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1.  Noncoding RNAs and DNA Methylation in Plants 
National science review  2014;1(2):219-229.
Cytosine DNA methylation is an epigenetic modification in eukaryotes that maintains genome integrity and regulates gene expression. The DNA methylation patterns in plants are more complex than those in animals, and plants and animals have common as well as distinct pathways in regulating DNA methylation. Recent studies involving genetic, molecular, biochemical and genomic approaches have greatly expanded our knowledge of DNA methylation in plants. The roles of many proteins as well as non-coding RNAs in DNA methylation have been uncovered.
doi:10.1093/nsr/nwu003
PMCID: PMC4307843  PMID: 25635229
siRNA; non-coding RNA; DNA methylation; Pol IV; Pol V; argonaute
2.  The Effectiveness of RECIST on Survival in Patients with NSCLC Receiving Chemotherapy with or without Target Agents as First-Line Treatment 
Scientific Reports  2015;5:7683.
We analyzed the correlation between survival and antitumor effect evaluated by RECIST in advanced NSCLC patients with chemotherapy plus target therapy or not as first-line treatment, to examine the applicability of RECIST in this population. The patients were screened from 4 clinical trials (12621, 12006, FASTACT-I, and FASTACT-II), and those who received chemotherapy plus target therapy or chemotherapy alone were eligible. Among the 59 enrolled patients, 29 received combination therapy, while the other 30 received chemotherapy only. In the combination therapy group, patients with PR or SD had longer overall survival (OS) than those with PD (P < 0.001 and P = 0.002, respectively). However, in the chemotherapy alone group, compared with PD patients, either PR or SD group had no significant overall survival benefit (P = 0.690 and P = 0.528, respectively). In summary, for advanced NSCLC patients receiving chemotherapy plus target therapy as first-line treatment and evaluated by RECIST criteria, SD has the same overall survival benefit as PR, suggesting that antitumor effective evaluation by RECIST criteria cannot be translated to overall survival benefit especially for this kind of patients. Therefore, developing a more comprehensive evaluation method to perfect RECIST criteria is thus warranted for patients received target therapy in NSCLC.
doi:10.1038/srep07683
PMCID: PMC4286759  PMID: 25567662
3.  Variation in smoking cessation after vascular operations 
Journal of vascular surgery  2013;57(5):1338-1344.e4.
Objective
Smoking is the most important modifiable risk factor for patients with vascular disease. The purpose of this study was to examine smoking cessation rates after vascular procedures and delineate factors predictive of postoperative smoking cessation.
Methods
The Vascular Study Group of New England registry was used to analyze smoking status preoperatively and at 1 year after carotid endarterectomy, carotid artery stenting, lower extremity bypass, and open and endovascular abdominal aortic aneurysm repair between 2003 and 2009. Of 10,734 surviving patients after one of these procedures, 1755 (16%) were lost to follow-up and 1172 (11%) lacked documentation of their smoking status at follow-up. The remaining 7807 patients (73%) were available for analysis. Patient factors independently associated with smoking cessation were determined using multivariate analysis. The relative contribution of patient and procedure factors including treatment center were measured by χ-pie analysis. Variation between treatment centers was further evaluated by calculating expected rates of cessation and by analysis of means. Vascular Study Group of New England surgeons were surveyed regarding their smoking cessation techniques (85% response rate).
Results
At the time of their procedure, 2606 of 7807 patients (33%) were self-reported current smokers. Of these, 1177 (45%) quit within the first year of surgery, with significant variation by procedure type (open abdominal aortic aneurysm repair, 50%; endovascular repair, 49%; lower extremity bypass, 46%; carotid endarterectomy, 43%; carotid artery stenting, 27%). In addition to higher smoking cessation rates with more invasive procedures, age >70 years (odds ratio [OR], 1.90; 95% confidence interval [CI], 1.30-2.76; P< .001) and dialysis dependence (OR, 2.38; 95% CI, 1.04-5.43; P = .04) were independently associated with smoking cessation, whereas hypertension (OR, 1.23; 95% CI, 1.00-1.51; P = .051) demonstrated a trend toward significance. Treatment center was the greatest contributor to smoking cessation, and there was broad variation in smoking cessation rates, from 28% to 62%, between treatment centers. Cessation rates were higher than expected in three centers and significantly lower than expected in two centers. Among survey respondents, 78% offered pharmacologic therapy or referral to a smoking cessation specialist, or both. The smoking cessation rate for patients of these surgeons was 48% compared with 33% in those who did not offer medications or referral (P< .001).
Conclusions
Patients frequently quit smoking after vascular surgery, and multiple patient-related and procedure-related factors contribute to cessation. However, we note significant influence of treatment center on cessation as well as broad variation in cessation rates between treatment centers. This variation indicates an opportunity for vascular surgeons to impact smoking cessation at the time of surgery.
doi:10.1016/j.jvs.2012.10.130
PMCID: PMC4279220  PMID: 23375433
4.  Superhydrophobic Photosensitizers. Mechanistic Studies of 1O2 Generation in the Plastron and Solid/Liquid Droplet Interface 
Journal of the American Chemical Society  2013;135(50):18990-18998.
