pneumonia; empyema; MALDI-TOF MS; 16S rRNA gene sequencing
14.  Usefulness of the heart-rate variability complex for predicting cardiac mortality after acute myocardial infarction 
Background
Previous studies indicate that decreased heart-rate variability (HRV) is related to the risk of death in patients after acute myocardial infarction (AMI). However, the conventional indices of HRV have poor predictive value for mortality. Our aim was to develop novel predictive models based on support vector machine (SVM) to study the integrated features of HRV for improving risk stratification after AMI.
Methods
A series of heart-rate dynamic parameters from 208 patients were analyzed after a mean follow-up time of 28 months. Patient electrocardiographic data were classified as either survivals or cardiac deaths. SVM models were established based on different combinations of heart-rate dynamic variables and compared to left ventricular ejection fraction (LVEF), standard deviation of normal-to-normal intervals (SDNN) and deceleration capacity (DC) of heart rate. We tested the accuracy of predictors by assessing the area under the receiver-operator characteristics curve (AUC).
Results
We evaluated a SVM algorithm that integrated various electrocardiographic features based on three models: (A) HRV complex; (B) 6 dimension vector; and (C) 8 dimension vector. Mean AUC of HRV complex was 0.8902, 0.8880 for 6 dimension vector and 0.8579 for 8 dimension vector, compared with 0.7424 for LVEF, 0.7932 for SDNN and 0.7399 for DC.
Conclusions
HRV complex yielded the largest AUC and is the best classifier for predicting cardiac death after AMI.
doi:10.1186/1471-2261-14-59
PMCID: PMC4023175  PMID: 24886422
Acute myocardial infarction; Cardiac death; Support vector machine; Heart-rate variability; Machine learning
15.  Application of ThinPrep Bronchial Brushing Cytology in the Early Diagnosis of Lung Cancer: A Retrospective Study 
PLoS ONE  2014;9(4):e90163.
The majority of lung cancer patients are diagnosed at advanced stages of disease. This study evaluated the diagnostic value of ThinPrep (TP) bronchial brushing cytology in lung cancer. A total of 595 patients with suspicious lung cancer were enrolled in this study. The bronchial brushing samples were prepared by TP. The data were then compared to histology of lung tissue samples. Histologically, 479 of these 595 patients were diagnosed with lung cancer, including 223 cases of lung squamous cell carcinoma (SCC), 77 cases of lung adenocarcinoma (ADC), and 152 cases of small cell lung carcinoma (SCLC). The TP cytology revealed a total of 460 cases of lung cancer (including 232 SCCs, 91 ADCs, and 108 SCLCs). The TP cytological technique had 87.06% sensitivity and 62.93% specificity in the diagnosis of lung cancer. Specifically, TP cytology confirmed 195 of 223 SCCs, 47 of 77 ADCs, and 94 of 152 SCLCs. The TP cytology showed 87.44% sensitivity and 90.05% specificity for the diagnosis of SCC, with a Matthew's correlation coefficient (MCC) of 0.820; while the sensitivity was reduced to 61.04% and the specificity was 90.93% for the diagnosis of ADC, with a MCC of 0.464. For the diagnosis of SCLC, the sensitivity was 61.84% and the specificity was 96.84%, with a MCC of 0.648. Thus, this study demonstrated the usefulness of TP bronchial brushing cytology in the early diagnosis of lung cancer, especially the early stage of lung SCC. A prospective clinical trial will verify these data before being translated into the clinic.
doi:10.1371/journal.pone.0090163
PMCID: PMC3997333  PMID: 24759600
16.  Systematic identification of trans-eQTLs as putative drivers of known disease associations 
Nature genetics  2013;45(10):1238-1243.
Identifying the downstream effects of disease-associated single nucleotide polymorphisms (SNPs) is challenging: the causal gene is often unknown or it is unclear how the SNP affects the causal gene, making it difficult to design experiments that reveal functional consequences. To help overcome this problem, we performed the largest expression quantitative trait locus (eQTL) meta-analysis so far reported in non-transformed peripheral blood samples of 5,311 individuals, with replication in 2,775 individuals. We identified and replicated trans-eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Although we did not study specific patient cohorts, we identified trait-associated SNPs that affect multiple trans-genes that are known to be markedly altered in patients: for example, systemic lupus erythematosus (SLE) SNP rs49170141 altered C1QB and five type 1 interferon response genes, both hallmarks of SLE2-4. Subsequent ChIP-seq data analysis on these trans-genes implicated transcription factor IKZF1 as the causal gene at this locus, with DeepSAGE RNA-sequencing revealing that rs4917014 strongly alters 3’ UTR levels of IKZF1. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.
doi:10.1038/ng.2756
PMCID: PMC3991562  PMID: 24013639
17.  Anti-Cyclic Citrullinated Peptide Antibody Is Associated with Interstitial Lung Disease in Patients with Rheumatoid Arthritis 
PLoS ONE  2014;9(4):e92449.
