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1.  Mast cell-derived serine proteinase regulates T helper 2 polarization 
Scientific Reports  2014;4:4649.
Although mast cells play a critical role in allergic reactions, the cells are also involved in the protective immunity in the body. This study aims to investigate the role of mast cells in immune regulation during aberrant T helper (Th)2 responses. In this study, an adoptive antigen-specific Th2 response model was established with mast cell-deficient mice to test the role of mast cell in the immune regulation. Cell culture was employed to test the role of mast cells in the modulation of the expression of B cell lymphoma 6 protein (Bcl-6) in Th2 cells. The results showed that after adoptive transfer with immune cells, the mast cell-deficient mice showed stronger Th2 pattern responses in the intestine than that in the mast cell-sufficient mice. Mast cell-derived mouse mast cell protease-6 increased the expression of Bcl-6 in Th2 cells. Bcl-6 inhibited the expression of GATA-3 in Th2 cells, subsequently, forkhead box P3 was increased and the Th2 cytokines were reduced in the cells; the cells thus showed the immune regulatory properties similar to regulatory T cells. We conclude that bedsides initiating immune inflammation, mast cells also contribute to the immune regulation on Th2 polarization.
doi:10.1038/srep04649
PMCID: PMC3983597  PMID: 24721951
2.  Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients 
Lung adenocarcinoma is the most common type of primary lung cancer. The purpose of this study was to delineate gene expression patterns for survival prediction in lung adenocarcinoma. Gene expression profiles of 82 (discovery set) and 442 (validation set 1) lung adenocarcinoma tumor tissues were analyzed using a systems biology-based network approach. We also examined the expression profiles of 78 adjacent normal lung tissues from 82 patients. We found a significant correlation of an expression module with overall survival (adjusted hazard ratio or HR=1.71; 95% CI=1.06-2.74 in discovery set; adjusted HR=1.26; 95% CI=1.08-1.49 in validation set 1). This expression module contained genes enriched in the biological process of the cell cycle. Interestingly, the cell cycle gene module and overall survival association were also significant in normal lung tissues (adjusted HR=1.91; 95% CI, 1.32-2.75). From these survival-related modules, we further defined three hub genes (UBE2C, TPX2 and MELK) whose expression-based risk indices were more strongly associated with poor 5-year survival (HR=3.85, 95% CI=1.34-11.05 in discovery set; HR=1.72, 95% CI=1.21-2.46 in validation set 1; and HR=3.35, 95% CI=1.08-10.04 in normal lung set). The 3-gene prognostic result was further validated using 92 adenocarcinoma tumor samples (validation set 2); patients with a high-risk gene signature have a 1.52 fold increased risk (95% CI, 1.02–2.24) of death than patients with a low-risk gene signature. These results suggest that network-based approach may facilitate discovery of key genes that are closely linked to survival in patients with lung adenocarcinoma.
doi:10.1016/j.lungcan.2012.12.022
PMCID: PMC3595338  PMID: 23357462
Lung cancer; survival; gene expression profiling; cell cycle; systems biology
3.  Non-invasive Characterization of the Histopathologic Features of Pulmonary Nodules of the Lung Adenocarcinoma Spectrum using Computer Aided Nodule Assessment and Risk Yield (CANARY) – a Pilot Study 
Introduction
Pulmonary nodules of the adenocarcinoma spectrum are characterized by distinctive morphological and radiological features and variable prognosis. Non-invasive high-resolution computed-tomography (HRCT)-based risk stratification tools are needed to individualize their management.
Methods
Radiological measurements of histopathologic tissue invasion were developed in a training set of 54 pulmonary nodules of the adenocarcinoma spectrum and validated in 86 consecutively resected nodules. Nodules were isolated and characterized by computer-aided analysis and data were analyzed by Spearman correlation, sensitivity, specificity as well as the positive and negative predictive values.
Results
Computer Aided Nodule Assessment and Risk Yield (CANARY) can non-invasively characterize pulmonary nodules of the adenocarcinoma spectrum. Unsupervised clustering analysis of HRCT data identified 9 unique exemplars representing the basic radiologic building blocks of these lesions. The exemplar distribution within each nodule correlated well with the proportion of histologic tissue invasion, Spearman R=0.87,p < 0.0001 and 0.89,p < 0.0001 for the training and the validation set, respectively. Clustering of the exemplars in three-dimensional space corresponding to tissue invasion and lepidic growth was used to develop a CANARY decision algorithm, which successfully categorized these pulmonary nodules as “aggressive” (invasive adenocarcinoma) or “indolent” (adenocarcinoma in situ and minimally invasive adenocarcinoma). Sensitivity, specificity, positive predictive value and negative predictive value of this approach for the detection of “aggressive” lesions were 95.4%, 96.8%, 95.4% and 96.8%, respectively in the training set and 98.7%, 63.6%, 94.9% and 87.5%, respectively in the validation set.