We describe here a physical-organic study of the first triphasic superhydrophobic sensitizer for photooxidations in water droplets. Control of synthetic parameters enables the mechanistic study of “borderline” two- and three-phase superhydrophobic sensitizer surfaces where 1O2 is generated in compartments that are wetted, partially wetted, or remain dry in the plastron (i.e., air layer beneath the droplet). The superhydrophobic surface is synthesized by partially embedding silicon phthalocyanine (Pc) sensitizing particles to specific locations on polydimethylsiloxane (PDMS) posts printed in a square array (1 mm tall posts on 0.5 mm pitch). In the presence of red light and oxygen, singlet oxygen is formed on the superhydrophobic surface and reacts with 9,10-anthracene dipropionate dianion (1) within a freestanding water droplet to produce an endoperoxide in 54–72% yields. Control of the 1O2 chemistry was achieved by the synthesis of superhydrophobic surfaces enriched with Pc particles either at the PDMS end-tips or at PDMS post bases. Much of the 1O2 that reacts with anthracene 1 in the droplets was generated by the sensitizer “wetted” at the Pc particle/water droplet interface and gave the highest endoperoxide yields. About 20% of the 1O2 can be introduced into the droplet from the plastron. The results indicate that the superhydrophobic sensitizer surface offers a unique system to study 1O2 transfer routes where a balance of gas and liquid contributions of 1O2 is tunable within the same superhydrophobic surface.
doi:10.1021/ja410529q
PMCID: PMC3930608  PMID: 24295210
5.  A Large-scale Cross-sectional Study of ALK Rearrangements and EGFR Mutations in Non-small-cell Lung Cancer in Chinese Han Population 
Scientific Reports  2014;4:7268.
The predictive power of age at diagnosis and smoking history for ALK rearrangements and EGFR mutations in non-small-cell lung cancer (NSCLC) remains not fully understood. In this cross-sectional study, 1160 NSCLC patients were prospectively enrolled and genotyped for EML4-ALK rearrangements and EGFR mutations. Multivariate logistic regression analysis was performed to explore the association between clinicopathological features and these two genetic aberrations. Receiver operating characteristic (ROC) curves methodology was applied to evaluate the predictive value. We showed that younger age at diagnosis was the only independent variable associated with EML4-ALK rearrangements (odds ratio (OR) per 5 years' increment, 0.68; p < 0.001), while lower tobacco exposure (OR per 5 pack-years' increment, 0.88; p < 0.001), adenocarcinoma (OR, 6.61; p < 0.001), and moderate to high differentiation (OR, 2.05; p < 0.001) were independently associated with EGFR mutations. Age at diagnosis was a very strong predictor of ALK rearrangements but poorly predicted EGFR mutations, while smoking pack-years may predict the presence of EGFR mutations and ALK rearrangements but with rather limited power. These findings should assist clinicians in assessing the likelihood of EML4-ALK rearrangements and EGFR mutations and understanding their biological implications in NSCLC.
doi:10.1038/srep07268
PMCID: PMC4248273  PMID: 25434695
6.  EBV-driven LMP1 and IFN-γ up-regulate PD-L1 in nasopharyngeal carcinoma: Implications for oncotargeted therapy 
Oncotarget  2014;5(23):12189-12202.
PD-L1 expression is a feature of Epstein-Barr virus (EBV) associated malignancies such as nasopharyngeal carcinoma (NPC). Here, we found that EBV-induced latent membrane protein 1 (LMP1) and IFN-γ pathways cooperate to regulate programmed cell death protein 1 ligand (PD-L1). Expression of PD-L1 was higher in EBV positive NPC cell lines compared with EBV negative cell lines. PD-L1 expression could be increased by exogenous and endogenous induction of LMP1 induced PD-L1. In agreement, expression of PD-L1 was suppressed by knocking down LMP1 in EBV positive cell lines. We further demonstrated that LMP1 up-regulated PD-L1 through STAT3, AP-1, and NF-κB pathways. Besides, IFN-γ was independent of but synergetic with LMP1 in up-regulating PD-L1 in NPC. Furthermore, we showed that PD-L1 was associated with worse disease-free survival in NPC patients. These results imply that blocking both the LMP1 oncogenic pathway and PD-1/PD-L1 checkpoints may be a promising therapeutic approach for EBV positive NPC patients.
PMCID: PMC4322961  PMID: 25361008
Nasopharyngeal carcinoma (NPC); latent membrane protein 1 (LMP1); PD-L1; Epstein–Barr virus (EBV)
7.  Interleukin-23A is associated with tumor growth in Helicobacter-pylori-related human gastric cancer 
Cancer Cell International  2014;14(1):104.
Background
Interleukin (IL)-23 is one of the newly identified inflammatory cytokines, and inflammation is also known to be related to the development of gastric cancer (GC). The role of IL-23 in gastric cancer, however, is largely unknown. In the present study, we investigated the expression and possible role of IL-23A in human GC.
Methods
The expression of IL-23A and IL-17A in human GC tissues was determined by immunohistochemistry, and the relationship between IL-23A expression and clinical characteristics of GC was investigated. The serum concentration of IL-23A and IL-17A was also tested by ELISA. The source and role of IL-23A in GC were studied in vitro by Flowcytometry, MTS (Owen’s reagent) assay and Western blot.
Results
IL-23A, IL-23 receptor (IL-23R) and IL-17A were all overexpressed in human GC tissues, and the level of IL-23A was well correlated with IL-17A in GC tissues as well as in patient’s serum. Macrophages and GC cells were the main source of IL-23A secretion upon stimulation of H. pylori lysate. Furthermore, we found that IL-23A promoted proliferation of GC cell lines via IL-17A/IL-17 receptor antagonist (IL-17RA) /nuclear factor-κB (NF-κB) signaling.