Objective
Patients with rheumatoid arthritis (RA) are at risk to develop RA-associated interstitial lung disease (RA-ILD). This retrospective study aimed to investigate the potential association of the positivity of serum anti-cyclic citrullinated peptide antibody (anti-CCP2) and rheumatoid factor (RF) with RA-ILD in RA patients.
Methods
A total of 285 RA patients were recruited at the inpatient service of Peking Union Medical College Hospital in China between 2004 and 2013. Individual patients were evaluated for the evidence of ILD. The concentrations of serum anti-CCP2 and RF in individual patients were measured. The potential risk factors for ILD in RA patients were assessed by univariate and multivariate models.
Results
There were 71 RA patients with RA-ILD, accounting for 24.9% in this population. The positive rates of anti-CCP2 and RF in the patients with RA-ILD were significantly higher than that in the patients with RA-only (88.7% vs. 67.3%, p<0.001; 84.5% vs. 70.6%, p = 0.02, respectively). Univariate and multivariate logistic regression analysis revealed that RA patients with positive serum anti-CCP2, but not RF, were associated with an increased risk of ILD (crude odds ratio [cOR] 3.83, 95% confidence interval [CI] 1.74–8.43, p<0.001; adjusted odds ratio [aOR] 3.50, 95% CI 1.52–8.04, p<0.001).
Conclusion
Our findings suggest that positive serum anti-CCP2, but not RF, may be associated with RA-ILD in RA patients.
doi:10.1371/journal.pone.0092449
PMCID: PMC3990563  PMID: 24743261
18.  GhMPK17, a Cotton Mitogen-Activated Protein Kinase, Is Involved in Plant Response to High Salinity and Osmotic Stresses and ABA Signaling 
PLoS ONE  2014;9(4):e95642.
Mitogen-activated protein kinase (MAPK) cascades play pivotal roles in mediating biotic and abiotic stress responses. Cotton (Gossypium hirsutum) is the most important textile crop in the world, and often encounters abiotic stress during its growth seasons. In this study, a gene encoding a mitogen-activated protein kinase (MAPK) was isolated from cotton, and designated as GhMPK17. The open reading frame (ORF) of GhMPK17 gene is 1494 bp in length and encodes a protein with 497 amino acids. Quantitative RT-PCR analysis indicated that GhMPK17 expression was up-regulated in cotton under NaCl, mannitol and ABA treatments. The transgenic Arabidopsis plants expressing GhMPK17 gene showed higher seed germination, root elongation and cotyledon greening/expansion rates than those of the wild type on MS medium containing NaCl, mannitol and exogenous ABA, suggesting that overexpression of GhMPK17 in Arabidopsis increased plant ABA-insensitivity, and enhanced plant tolerance to salt and osmotic stresses. Furthermore, overexpression of GhMPK17 in Arabidopsis reduced H2O2 level and altered expression of ABA- and abiotic stress-related genes in the transgenic plants. Collectively, these data suggested that GhMPK17 gene may be involved in plant response to high salinity and osmotic stresses and ABA signaling.
doi:10.1371/journal.pone.0095642
PMCID: PMC3990703  PMID: 24743296
19.  Nitrite Promotes the Growth and Decreases the Lignin Content of indica Rice Calli: A Comprehensive Transcriptome Analysis of Nitrite-Responsive Genes during In Vitro Culture of Rice 
PLoS ONE  2014;9(4):e95105.
As both major macronutrients and signal molecules, nitrogen metabolites, such as nitrate and nitrite, play an important role in plant growth and development. In this study, the callus growth of indica rice cv. 9311 was significantly enhanced by nitrite, whereas the soluble protein content remained unchanged. The deep RNA sequencing technology (RNA-seq) showed that the transcriptional profiles of cv. 9311 calli were significantly changed after adding nitrite to the nitrate-free medium, and these nitrite-responsive genes were involved in a wide range of plant processes, particularly in the secondary metabolite pathways. Interestingly, most of the genes involved in phenylpropanoid-related pathways were coordinately down-regulated by nitrite, such as four cinnamoyl-CoA reductase, and these in turn resulted in the decrease of lignin content of indica calli. Furthermore, several candidate genes related to cell growth or stress responses were identified, such as genes coding for expansins, SMALL AUXIN UP RNA (SAUR) and HSP20s, and these suggested that nitrite could probably serve as a transcriptome signal to enhance the indica calli growth by regulation of various downstream genes expression. This study contributes to a better understanding of the function of nitrite during the process of plant tissue culture and could aid in the application of this technology to improved indica genetic transformation efficiency.
doi:10.1371/journal.pone.0095105
PMCID: PMC3989302  PMID: 24740395
20.  Prognostic Significance of Cyclin D1 Expression in Colorectal Cancer: A Meta-Analysis of Observational Studies 
PLoS ONE  2014;9(4):e94508.