Conclusion
CANARY represents a promising tool to non-invasively risk stratify pulmonary nodules of the adenocarcinoma spectrum.
doi:10.1097/JTO.0b013e3182843721
PMCID: PMC3597987  PMID: 23486265
Pulmonary nodules; lung adenocarcinoma; risk stratification; computer aided image analysis
4.  Mass spectrometry-based serum peptide profiling in hepatocellular carcinoma with bone metastasis 
AIM: To investigate the potential of serum peptides as a diagnostic tool for hepatocellular carcinoma (HCC) with bone metastasis.
METHODS: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) was used to characterize the serum peptide profile of HCC patients with bone metastasis. Serum samples from 138 HCC patients (66 cases with and 72 cases without bone metastasis) were randomly assigned into a training set (n = 76) and a test set (n = 62). Differential serum peptides were examined using ClinProt magnetic bead-based purification followed by MALDI-TOF-MS. The sequences of differentially expressed serum peptides were identified using liquid chromatography-mass spectrometry. A diagnostic model was established using a learning algorithm of radial basis function neural network verified by a single blind trial. Receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic power of the established model.
RESULTS: Ten peptide peaks were significantly different between HCC patients with or without bone metastasis (P < 0.001). Sequences of seven peptides with mass to charge ratios (m/z) of 1780.7, 1866.5, 2131.6, 2880.4, 1532.4, 2489.8, and 2234.3 were successfully identified. These seven peptides were derived from alpha-fetoprotein, prothrombin, serglycin, isoform 2 of inter-alpha-trypsin inhibitor heavy chain H4, isoform 1 of autophagy-related protein 16-2, and transthyretin and fibrinogen beta chains, respectively. The recognition rate and predictive power of a diagnostic model established on the basis of six significant peptides (m/z for these six peptides were 1535.4, 1780.7, 1866.5, 2131.6, 2880.4, and 2901.9) were 89.47% and 82.89%, respectively. The sensitivity and specificity of this model based upon a single blind trial were 85.29% and 85.71%, respectively. ROC analysis found that the AUC (area under the ROC curve) value was 0.911.
CONCLUSION: Our study suggested that serum peptides may serve as a diagnosis tool for HCC bone metastasis.
doi:10.3748/wjg.v20.i11.3025
PMCID: PMC3961966  PMID: 24659894
Hepatocellular carcinoma; Serum; Peptides; Matrix-assisted laser desorption ionization-time of flight mass spectrometry; Tumor biomarker
5.  Worse disease-free survival in never-smokers with ALK+ lung adenocarcinoma 
Introduction
The EML4–anaplastic lymphoma kinase (ALK) translocation is a recognized oncogenic driver in non-small cell lung cancer. We investigated immunohistochemistry (IHC) screening with fluorescence in-situ hybridization (FISH) confirmation for ALK detection and estimated the prevalence of ALK-positivity in our patient cohort of never smokers, together with differences in clinical outcomes and prognostic factors for patients with ALK-positive and ALK-negative tumors.
Methods
We designed a three-phase study (training, validation, and testing) in 300 never-smokers with lung adenocarcinoma from the observational Mayo Clinic Lung Cancer Cohort. Tumor samples were tested using IHC and FISH, and concordance between the methods was assessed. Clinical outcomes were assessed via 5-year progression or recurrence-free survival from diagnosis. Prognostic factors for ALK-positive tumors and metastases were also investigated.
Results
ALK-positive patients were significantly (p<0·05) younger and had higher-grade tumors than ALK-negative patients. ALK-positivity was 12.2% by IHC and confirmed at 8.2% of tumors by FISH, with complete concordance between IHC 3+/0 and FISH+/− assessments, respectively. Five-year risk of progression or recurrence was doubled for patients with ALK-positive compared with ALK-negative tumors; ALK-positive tumors also appeared to be associated with a higher risk of brain and liver metastases.