Conclusions
The high expression of IL-23A is associated with GC. IL-23A can promoted GC cells growth by inducing the secretion of IL-17A in tumor microenvironment. Our results suggest that the serum concentration of IL-23A is a good biomarker of poor clinical prognosis in GC patients.
doi:10.1186/s12935-014-0104-x
PMCID: PMC4207902  PMID: 25349535
Interleukin-23A; Interleukin-17A; Nuclear factor-κB; Gastric cancer
8.  Risk of treatment-related deaths with vascular endothelial growth factor receptor tyrosine kinase inhibitors: a meta-analysis of 41 randomized controlled trials 
OncoTargets and therapy  2014;7:1851-1867.
Background
Vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitors (TKIs) have widely been used in advanced cancer. However, these drugs may also lead to serious adverse events. The present meta-analysis aimed to determine the overall incidence and risk of deaths due to VEGFR-TKIs with more detailed subgroup analysis.
Materials and methods
PubMed, Web of Science, and Cochrane databases were searched for randomized controlled trials (RCTs) that compared VEGFR-TKIs with non-VEGFR-TKIs in the treatment of solid cancer. Pooled incidence, odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using random-effects or fixed-effects models based on the heterogeneity of included trials.
Results
A total of 14,139 participants from 41 RCTs were enrolled. The pooled incidence of death due to VEGFR-TKIs was 1.9% (95% CI: 1.6%–2.3%) with an OR of 1.85 (95% CI: 1.33–2.58; P<0.01) when compared with control groups. On subgroup analysis, significantly increased risk of death was found in patients with nonsmall-cell lung cancer (OR: 2.37; 95% CI: 1.19–4.73; P=0.01) and colorectal cancer (OR: 2.84; 95% CI: 1.02–7.96; P=0.05). Among different VEGFR-TKIs, sorafenib and sunitinib had significant risk of death when compared with control arms, respectively. VEGFR-TKIs in combination with other antineoplastic agents, but not VEGFR-TKI monotherapy, significantly increased the risk of treatment-related deaths. No heterogeneity was noted across all the prespecified subgroups regarding ORs.
Conclusion
The present work pointed out a significantly increased risk of death due to VEGFR-TKIs. Close monitoring should be emphasized in patients receiving these drugs.
doi:10.2147/OTT.S68386
PMCID: PMC4199796  PMID: 25336977
cancer; tyrosine kinase inhibitors; treatment-related death; meta-analysis
9.  DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis 
PLoS Genetics  2014;10(7):e1004446.
RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology.
Author Summary
DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. Here, we uncovered an unexpected role of DNA topoisomerase 1α (TOP1α) in the maintenance of genome stability. Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. Two plant-specific RNA polymerases, Pol IV and Pol V, generate small and long noncoding RNAs, respectively, from TEs and repeats. These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. The role of TOP1α in RdDM could be attributed to its promotion of Pol V, but not Pol IV, transcription to generate long noncoding RNAs.
doi:10.1371/journal.pgen.1004446
PMCID: PMC4080997  PMID: 24992598
10.  Phytochrome B-mediated activation of lipoxygenase modulates an excess red light-induced defence response in Arabidopsis  
Journal of Experimental Botany  2014;65(17):4907-4918.
Summary
Excess red light induces a defence response by activating lipoxygenase at both the transcript and activity levels.
Lipoxygenase (LOX), a non-haem-iron-containing dioxygenase, is activated under various biotic or abiotic stresses to trigger a series resistance response, but the molecular mechanism of LOX activation remains unclear. This work investigated the activation of LOX during the plant defence response induced by excess red light (RL). In conditions of RL-induced defence, Arabidopsis LOX activity and transcription levels of LOX2, LOX3, and LOX4 were both upregulated. Under RL, phytochrome B promoted the degradation of phytochrome-interacting factor 3 (PIF3), a factor that inhibited the expression levels of LOXs, and thus the transcription levels of LOX2, LOX3, and LOX4 were increased. Upon pathogen infection, the activity of mitogen-activated protein kinase 3 (MPK3) and MPK6 was increased in plants pre-treated with RL. Moreover, experiments with the inhibitor PD98059 and mutants mpk3 and mpk6-2 demonstrated that MPK3 and MPK6 were both responsible for LOX activation. Further results showed that, in response to RL, an increase in cytoplasmic calcium concentration and upregulation of calmodulin 3 (CaM3) transcript level occurred upstream of MPK3 and MPK6 activation. Collectively, these results suggested that activation of LOX both at the transcript level and in terms of activity modulates the defence response induced by RL, providing a new insight into the mechanistic study of LOX during plant defences.
doi:10.1093/jxb/eru247
PMCID: PMC4144769  PMID: 24916071
Arabidopsis; defence response; excess red light; lipoxygenase; MAPK; phytochrome B.
11.  BRG1 variant rs1122608 on chromosome 19p13.2 confers protection against stroke and regulates expression of pre-mRNA-splicing factor SFRS3 
Human genetics  2013;133(5):499-508.