Objective
Cyclin D1 plays a vital role in cancer cell cycle progression and is overexpressed in many human cancers, including colorectal cancer (CRC). However, the prognostic value of cyclin D1 overexpression in colorectal cancer is conflicting and heterogeneous. We conducted a meta-analysis to more precisely evaluate its prognostic significance.
Methods
A comprehensive literature search for relevant studies published up to January 2014 was performed using PubMed, EMBASE, and ISI Web of Science. The pooled hazard ratio (HR) with 95% confidence intervals (CI) was used to estimate the effects.
Results
22 studies with 4150 CRC patients were selected to evaluate the association between cyclin D1 and overall survival (OS), disease-free survival (DFS) and clinicopathological parameters. In a random-effects model, the results showed that cyclin D1 overexpression in CRC was significantly associated with both poor OS (HR = 0.73, 95% CI: 0.63–0.85, P<0.001) and DFS (HR = 0.60, 95% CI: 0.44–0.82, P = 0.001). Additionally, cyclin D1 overexpression was significantly associated with more relative older patients (≥60 years) (OR 0.62, 95% CI 0.44–0.89, P = 0.009), T3,4 tumor invasion (OR 0.70, 95% CI 0.57–0.85, P<0.001), N positive (OR 0.75, 95% CI 0.60–0.95, P = 0.016) and distant metastasis (OR 0.60, 95% CI 0.36–0.99, P = 0.047) of CRC.
Conclusion
The meta-analysis results indicated that cyclin D1 is an unfavorable prognostic factor for CRC. Cyclin D1 overexpression might be associated with poor clinical outcome and some clinicopathological factors such as age, T category, N category and distant metastasis in CRC patients.
doi:10.1371/journal.pone.0094508
PMCID: PMC3984178  PMID: 24728073
21.  Three-Dimensional Sulfur/Graphene Multifunctional Hybrid Sponges for Lithium-Sulfur Batteries with Large Areal Mass Loading 
Scientific Reports  2014;4:4629.
In this communication, we introduce the concept of three dimensional (3D) battery electrodes to enhance the capacity per footprint area for lithium-sulfur battery. In such a battery, 3D electrode of sulfur embedded into porous graphene sponges (S-GS) was directly used as the cathode with large areal mass loading of sulfur (12 mg cm−2), approximately 6–12 times larger than that of most reports. The graphene sponges (GS) worked as a framework that can provide high electronic conductive network, abilities to absorb the polysulfides intermediate, and meanwhile mechanical support to accommodate the volume changes during charge and discharge. As a result, the S-GS electrode with 80 wt.% sulfur can deliver an extremely high areal specific capacitance of 6.0 mAh cm−2 of the 11th cycle, and maintain 4.2 mAh cm−2 after 300 charge−discharge cycles at a rate of 0.1C, representing an extremely low decay rate (0.08% per cycle after 300 cycles), which could be the highest areal specific capacity with comparable cycle stability among the rechargeable Li/S batteries reported ever.
doi:10.1038/srep04629
PMCID: PMC3982171  PMID: 24717445
22.  BHBA Suppresses LPS-Induced Inflammation in BV-2 Cells by Inhibiting NF-κB Activation 
Mediators of Inflammation  2014;2014:983401.
β-Hydroxybutyric acid (BHBA) has neuroprotective effects, but the underlying molecular mechanisms are unclear. Microglial activation plays an important role in neurodegenerative diseases by producing several proinflammatory enzymes and proinflammatory cytokines. The current study investigates the potential mechanisms whereby BHBA affects the expression of potentially proinflammatory proteins by cultured murine microglial BV-2 cells stimulated with lipopolysaccharide (LPS). The results showed that BHBA significantly reduced LPS-induced protein and mRNA expression levels of iNOS, COX-2, TNF-α, IL-1β, and IL-6. Blocking of GPR109A by PTX resulted in a loss of this anti-inflammatory effect in BV-2 cells. Western blot analysis showed that BHBA reduced LPS-induced degradation of IκB-α and translocation of NF-κB, while no effect was observed on MAPKs phosphorylation. All results imply that BHBA significantly reduces levels of proinflammatory enzymes and proinflammatory cytokines by inhibition of the NF-κB signaling pathway but not MAPKs pathways, and GPR109A is essential to this function. Overall, these data suggest that BHBA has a potential as neuroprotective drug candidate in neurodegenerative diseases.
doi:10.1155/2014/983401
PMCID: PMC3997897  PMID: 24803746
23.  Ang (1–7) Protects Islet Endothelial Cells from Palmitate-Induced Apoptosis by AKT, eNOS, p38 MAPK, and JNK Pathways 
Journal of Diabetes Research  2014;2014:391476.