Conclusions
Our findings suggest that ALK-positivity is associated with a significantly poor outcome in non-smoking-related adenocarcinoma, and that ALK-positive tumors may be associated with an increased risk of brain and liver metastases compared with ALK-negative disease. Consequently, an unmet medical need exists in ALK-positive lung cancer patients, and effective ALK-specific therapies are needed now.
doi:10.1097/JTO.0b013e31823c5c32
PMCID: PMC3931519  PMID: 22134072
EML4-anaplastic lymphoma kinase (ALK); non small cell lung cancer (NSCLC); immunohistochemistry (IHC); fluorescence in-situ hybridization (FISH); progression and recurrence free survival (PFS/RFS)
6.  Alpha 1-Antitrypsin Deficiency Carriers, Serum Alpha 1-Antitrypsin Concentration, and Non-Small-Cell Lung Cancer Survival 
Introduction
Although the association between alpha 1-antitrypsin deficiency (α1ATD) carriers and lung cancer risk has been found, the effects of α1ATD carriers and serum alpha 1-antitrypsin (α1AT) concentration on non-small-cell lung cancer (NSCLC) survival remained unclear.
Methods
Patients were selected from the Epidemiology and Genetics of Lung Cancer study at the Mayo Clinic with the criteria of 1) primary NSCLC diagnosis, and 2) available α1ATD carrier status tested by isoelectric focusing serum α1AT concentration by immunonephelometry. The effects of carrier status and serum α1AT concentration on survival were evaluated by Cox proportional hazards models with (1) a landmark approach where overall survival was defined from the time of blood draw to death from any cause, and (2) included only patients with blood draw time prior to initial treatment.
Results
1,321 patients were included in this study, with 179 α1ATD carriers and 1,142 non-carriers. No differences in overall survival by α1ATD carrier status were found [adjusted hazard ratio (AHR): 0.98; 95% CI: 0.82-1.18]. However, serum α1AT concentration was significantly associated with survival among all patients in the landmark model [AHR per 50 mg/dL increments: 1.15; 95% CI: 1.10-1.20] and among patients whose blood were drawn for serum α1AT level assessment before any treatment [AHR per 50 mg/dL increments: 1.44; 95% CI: 1.21-1.71].
Conclusions
Being an α1ATD carrier had no significant effect on NSCLC survival. The increased serum α1AT concentration was a poor prognosis marker for NSCLC, regardless of carrier status.
doi:10.1097/JTO.0b013e31820213fb
PMCID: PMC3927968  PMID: 21173712
alpha 1-antitrypsin; alpha 1-antitrypsin deficiency; non-small-cell lung cancer; survival
7.  Variants in inflammation genes are implicated in risk of lung cancer in never smokers exposed to second-hand smoke 
Cancer discovery  2011;1(5):420-429.
Lung cancer in lifetime never smokers is distinct from that in smokers, but the role of separate or overlapping carcinogenic pathways has not been explored. We therefore evaluated a comprehensive panel of 11,737 SNPs in inflammatory-pathway genes in a discovery phase (451 lung cancer cases, 508 controls from Texas). SNPs that were significant were evaluated in a second external population (303 cases, 311 controls from the Mayo Clinic). An intronic SNP in the ACVR1B gene, rs12809597, was replicated with significance and restricted to those reporting adult exposure to environmental tobacco smoke Another promising candidate was a SNP in NR4A1, although the replication OR did not achieve statistical significance. ACVR1B belongs to the TGFR-β superfamily, contributing to resolution of inflammation and initiation of airway remodeling. An inflammatory microenvironment, (second hand smoking, asthma, or hay fever) is necessary for risk from these gene variants to be expressed. These findings require further replication, followed by targeted resequencing, and functional validation.
doi:10.1158/2159-8290.CD-11-0080
PMCID: PMC3919666  PMID: 22586632
lung cancer; never smokers; inflammation genes; sidestream exposure
8.  Mechanisms of Ghrelin Anti-Heart Failure: Inhibition of Ang II-Induced Cardiomyocyte Apoptosis by Down-Regulating AT1R Expression 
PLoS ONE  2014;9(1):e85785.
Background
Ghrelin is a novel growth hormone–releasing peptide administered to treat chronic heart failure (CHF). However, the underlying mechanism of its protective effects against heart failure (HF) remains unclear.
Methods and Results
A total of 68 patients with CHF and 20 healthy individuals were included. The serum levels of Angiotensin II (Ang II) and ghrelin were measured using ELISA. The results showed that Ang II and ghrelin were both significantly increased in CHF patients and that the ghrelin levels were significantly positively correlated with Ang II. The left anterior descending coronary artery was ligated to establish a rat model of CHF, and cultured cardiomyocytes from neonatal rats were stimulated with Ang II to explore the role of ghrelin in CHF. The results showed that ghrelin inhibited cardiomyocyte apoptosis both in vivo and in vitro. Furthermore, caspase-3 expression was examined, and the results revealed that Ang II induces cardiomyocyte apoptosis through the caspase-3 pathway, whereas ghrelin inhibits this action. Lastly, to further elucidate the mechanism by which ghrelin inhibits Ang II action, the expression of the AT1 and AT2 receptors was evaluated; the results showed that Ang II up-regulates the AT1 and AT2 receptors in cardiomyocytes, whereas ghrelin inhibits AT1 receptor up-regulation but does not affect AT2 receptor expression.