A single nucleotide polymorphism (SNP) rs1122608 on chromosome 19p13.2 and in the BRG1/SMARCA4 gene was previously associated with coronary artery disease (CAD). CAD and ischemic stroke are both associated with atherosclerosis. Thus, we tested the hypothesis that rs1122608 is associated with ischemic stroke. Further studies were used to identify the most likely mechanism by which rs1122608 regulates atherosclerosis. For case–control association studies, two independent Chinese Han GeneID cohorts were used, including a Central cohort with 1,075 cases and 2,685 controls and the Northern cohort with 1,208 cases and 824 controls. eQTL and real-time RT-PCR analyses were used to identify the potential candidate gene(s) affected by rs1122608. The minor allele T of SNP rs1122608 showed significant association with a decreased risk of ischemic stroke in the Central GeneID cohort (adjusted Padj = 2.1 × 10−4, OR 0.61). The association was replicated in an independent Northern GeneID cohort (Padj = 6.00 × 10−3, OR 0.69). The association became more significant in the combined population (Padj = 7.86 × 10−5, OR 0.73). Allele T of SNP rs1122608 also showed significant association with a decreased total cholesterol level (Padj = 0.013). Allele T of rs1122608 was associated with an increased expression level of SFRS3 encoding an mRNA splicing regulator, but not with the expression of BRG1/SMARCA4 or LDLR (located 36 kb from rs1122608). Increased expression of SFSR3 may decrease IL-1β expression and secretion, resulting in reduced risk of atherosclerosis and stroke. This is the first study that demonstrates that rs1122608 confers protection against ischemic stroke and implicates splicing factor SFSR3 in the disease process.
doi:10.1007/s00439-013-1389-x
PMCID: PMC3988217  PMID: 24190014
12.  Innovative pharmaceutical development based on unique properties of nanoscale delivery formulation 
Nanoscale  2013;5(18):8307-8325.
The advent of nanotechnology has reignited interest in the field of pharmaceutical science for the development of nanomedicine. Nanomedicinal formulations are nanometer-sized carrier materials designed for increasing the drug tissue bioavailability, thereby improving the treatment of systemically applied chemotherapeutic drugs. Nanomedicine is a new approach to deliver the pharmaceuticals through different routes of administration with safer and more effective therapies compared to conventional methods. To date, various kinds of nanomaterials have been developed over the years to make delivery systems more effective for the treatment of various diseases. Even though nanomaterials have significant advantages due to their unique nanoscale properties, there are still significant challenges in the improvement and development of nanoformulations with composites and other materials. Here in this review, we highlight the nanomedicinal formulations aiming to improve the balance between the efficacy and the toxicity of therapeutic interventions through different routes of administration and how to design nanomedicine for safer and more effective ways to improve the treatment quality. We also emphasize the environmental and health prospects of nanomaterials for human health care.
doi:10.1039/c3nr01525d
PMCID: PMC3934102  PMID: 23860639
13.  Network Meta-Analysis of Erlotinib, Gefitinib, Afatinib and Icotinib in Patients with Advanced Non-Small-Cell Lung Cancer Harboring EGFR Mutations 
PLoS ONE  2014;9(2):e85245.
Background
Several EGFR-tyrosine kinase inhibitors (EGFR-TKIs) including erlotinib, gefitinib, afatinib and icotinib are currently available as treatment for patients with advanced non-small-cell lung cancer (NSCLC) who harbor EGFR mutations. However, no head to head trials between these TKIs in mutated populations have been reported, which provides room for indirect and integrated comparisons.
Methods
We searched electronic databases for eligible literatures. Pooled data on objective response rate (ORR), progression free survival (PFS), overall survival (OS) were calculated. Appropriate networks for different outcomes were established to incorporate all evidences. Multiple-treatments comparisons (MTCs) based on Bayesian network integrated the efficacy and specific toxicities of all included treatments.
Results
Twelve phase III RCTs that investigated EGFR-TKIs involving 1821 participants with EGFR mutation were included. For mutant patients, the weighted pooled ORR and 1-year PFS of EGFR-TKIs were significant superior to that of standard chemotherapy (ORR: 66.6% vs. 30.9%, OR 5.46, 95%CI 3.59 to 8.30, P<0.00001; 1-year PFS: 42.9% vs. 9.7%, OR 7.83, 95%CI 4.50 to 13.61; P<0.00001) through direct meta-analysis. In the network meta-analyses, no statistically significant differences in efficacy were found between these four TKIs with respect to all outcome measures. Trend analyses of rank probabilities revealed that the cumulative probabilities of being the most efficacious treatments were (ORR, 1-year PFS, 1-year OS, 2-year OS): erlotinib (51%, 38%, 14%, 19%), gefitinib (1%, 6%, 5%, 16%), afatinib (29%, 27%, 30%, 27%) and icotinib (19%, 29%, NA, NA), respectively. However, afatinib and erlotinib showed significant severer rash and diarrhea compared with gefitinib and icotinib.
Conclusions
The current study indicated that erlotinib, gefitinib, afatinib and icotinib shared equivalent efficacy but presented different efficacy-toxicity pattern for EGFR-mutated patients. Erlotinib and afatinib revealed potentially better efficacy but significant higher toxicities compared with gefitinib and icotinib.
doi:10.1371/journal.pone.0085245
PMCID: PMC3922700  PMID: 24533047
14.  Growing Impact of Restenosis on the Surgical Treatment of Peripheral Arterial Disease 
Background
Patients with peripheral arterial disease often experience treatment failure from restenosis at the site of a prior peripheral endovascular intervention (PVI) or lower extremity bypass (LEB). The impact of these treatment failures on the utilization and outcomes of secondary interventions is poorly understood.