This study aimed to explore the effect of angiotensin (1–7) (Ang (1–7)) on palmitate-induced apoptosis in islet endothelial cells and the mechanism of action. MS-1 cells were treated with palmitate in the presence or absence of Ang (1–7). The percentage of apoptotic cells was determined by DNA fragmentation and flow cytometry. Reactive oxygen species (ROS) production was measured using a Reactive Oxygen Species Assay Kit. Expression of AKT, eNOS, C-Jun N-terminal kinase (JNK), and p38 was detected by western blotting. Compared with palmitate treated group, palmitate-induced apoptosis was decreased in MS-1 cells which were preincubated with Ang (1–7) (P < 0.05). Palmitate decreased the phosphorylation of AKT and eNOS, and Ang (1–7) increased the phosphorylation of these kinases (P < 0.05), with a concomitant reduction in MS-1 cells apoptosis. Ang (1–7) also inhibited the palmitate-induced ROS production and attenuated the apoptosis-related signaling molecule JNK and p38 activation (all P < 0.05). PI3K/AKT, eNOS, p38 MAPK, and JNK inhibitors blocked the antilipoapoptosis of Ang (1–7) (all P < 0.05). Our findings suggest that Ang (1–7) reduces palmitate-induced islet endothelial cells apoptosis. AKT/eNOS/NO signaling and JNK and p38 pathway are involved in the Ang (1–7)-mediated modulation of islet endothelial cells lipoapoptosis.
doi:10.1155/2014/391476
PMCID: PMC3996957  PMID: 24804268
24.  Triptycene-based Bis(benzimidazole) Carboxylate-Bridged Biomimetic Diiron(II) Complexes 
European journal of inorganic chemistry  2013;2013(12):2011-2019.
A triptycene-based bis(benzimidazole) ester ligand, L3, was designed to enhance the electron donating ability of the heterocyclic nitrogen atoms relative to those of the first generation bis(benzoxazole) analogs, L1 and L2. A convergent synthesis of L3 was designed and executed. Three-component titration experiments using UV-visible spectroscopy revealed that the desired diiron(II) complex could be obtained with a 1:2:1 ratio of L3:Fe(OTf)2(MeCN)2:external carboxylate reactants. X-ray crystallographic studies of two diiron complexes derived in this manner from L3 revealed their formulas to be [Fe2L3(μ-OH)(μ-O2CR)(OTf)2], where R = 2,6-bis(p-tolyl)benzoate (7) or triphenylacetate (8). The structures are similar to that of a diiron complex derived from L1, [Fe2L1(μ-OH)(μ-O2CArTol)(OTf)2] (9) with a notable difference being that, in 7 and 8, the geometry at iron more closely resembles square-pyramidal than trigonal-bipyramidal. Mössbauer spectroscopic analyses of 7 and 8 indicate the presence of high-spin diiron(II) cores. These results demonstrate the importance of substituting benzimidazole for benzoxazole for assembling biomimetic diiron complexes with syn disposition of two N-donor ligands, as found in O2-activating carboxylate-bridged diiron centers in biology.
doi:10.1002/ejic.201201387
PMCID: PMC3625018  PMID: 23585728
25.  Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity 
Age  2011;35(2):301-314.
The genetic basis of the large species differences in longevity and aging remains a mystery. Thanks to recent large-scale genome sequencing efforts, the genomes of multiple species have been sequenced and can be used for cross-species comparisons to study species divergence in longevity. By analyzing proteins under accelerated evolution in several mammalian lineages where maximum lifespan increased, we identified genes and processes that are candidate targets of selection when longevity evolves. We identified several proteins with longevity-specific selection patterns, including COL3A1 that has previously been related to aging and proteins related to DNA damage repair and response such as DDB1 and CAPNS1. Moreover, we found that processes such as lipid metabolism and cholesterol catabolism show such patterns of selection and suggest a link between the evolution of lipid metabolism, cholesterol catabolism, and the evolution of longevity. Lastly, we found evidence that the proteasome–ubiquitin system is under selection specific to lineages where longevity increased and suggest that its selection had a role in the evolution of longevity. These results provide evidence that natural selection acts on species when longevity evolves, give insights into adaptive genetic changes associated with the evolution of longevity in mammals, and provide evidence that at least some repair systems are selected for when longevity increases.
Electronic supplementary material
The online version of this article (doi:10.1007/s11357-011-9361-y) contains supplementary material, which is available to authorized users.
doi:10.1007/s11357-011-9361-y
PMCID: PMC3592953  PMID: 22205409
Aging; Evolutionary genomics; Protein evolution; Mammals; Proteasome

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