Conclusions
These data suggest that the serum levels of ghrelin are significantly positively correlated with Ang II in CHF patients and that ghrelin can inhibit Ang II-induced cardiomyocyte apoptosis by down-regulating AT1R, thereby playing a role in preventing HF.
doi:10.1371/journal.pone.0085785
PMCID: PMC3897516  PMID: 24465706
9.  HCV Core Protein-Induced Down-Regulation of microRNA-152 Promoted Aberrant Proliferation by Regulating Wnt1 in HepG2 Cells 
PLoS ONE  2014;9(1):e81730.
Background
Hepatitis C virus (HCV) has been reported to regulate cellular microRNAs (miRNAs). The HCV core protein is considered to be a potential oncoprotein in HCV-related hepatocellular carcinoma (HCV-HCC), but HCV core-regulated miRNAs are largely unknown. Our preliminary experiments revealed significant down-regulation of microRNA-152 (miR-152) by HCV core protein in HepG2 cells. Through target gene prediction softwares, Wnt1 was predicted to be a potential target of miR-152. The present study was initiated to investigate whether miR-152 is aberrantly regulated by the HCV core protein, and involved in the regulation of the aberrant proliferation of HCV-HCC cells.
Methods
MiR-152 levels were examined by stem-loop real-time RT-PCR (SLqRT-PCR). Cell proliferation was analyzed by MTT and colony formation assay. Cell cycle analysis was performed by flow cytometry. Luciferase reporter assay was conducted to confirm miRNA-target association. Wnt1 expression was determined by real-time qPCR and Western blotting.
Results
HCV core protein significantly suppressed miR-152 expression, and led to significant Wnt1 up-regulation with a concomitant aberrantly promoted proliferation. Moreover, we validated that miR-152 inhibition promoted, while miR-152 mimics inhibited cell proliferation. Using, qRT–PCR and western blot, Wnt1 was demonstrated to be regulated by miR-152. Luciferase activity assay showed that while miR-152 mimics significantly reduced the luciferase activity by 83.76% (P<0.0001), miR-152 inhibitor showed no effect on luciferase reporter. Most notably, salvage expression of miR-152 after Ad-HCV core infection for 24 h almost totally reversed the proliferation-promoting effect of the HCV core protein, and meanwhile, reduced the expression of both Wnt1 mRNA and protein to basal levels.
Conclusion
These findings provide important evidence that the reduced miR-152 expression by HCV core protein can indirectly lose an inhibitory effect on Wnt1, which might, at least partially lead to cell proliferation of liver cancer cells. MiR-152 may have a therapeutic potential to suppress liver cancer proliferation.
doi:10.1371/journal.pone.0081730
PMCID: PMC3886937  PMID: 24416131
11.  Physical activity level and quality of life in long term lung cancer survivors 
Lung cancer (Amsterdam, Netherlands)  2012;77(3):10.1016/j.lungcan.2012.05.096.
Purpose
Lung cancer is associated with a multitude of challenges, and lung cancer survivors report significantly lower quality of life (QOL) than other cancer survivors.
Methods
This study aimed to examine the relationship between physical activity level and QOL in a large sample of long term lung cancer survivors (N = 1937). Average age at diagnosis was 65 years, 92% were Caucasian, and 51% male. Surveys were completed at lung cancer diagnosis and then average 4.2 years post-diagnosis.
Results
Most survivors reported having a sedentary lifestyle at both timepoints. However, 256 survivors reported a change in physical activity level from diagnosis to follow-up. Decreased physical activity (n = 140) was associated with decreased overall, mental, physical, emotional, social, and spiritual QOL (all ps < .001) and decreased symptom control as seen in reported pain, dry coughing, coughing with phlegm, shortness of breath, and level of fatigue (all ps < .05). In contrast, increased physical activity (n = 116) was associated with improved QOL (all ps < .05), and improved symptom control as seen in frequency and severity of pain (p < .01). For all participants, those engaging in regular physical activity (30 min or more per day, at least five days per week) reported significantly higher QOL scores (all ps < .001), and better symptom control than more sedentary survivors.
Conclusions
Results indicate a significant association between change in physical activity and QOL and symptom control for long term lung cancer survivors, and research exploring interventions designed to improve activity level for lung cancer survivors is further warranted.
doi:10.1016/j.lungcan.2012.05.096
PMCID: PMC3882512  PMID: 22681871
Long term lung cancer survivors; Physical activity; Exercise; Quality of life; Symptom control
12.  A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma 
Background
We propose a two-step model-based approach, with correction for ascertainment, to linkage analysis of a binary trait with variable age of onset and apply it to a set of multiplex pedigrees segregating for adult glioma.