Methods and Results
In our regional vascular quality improvement collaborative, we compared 2350 patients undergoing primary infrainguinal LEB with 1154 patients undergoing secondary infrainguinal LEB (LEB performed after previous revascularization in the index limb) between 2003 and 2011. The proportion of patients undergoing secondary LEB increased by 72% during the study period (22% of all LEBs in 2003 to 38% in 2011, P<0.001). In‐hospital outcomes, such as myocardial infarction, death, and amputation, were similar between primary and secondary LEB groups. However, in both crude and propensity‐weighted analyses, secondary LEB was associated with significantly inferior 1‐year outcomes, including major adverse limb event‐free survival (composite of death, new bypass graft, surgical bypass graft revision, thrombectomy/thrombolysis, or above‐ankle amputation; Secondary LEB MALE‐free survival = 61.6% vs primary LEB MALE‐free survival = 67.5%, P=0.002) and reintervention or amputation‐free survival (composite of death, reintervention, or above‐ankle amputation; Secondary LEB RAO‐free survival = 58.9% vs Primary LEB RAO‐free survival 64.1%, P=0.003). Inferior outcomes for secondary LEB were observed regardless of the prior failed treatment type (PVI or LEB).
Conclusions
In an era of increasing utilization of PVI, a growing proportion of patients undergo LEB in the setting of a prior failed PVI or surgical bypass. When caring for patients with peripheral arterial disease, physicians should recognize that first treatment failure (PVI or LEB) affects the success of subsequent revascularizations.
doi:10.1161/JAHA.113.000345
PMCID: PMC3886769  PMID: 24275626
angioplasty; bypass; peripheral vascular disease; restenosis; revascularization; stents
15.  Serum proteomic study on EGFR-TKIs target treatment for patients with NSCLC 
OncoTargets and therapy  2013;6:1481-1491.
Background
Although epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are widely used for EGFR mutated non-small-cell lung cancer (NSCLC) patients, tumor sample availability and heterogeneity of the tumor remain challenging for physicians’ selection of these patients. Here, we developed a serum proteomic classifier based on matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) to predict the clinical outcome of patients treated with EGFR-TKIs.
Method
A total of 68 patients were included in this study. All patients received EGFR-TKIs as second or third line treatment and blood samples were collected before treatment. Using magnetic bead assisted serum peptide capture coupled to MALDI-TOF-MS, pretreatment serum from 24 NSCLC patients was analyzed to develop a proteomic classifier (training set). In a blinded test set with 44 patients, each sample was classified into “good” or “poor” groups using this classifier. Survival analysis of each group was done based on this classification.
Result
A 3-peptide proteomic classifier was developed from the training set. In the testing set, the classifier was able to distinguish patients of “good” or “poor” outcomes with 93% accuracy, sensitivity, and specificity. The overall survival and progression free survival of the predicted good group were found to be significantly longer than the poor group, not only in the whole population but also in certain subgroups, such as pathological adenocarcinoma and nonsmokers. With respect to the tumor samples available for EGFR mutation detection, all eight EGFR mutant tumors and three of the 12 wild type EGFR tumors were classified as good while nine of the 12 wild type EGFR tumors were classified as poor.
Conclusion
The current study has shown that a proteomic classifier can predict the outcome of patients treated with EGFR-TKIs and may aid in patient selection in the absence of available tumor tissue. Further studies are necessary to confirm these findings.
doi:10.2147/OTT.S51887
PMCID: PMC3818102  PMID: 24204163
non-small-cell lung cancer; matrix assisted laser desorption ionization time of flight mass spectrometry; proteomic classifier; survival
16.  Mechanisms that impact microRNA stability in plants 
RNA Biology  2012;9(10):1218-1223.
microRNAs (miRNAs) are 20–24 nucleotide RNAs that regulate a variety of developmental and metabolic processes. The accumulation of miRNAs in vivo can be controlled at multiple levels. In addition to miRNA biogenesis, mechanisms that lead to RNA degradation, such as 3′ uridylation and 3′ truncation, also affect the steady-state levels of miRNAs. On the other hand, 2’-O-methylation in plant miRNAs protects their 3′ ends from truncation and uridylation. The recent identification of HESO1 as the key enzyme responsible for miRNA uridylation in Arabidopsis was a first step toward a full understanding of the mechanisms underlying miRNA turnover. Analyses of the heso1 mutant predicted the existence of another uridylation activity and a previously unknown nuclease that act on miRNAs. The future identification of these enzymes will enrich our understanding of miRNA turnover.
doi:10.4161/rna.22034
PMCID: PMC3583851  PMID: 22995833
argonaute; HEN1; HESO1; methylation; microRNA; miRNA stability; miRNA turnover; uridylation
17.  Efficacy of epidermal growth factor receptor-tyrosine kinase inhibitors for Chinese patients with squamous cell carcinoma of lung harboring EGFR mutation 
Journal of Thoracic Disease  2013;5(5):585-592.
Objective
Epidermal growth factor receptor (EGFR) mutation mostly occurred in lung adenocarcinoma, rarely in squamous cell carcinoma (SQCC). EGFR mutation rate in SQCC varied in previous reports, and the efficacy of EGFR tyrosine kinase inhibitors (TKIs) in SQCC harboring EGFR mutation has not yet been fully evaluated. The aim of this study was to investigate the efficacy EGFR-TKIs for Chinese patients with SQCC of lung harboring EGFR mutation.