Methods
First, we fit segregation models by formulating the likelihood for a person to have a bivariate phenotype, affection status and age of onset, along with other covariates, and from these we estimate population trait allele frequencies and penetrance parameters as a function of age (N=281 multiplex glioma pedigrees). Second, the best fitting models are used as trait models in multipoint linkage analysis (N=74 informative multiplex glioma pedigrees). To correct for ascertainment, a prevalence constraint is used in the likelihood of the segregation models for all 281 pedigrees. Then the trait allele frequencies are re-estimated for the pedigree founders of the subset of 74 pedigrees chosen for linkage analysis.
Results
Using the best fitting segregation models in model-based multipoint linkage analysis, we identified two separate peaks on chromosome 17; the first agreed with a region identified by Shete et al. who used model-free affected-only linkage analysis, but with a narrowed peak: and the second agreed with a second region they found but had a larger maximum log of the odds (LOD).
Conclusions/Impact
Our approach has the advantage of not requiring markers to be in linkage equilibrium unless the minor allele frequency is small (markers which tend to be uninformative for linkage), and of using more of the available information for LOD-based linkage analysis.
doi:10.1158/1055-9965.EPI-12-0703
PMCID: PMC3518573  PMID: 22962404
Glioma; model-based linkage; segregation; age of onset; prevalence constraint
13.  Assessing the optimal dose for Cetrorelix in Chinese women undergoing ovarian stimulation during the course of IVF-ET treatment 
We conducted a prospective, randomized, and controlled trial to assess the optimal dose for GnRH antagonist, cetrorelix, for Chinese women during the course of ovarian stimulation. The patients were randomly divided into two groups, in which 48 patients were advised to inject 0.25 mg Cetrorelix daily (the 0.25 mg group), while 39 patients were instructed to receive a daily dose of 0.125 mg cetrorelix (the 0.125 mg group). In general, a daily dose of 0.125 mg cetrorelix could be more optimal for Chinese women as manifested by the lower cancellation rate, higher implantation rate and clinical pregnancy rate. Specifically, daily administration of 0.125 mg cetrorelix for patients under 35 years old is associated with a 3-fold higher implantation rate and a 5-fold higher clinical pregnancy rate as compared with that of those patients ≥ 35 years old. On the contrary, higher rates for implantation and clinical pregnancy were noted by daily injection of 0.25 mg cetrorelix in elder patients (≥ 35 years old) as compared with that of young patients (< 35 years old). Together, our data suggest that a daily dose of 0.125 mg cetrorelix could be more optimal for patients < 35 years old, while 0.25 mg/day of cetrorelix are likely conducive to higher implantation and clinical pregnancy rate for those patients ≥ 35 years old. These data could be important for preventing LH surge while maintaining optimal LH levels necessary for embryo implantation for Chinese women during the course of IVF-ET treatment.
PMCID: PMC3853427  PMID: 24349624
IVF-ET; GnRH antagonist; cetrorelix; ovarian stimulation
14.  Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum) 
BMC Genomics  2013;14:793.
Background
Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has attracted interest as an alternative plant model species with high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still incomplete and transcriptomic information is scarce. In addition, functional genomics investigations in this species are severely hampered by a lack of affordable tools for genome-wide gene expression studies.
Results
Here, we report the results of Thellungiella de novo transcriptome assembly and annotation based on 454 pyrosequencing and development and validation of a T. salsuginea microarray. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from samples covering different tissues and abiotic stress conditions. Both libraries yielded partially unique sequences, indicating their necessity to obtain comprehensive transcriptome coverage. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. These unigenes were compared to all available Thellungiella genome sequence information. In addition, the groups of Late Embryogenesis Abundant (LEA) proteins, Mitogen Activated Protein (MAP) kinases and protein phosphatases were annotated in detail. We also predicted the target genes for 384 putative miRNAs. From the sequence information, we constructed a 44 k Agilent oligonucleotide microarray. Comparison of same-species and cross-species hybridization results showed superior performance of the newly designed array for T. salsuginea samples. The developed microarrays were used to investigate transcriptional responses of T. salsuginea and Arabidopsis during cold acclimation using the MapMan software.
Conclusions
This study provides the first comprehensive transcriptome information for the extremophile Arabidopsis relative T. salsuginea. The data constitute a more than three-fold increase in the number of publicly available unigene sequences and will greatly facilitate genome annotation. In addition, we have designed and validated the first genome-wide microarray for T. salsuginea, which will be commercially available. Together with the publicly available MapMan software this will become an important tool for functional genomics of plant stress tolerance.
doi:10.1186/1471-2164-14-793
PMCID: PMC3832907  PMID: 24228715
Arabidopsis thaliana; Cold acclimation; Gene annotation; LEA proteins; MAP kinases; Microarray design; microRNAs; Protein phosphatases; Thellungiella salsuginea; Transcriptome sequencing
15.  On-line amino acid-based capillary isoelectric focusing-ESI-MS/MS for protein digests analysis 
Analytica chimica acta  2012;750:207-211.
Six amino acids with pIs that ranged from 3.2 to 9.7 were used as ampholytes to establish a pH gradient in capillary isoelectric focusing. This amino acid-based capillary isoelectric focusing (cIEF) was coupled with ESI-MS/MS using an electrokinetically pumped sheath-flow interface for peptide analysis. Amino acid-based isoelectric focusing generates a two-order of magnitude lower background signal than commercial ampholytes in the important m/z range of 300–1800. Good focusing was achieved for insulin receptor, which produced ~10-s peak width. For 0.1 mg/mL bovine serum albumin (BSA) digests, 24 ± 1 peptides (sequence coverage 47 ± 4 %) were identified in triplicate analysis. As expected, the BSA peptides were separated according to their pI. The concentration detection limit for the BSA digests is 7 nM and the mass detection limit is 7 fmole. A solution of six bovine protein tryptic digests spanning 5 orders of magnitude in concentration was analyzed by amino acid based cIEF-ESI-MS/MS. Five proteins with a concentration range spanning 4 orders of magnitude were identified in triplicate runs. Using amino acid based cIEF-ESI-MS/MS, 112 protein groups and 303 unique peptides were identified in triplicate runs of a RAW 264.7 cell homogenate protein digest. In comparison with ampholyte based cIEF-ESI-MS/MS, amino acid based cIEF-ESI-MS/MS produces higher resolution of five acidic peptides, much cleaner mass spectra, and higher protein spectral counts.
doi:10.1016/j.aca.2012.04.026
PMCID: PMC3474973  PMID: 23062442
16.  Coupling methanol denaturation, immobilized trypsin digestion, and accurate mass and time tagging for liquid chromatography-based shotgun proteomics of low nanogram amounts of RAW 264.7 cell lysate 
Analytical chemistry  2012;84(20):8715-8721.
We report the shotgun proteomic analysis of mammalian cell lysates that contain low nanogram amounts of protein. Proteins were denatured using methanol, digested using immobilized trypsin, and analyzed by UPLC-ESI-MS/MS. The approach generated more peptides and higher sequence coverage for a mixture of three standard proteins than the use of free trypsin solution digestion of heat- or urea-denatured proteins. We prepared triplicate RAW 264.7 cell lysates that contained 6 ng, 30 ng, 120 ng, and 300 ng of protein. An average of 2 ± 1, 23 ± 2, 134 ± 11, and 218 ± 26 proteins were detected for each sample size, respectively. The numbers of both protein and peptide IDs scaled linearly with the amount of sample taken for analysis. Our approach also outperformed traditional methods (free trypsin digestion of heat- or urea-denatured proteins) for 6 ng to 300 ng RAW 264.7 cell protein analysis in terms of number of peptides and proteins identified. The use of accurate mass and time (AMT) tags resulted in the identification of an additional 16 proteins based on 20 peptides from the 6 ng cell lysate prepared with our approach. When AMT analysis was performed for the 6 ng cell lysate prepared with traditional methods, no reasonable peptide signal could be obtained. In all cases, roughly ~30% of the digested sample was taken for analysis, corresponding to the analysis of a 2 ng aliquot of homogenate from the 6 ng cell lysate.
doi:10.1021/ac3019608
PMCID: PMC3477608  PMID: 22971241
17.  Previous Lung Diseases and Lung Cancer Risk: A Pooled Analysis From the International Lung Cancer Consortium 
American Journal of Epidemiology  2012;176(7):573-585.