Patients and methods
Two cohorts of patients were analyzed. The first cohort included 146 consecutive post-operation SQCC patients from January 2008 to October 2012. The second cohort included 63 patients with advanced SQCC receiving EGFR-TKIs treatment. EGFR mutation analysis was performed with Real-time PCR method. The pathologic diagnosis was validated with immunohistochemistry (IHC) for patients harboring activated EGFR mutation. And the efficacy of EGFR-TKIs in squamous cell carcinoma of lung (SQCC) was evaluated in patients with activated EGFR mutations.
Results
In the first cohort, 146 resected patients, EGFR mutations were detected in 3 patients, with the mutation rate of 2.0%. In cohort two, 63 patients treated with EGFR-TKIs, 15 patients possessed activated EGFR mutations. The response rate and disease control rate in these patients was 26.7% and 66.7% respectively. 5 patients had disease control over 6 months. The progression free survival (PFS) in EGFR-mutated patients was 3.9 months.
Conclusions
In Chinese SQCC patients, EGFR mutation rate was extremely low. EGFR-TKIs seemed to be less effective in EGFR-mutated SQCC patients, but some patients could still obtain benefit from EGFR-TKIs. To identify this part of patients, further study was warranted in the future.
doi:10.3978/j.issn.2072-1439.2013.09.15
PMCID: PMC3815724  PMID: 24255770
Squamous cell carcinoma of lung (SQCC); immunohistochemistry (IHC); epidermal growth factor receptor mutation (EGFR mutation); epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs)
18.  Clinical significance of the thymidylate synthase, dihydropyrimidine dehydrogenase, and thymidine phosphorylase mRNA expressions in hepatocellular carcinoma patients receiving 5-fluorouracil-based transarterial chemoembolization treatment 
OncoTargets and therapy  2013;6:811-818.
Purpose
To determine whether 5-fluorouracil (5-FU) sensitivity is associated with the mRNA expressions of thymidylate synthase (TS), dihydropyrimidine dehydrogenase (DPD), and thymidine phosphorylase (TP) in patients with hepatocellular carcinoma (HCC) treated with 5-FU-based transarterial chemoembolization (TACE).
Methods
Formalin-fixed, paraffin-embedded tumor specimens from 40 patients treated with 5-FU-based TACE were selected for the examination of TS, DPD, and TP expression level by a quantitative real-time reverse transcription- polymerase chain reaction (PCR) technique. Patients were categorized into high and low expression groups according to the median expression level of each enzyme. Associations between the mRNA expression levels of TS, DPD, and TP and clinical parameters including treatment efficacies, clinicopathological factors, and prognosis were assessed.
Results
High DPD expression was associated with worse treatment outcome, including intrahepatic disease progression rate (hazard ratio [HR] for high DPD versus low DPD, 2.212; 95% confidence interval [CI], 1.030–4.753; P = 0.042), extrahepatic disease progression rate (HR for high versus low DPD, 3.171; 95% CI, 1.003–10.023; P = 0.049), and progression-free survival (HR for high versus low DPD, 2.308; 95% CI, 1.102–4.836; P = 0.027). No correlation was found between the mRNA expression of TS/TP and treatment outcome.
Conclusion
DPD mRNA expression level was negatively correlated with the clinical outcomes of HCC patients treated with 5-FU-based TACE. These results provide indirect evidence that high DPD mRNA expression is a predictive marker of treatment resistance for 5-FU.
doi:10.2147/OTT.S46498
PMCID: PMC3704606  PMID: 23861589
dihydropyrimidine dehydrogenase; 5-fluorouracil; hepatocellular carcinoma; thymidylate synthase; thymidine phosphorylase; transarterial chemoembolization
19.  COX5B Regulates MAVS-mediated Antiviral Signaling through Interaction with ATG5 and Repressing ROS Production 
PLoS Pathogens  2012;8(12):e1003086.
Innate antiviral immunity is the first line of the host defense system that rapidly detects invading viruses. Mitochondria function as platforms for innate antiviral signal transduction in mammals through the adaptor protein, MAVS. Excessive activation of MAVS-mediated antiviral signaling leads to dysfunction of mitochondria and cell apoptosis that likely causes the pathogenesis of autoimmunity. However, the mechanism of how MAVS is regulated at mitochondria remains unknown. Here we show that the Cytochrome c Oxidase (CcO) complex subunit COX5B physically interacts with MAVS and negatively regulates the MAVS-mediated antiviral pathway. Mechanistically, we find that while activation of MAVS leads to increased ROS production and COX5B expression, COX5B down-regulated MAVS signaling by repressing ROS production. Importantly, our study reveals that COX5B coordinates with the autophagy pathway to control MAVS aggregation, thereby balancing the antiviral signaling activity. Thus, our study provides novel insights into the link between mitochondrial electron transport system and the autophagy pathway in regulating innate antiviral immunity.
Author Summary
Pattern recognition receptors are vital to innate immunity. In the antiviral innate immunity, retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs), such as RIG-I and MDA5, sense viral RNAs through their C-terminal helicase domains, then initiate the antiviral response through interaction with the essential adaptor protein MAVS, which is located in mitochondrial outer membrane. Although cumulative studies have showed that mitochondria-associated MAVS plays an important role in antiviral signaling, much remains unknown about the mechanism of MAVS activity related to mitochondrial membrane localization. In this article we demonstrate that the CcO complex subunit COX5B negatively regulates the MAVS-mediated antiviral pathway through interaction with MAVS. At the mechanistic level, we show that COX5B inhibits MAVS-mediated antiviral pathway by suppressing ROS production, and coordinating with the autophagy pathway to control MAVS aggregation. Our data support a notion that mitochondrial electron transport system coordinates with the autophagy pathway to regulate MAVS-mediated signaling for a tight control of innate antiviral immunity.
doi:10.1371/journal.ppat.1003086
PMCID: PMC3534373  PMID: 23308066
20.  Comparison of different methods for detecting epidermal growth factor receptor mutations in peripheral blood and tumor tissue of non-small cell lung cancer as a predictor of response to gefitinib 
OncoTargets and therapy  2012;5:439-447.
Background
Previous studies have reported that epidermal growth factor receptor (EGFR) mutation in tumor tissue and peripheral blood can predict the response to EGFR tyrosine kinase inhibitor (TKI) in non-small cell lung cancer (NSCLC). However, the heterogeneity of the sample sources makes it difficult to evaluate the detecting methodologies. The goal of this study is to compare different methods for analyzing EGFR mutation in blood and tumor tissue.
Materials and methods
Fifty-one advanced NSCLC patients treated with gefitinib were included in the study. The EGFR mutation status of each patients’ blood was analyzed by denaturing high-performance liquid chromatography (DHPLC), mutant-enriched liquidchip (ME-Liquidchip), and Scorpion Amplification Refractory Mutation System (Scorpion-ARMS) kits. EGFR mutation information in paired tumor samples detected by Scorpion-ARMS served as a reference. Comparative analyses were performed on mutation status results obtained from different methods and on the association between the clinical outcome of TKI treatment and EGFR mutation status.
Results
The response rate (RR) in the whole group was 33.3%. EGFR mutation rates were identified as 15.7%, 27.5%, and 29.4% by DHPLC, ME-Liquidchip, and Scorpion-ARMS in blood, respectively. In 34 cases that had paired tumor samples, the mutation rate in tissue was 41.2%. The RRs of patients with mutation detected by different methods were 71.4% (tumor), 62.5% (blood, DHPLC), 50.0% (blood, ME-Liquidchip), and 66.7% (blood, Scorpion-ARMS). EGFR mutation detected by Scorpion-ARMS in blood and tumor tissues had better prediction of RR to EGFR-TKI (P = 0.002 and P = 0.001) than mutation detected with DHPLC and ME-Liquidchip.
Conclusion
Tumor tissue sample is the best source for EGFR mutation analysis in NSCLC patients. Peripheral blood samples may be used as an alternative source only in special conditions. Scorpion-ARMS, DHPLC, or ME-Liquidchip methods are all optional for detecting tumor EGFR mutation from blood.
doi:10.2147/OTT.S37289
PMCID: PMC3525047  PMID: 23251095
non-small cell lung cancer; EGFR mutation; mutation detection methods; gefitinib
21.  The impact of tumor size change after target therapy on survival: analysis of patients enrolled onto three clinical trials of advanced NSCLC from one institution 
OncoTargets and therapy  2012;5:349-355.
Purpose
To explore whether changes in tumor size impact survival in advanced non-small-cell lung cancer (NSCLC) after target therapy, especially in patients with evaluation of stable disease (SD), and to review the applicability of the Response Evaluation Criteria in Solid Tumors (RECIST) criteria in target therapy.
Patients and methods
Data from 88 NSCLC patients receiving gefitinib (250 mg, daily [qd]), erlotinib (150 mg, qd), and ZD6474 (100 mg, qd) in three clinical trials (IRESSA registration clinical trial, TRUST study, ZD6474 study) during November 2003 to June 2005 were retrospectively analyzed. The treatment effect (complete response, partial response, stable disease [SD], or progressive disease) was evaluated with radiologic assessment according to the RECIST criteria. SD patients were divided into two groups: SD−/0, in which the sum of the longest diameter of target lesions decreased by less than 30% or did not change; and SD+, in which the sum of the longest diameter of target lesions increased by less than 20%. The differences of progression-free survival (PFS) and overall survival (OS) between these groups were analyzed.
Results
In the whole group, 27 patients achieved complete response or partial response as best response, 40 achieved SD, and 22 had progressive disease. The median PFS and OS were 4 months and 11.1 months, respectively. In SD patients, 27 were SD−/0 and 13 patients were SD+. The PFS and OS of SD+ patients was shorter than that of SD−/0 patients (5.65 months vs 2.03 days, P < 0.001 and 12.2 months vs 7.1 months, P < 0.001).
Conclusion
The applicability of RECIST criteria was called into question in the evaluation of target therapy. Change in tumor size might predict survival in advanced NSCLC patients with target therapy and may be a surrogate endpoint for efficacy in target therapy.
doi:10.2147/OTT.S38441
PMCID: PMC3501954  PMID: 23172990
non-small-cell lung cancer; target therapy; stable disease; prognostic factor
22.  HESO1, a nucleotidyl transferase in Arabidopsis, uridylates unmethylated miRNAs and siRNAs to trigger their degradation 
Current biology : CB  2012;22(8):689-694.