To clarify the role of previous lung diseases (chronic bronchitis, emphysema, pneumonia, and tuberculosis) in the development of lung cancer, the authors conducted a pooled analysis of studies in the International Lung Cancer Consortium. Seventeen studies including 24,607 cases and 81,829 controls (noncases), mainly conducted in Europe and North America, were included (1984–2011). Using self-reported data on previous diagnoses of lung diseases, the authors derived study-specific effect estimates by means of logistic regression models or Cox proportional hazards models adjusted for age, sex, and cumulative tobacco smoking. Estimates were pooled using random-effects models. Analyses stratified by smoking status and histology were also conducted. A history of emphysema conferred a 2.44-fold increased risk of lung cancer (95% confidence interval (CI): 1.64, 3.62 (16 studies)). A history of chronic bronchitis conferred a relative risk of 1.47 (95% CI: 1.29, 1.68 (13 studies)). Tuberculosis (relative risk = 1.48, 95% CI: 1.17, 1.87 (16 studies)) and pneumonia (relative risk = 1.57, 95% CI: 1.22, 2.01 (12 studies)) were also associated with lung cancer risk. Among never smokers, elevated risks were observed for emphysema, pneumonia, and tuberculosis. These results suggest that previous lung diseases influence lung cancer risk independently of tobacco use and that these diseases are important for assessing individual risk.
doi:10.1093/aje/kws151
PMCID: PMC3530374  PMID: 22986146
bronchitis; chronic; emphysema; lung diseases; lung neoplasms; meta-analysis; pneumonia; pulmonary disease; chronic obstructive; tuberculosis
18.  A Novel Mechanism Underlies the Hepatotoxicity of Pyrazinamide 
Relatively little is known about the hepatotoxicity of pyrazinamide (PZA). PZA requires activation by amidase to form pyrazinoic acid (PA). Xanthine oxidase then hydroxylates PA to form 5-hydroxypyrazinoic acid (5-OH-PA). PZA can also be directly oxidized to form 5-OH-PZA. Before this study, it was unclear which metabolic pathway or PZA metabolites led to hepatotoxicity. This study determines whether PZA metabolites are responsible for PZA-induced hepatotoxicity. PZA metabolites were identified and cytotoxicity in HepG2 cells was assessed. Potential PZA and PA hepatotoxicity was then tested in rats. Urine specimens were collected from 153 tuberculosis (TB) patients, and the results were evaluated to confirm whether a correlation existed between PZA metabolite concentrations and hepatotoxicity. This led to the hypothesis that coadministration of amidase inhibitor (bis-p-nitrophenyl phosphate [BNPP]) decreases or prevents PZA- and PZA metabolite-induced hepatotoxicity in rats. PA and 5-OH-PA are more toxic than PZA. Electron microscopy showed that PZA and PA treatment of rats significantly increases aspartate transaminase (AST) and alanine aminotransferase (ALT) activity and galactose single-point (GSP) levels (P < 0.005). PA and 5-OH-PA levels are also significantly correlated with hepatotoxicity in the urine of TB patients (P < 0.005). Amidase inhibitor, BNPP, decreases PZA-induced, but not PA-induced, hepatotoxicity. This is the first report of a cell line, animal, and clinical trial confirming that the metabolite 5-OH-PA is responsible for PZA-induced hepatotoxicity.
doi:10.1128/AAC.01866-12
PMCID: PMC3623344  PMID: 23357778
19.  All-trans-Retinal Sensitizes Human RPE Cells to Alternative Complement Pathway–Induced Cell Death 
Purpose.
Retinal pigment epithelial (RPE) cell death occurs early in the pathogenesis of age-related macular degeneration (AMD) and Stargardt's disease. Emerging evidence suggests that all-trans-retinal (atRal) and alternative complement pathway (AP) activation contribute to RPE cell death in both of these retinal disorders. The aim of this study was to investigate the combined effect of atRal and AP activation on RPE cell viability.
Methods.
RPE cells were treated with atRal and then incubated with a complement-fixing antibody followed by stimulation with C1q-depleted serum to activate AP. Cell viability was assessed by tetrazolium salt and lactate dehydrogenase release assays. Changes in cell surface CD46 and CD59 expression were assessed by flow cytometry. Cells were pretreated with the antioxidant resveratrol, and C1q-depleted serum was incubated with an anti-C5 antibody prior to initiating AP attack to determine the protective effects of antioxidant therapy and complement inhibition, respectively.
Results.
Both atRal and AP activation independently caused RPE cell death. When AP attack was initiated following atRal treatment, a synergistic increase in cell death was observed. Following 24-hour atRal treatment, CD46 and CD59 expression decreased, corresponding temporally to increased susceptibility to AP attack. Resveratrol and the anti-C5 antibody both protected against AP-induced cell death following atRal exposure and were most effective when used in combination.
Conclusions.
atRal sensitizes RPE cells to AP attack, which may be mediated in part by atRal-induced downregulation of CD46 and CD59. Despite increased susceptibility to AP attack following exposure to atRal, resveratrol and anti-C5 antibody effectively prevent AP-mediated cell death.