SUMMARY
microRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs) impact numerous biological processes in eukaryotes. In addition to biogenesis, turnover contributes to the steady-state levels of small RNAs. One major factor that stabilizes miRNAs and siRNAs in plants as well as siRNAs and piRNAs in animals is 2′;-O-methylation on the 3′; terminal ribose by the methyltransferase HUA ENHANCER1 (HEN1) [1–6]. Genetic studies with Arabidopsis, Drosophila and zebrafish hen1 mutants show that 2′-O-methylation protects small RNAs from 3′-to-5′ truncation and 3′ uridylation, the addition of non-templated nucleotides, predominantly uridine [2, 7, 8]. Uridylation is a widespread phenomenon that is not restricted to small RNAs in hen1 mutants, and is often associated with their reduced accumulation ([7, 9, 10]; reviewed in [11]). The enzymes responsible for 3′ uridylation of small RNAs when they lack methylation in plants or animals have remained elusive. Here, we identify the Arabidopsis HEN1 SUPPRESSOR1 (HESO1) gene as responsible for small RNA uridylation in hen1 mutants. HESO1 exhibits terminal nucleotidyl transferase activity, prefers uridine as the substrate nucleotide, and is completely inhibited by 2′-O-methylation. We show that uridylation leads to miRNA degradation, and the degradation is most likely through an enzyme that is distinct from that causing the 3′ truncation in hen1 mutants.
doi:10.1016/j.cub.2012.02.051
PMCID: PMC3350747  PMID: 22464194
miRNA; siRNA; HESO1; nucleotidyl transferase; methylation; uridylation
23.  Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing 
BMC Plant Biology  2012;12:146.
Background
Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date.
Results
To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated.
Conclusions
We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.
doi:10.1186/1471-2229-12-146
PMCID: PMC3462689  PMID: 22894611
Chinese fir; miRNA; rasiRNA; tasiRNA; Cunninghamia lanceolata
24.  Development of a luciferase-based reporter of transcriptional gene silencing that enables bidirectional mutant screening in Arabidopsis thaliana 
Silence  2012;3:6.
Background
Cytosine methylation is an important chromatin modification that maintains genome integrity and regulates gene expression through transcriptional gene silencing. Major players in de novo methylation guided by siRNAs (known as RNA-directed DNA methylation, or RdDM), maintenance methylation, and active demethylation have been identified in Arabidopsis. However, active demethylation only occurs at a subset of RdDM loci, raising the question of how the homeostasis of DNA methylation is achieved at most RdDM loci. To identify factors that regulate the levels of cytosine methylation, we aimed to establish a transgenic reporter system that allows for forward genetic screens in Arabidopsis.
Results
We introduced a dual 35 S promoter (d35S) driven luciferase reporter, LUCH, into Arabidopsis and isolated a line with a moderate level of luciferase activity. LUCH produced transgene-specific 24 nucleotide siRNAs and its d35S contained methylated cytosine in CG, CHG and CHH contexts. Treatment of the transgenic line with an inhibitor of cytosine methylation de-repressed luciferase activity. Mutations in several components of the RdDM pathway but not the maintenance methylation genes resulted in reduced d35S methylation, especially CHH methylation, and de-repression of luciferase activity. A mutation in MOM1, which is known to cooperate with RdDM to silence transposons, reduced d35S DNA methylation and de-repressed LUCH expression. A mutation in ROS1, a cytosine demethylation enzyme, increased d35S methylation and reduced LUCH expression.
Conclusion
We developed a luciferase-based reporter, LUCH, which reports both DNA methylation directed by small RNAs and active demethylation by ROS1 in Arabidopsis. The moderate basal level of LUCH expression allows for bi-directional genetic screens that dissect the mechanisms of DNA methylation as well as demethylation.
doi:10.1186/1758-907X-3-6
PMCID: PMC3548752  PMID: 22676624
Cytosine methylation; Demethylation; RdDM; MOM1; Transcriptional gene silencing; siRNA
25.  Transcriptome-wide identification and characterization of miRNAs from Pinus densata 
BMC Genomics  2012;13:132.
Background
MicroRNAs (miRNAs) play key roles in diverse developmental processes, nutrient homeostasis and responses to biotic and abiotic stresses. The biogenesis and regulatory functions of miRNAs have been intensively studied in model angiosperms, such as Arabidopsis thaliana, Oryza sativa and Populus trichocarpa. However, global identification of Pinus densata miRNAs has not been reported in previous research.
Results
Here, we report the identification of 34 conserved miRNAs belonging to 25 miRNA families from a P. densata mRNA transcriptome database using local BLAST and MIREAP programs. The primary and/or precursor sequences of 29 miRNAs were further confirmed by RT-PCR amplification and subsequent sequencing. The average value of the minimal folding free energy indexes of the 34 miRNA precursors was 0.92. Nineteen (58%) mature miRNAs began with a 5' terminal uridine residue. Analysis of miRNA precursors showed that 19 mature miRNAs were novel members of 14 conserved miRNA families, of which 17 miRNAs were further validated by subcloning and sequencing. Using real-time quantitative RT-PCR, we found that the expression levels of 7 miRNAs were more than 2-fold higher in needles than in stems. In addition, 72 P. densata mRNAs were predicted to be targets of 25 miRNA families. Four target genes, including a nodal modulator 1-like protein gene, two GRAS family transcription factor protein genes and one histone deacetylase gene, were experimentally verified to be the targets of 3 P. densata miRNAs, pde-miR162a, pde-miR171a and pde-miR482a, respectively.
Conclusions
This study led to the discovery of 34 conserved miRNAs comprising 25 miRNA families from Pinus densata. These results lay a solid foundation for further studying the regulative roles of miRNAs in the development, growth and responses to environmental stresses in P. densata.
doi:10.1186/1471-2164-13-132
PMCID: PMC3347991  PMID: 22480283
Pinus densata; miRNA; Transcriptome

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