All-trans-retinal sensitizes RPE cells to alternative complement pathway attack, which is mediated by all-trans-retinal-induced downregulation of CD46 and CD59. Resveratrol and an anti-C5 antibody effectively attenuate the combined cytotoxic effects of all-trans-retinal and complement activation.
doi:10.1167/iovs.12-11020
PMCID: PMC3630820  PMID: 23518773
age-related macular degeneration; retinal pigment epithelium; oxidative damage; alternative complement pathway; all-trans-retinal
20.  CZE-ESI-MS/MS system for analysis of subnanogram amounts of tryptic digests of a cellular homogenate 
Proteomics  2012;12(0):3013-3019.
We report the performance of capillary zone electrophoresis coupled with an electrokinetically pumped electrospray interface and an Orbitrap-Velos mass spectrometer for high sensitivity protein analysis. We first investigated the system for quantitation of the tryptic digest of bovine serum albumin (BSA). The system produced outstanding linearity with respect to peak height, number of peptide IDs, and spectral counts across the range of 12 nM to 750 nM (60 amol to 3.5 fmol) of BSA injected. One peptide produced a detection limit of 0.3 nM (1.5 amol) injected. We also analyzed 700 pg of a tryptic digest prepared from a RAW264.7 cell lysate; 10 proteins were identified in triplicate analyses after filtering the data with peptide confidence value as high. This sample size corresponds to the protein content of ~10 eukaryotic cells.
doi:10.1002/pmic.201200100
PMCID: PMC3670668  PMID: 22888077
Electrokinetically driven sheath flow interface; CZE-ESI-MS/MS; Protein digests
21.  Quantitative changes of nitrergic neurons during postnatal development of chicken myenteric plexus*  
Objective: Information regarding the development of the enteric nervous system (ENS) is important for understanding the functional abnormalities of the gut. Because fertilized chicken eggs provide easy access to embryos, chicken models have been widely used to study embryonic development of myenteric plexus; however, no study has been focused on the postnatal period. The aim of this study was to perform a qualitative and quantitative analysis of the nitrergic neurons in the myenteric plexus of developing chickens in the postnatal period. Methods: Whole-mount preparations of the myenteric plexus were made in 7-d, 15-d, and 40-d old (adult) chickens of either sex (n=15). The myenteric plexus was studied after nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) histochemistry using light microscopy, digital photography, and Image-Pro Plus 6.0 software. The numbers of positively stained neurons and ganglia were counted in the duodenum, jejunum, ileum, caecum, and colon in the different age groups. Data were expressed as mean±standard deviation (SD), and statistical analysis was performed using a one-way analysis of variance (ANOVA) test. Results: The positively stained neurons showed various morphologies and staining intensities, and formed bead-shaped and U-shaped arrangements in the myenteric plexus. The densities of neurons and ganglia increased with age. However, the number of positive neurons per ganglion increased. The number of NADPH-d-positive neurons was highest in the colon, followed by the ileum, the jejunum, the duodenum, and the caeca in all age groups. Conclusions: Developmental changes in the myenteric plexus of chickens continue in the postnatal period, indicating that the maturation process of the gastrointestinal function is gradual. In addition, no significant difference is happening among different intestinal segments during postnatal development, suggesting that the function of different intestinal segments had been determined after birth.
doi:10.1631/jzus.B1300005
PMCID: PMC3796640  PMID: 24101205
NADPH-d histochemistry; Enteric nervous system (ENS); Development; Myenteric plexus; Chicken
22.  Past and Future Work on Radiobiology Mega Studies: A Case Study at Argonne National Laboratory 
Health physics  2011;100(6):613-621.
Between 1952 and 1992 more than 200 large radiobiology studies were conducted in research institutes throughout Europe, North America and Japan to determine the effects of external irradiation and internal emitters on the life span and tissue toxicity development in animals. At Argonne National Laboratory, 22 external beam studies were conducted on nearly 700 beagle dogs and 50,000 mice between 1969 and 1992. These studies helped to characterize the effects of neutron and gamma irradiation on lifespan, tumorigenesis, and mutagenesis across a range of doses and dosing patterns. The records and tissues collected at Argonne during that time period have been carefully preserved and redisseminated. Using these archived data ongoing statistical work has been done and continues to characterize quality of radiation, dose, dose rate, tissue, and gender specific differences in the radiation responses of exposed animals. The ongoing application of newly developed molecular biology techniques to the archived tissues has revealed gene specific mutation rates following exposure to ionizing irradiation. The original and ongoing work with this tissue archive is presented here as a case study of a more general trend in the radiobiology mega studies. These experiments helped form the modern understanding of radiation responses in animals, and continue to inform development of new radiation models. Recent archival efforts have facilitated open access to the data and materials produced by these studies and so a unique opportunity exists to expand this continued research.
doi:10.1097/HP.0b013e3181febad3
PMCID: PMC3784403  PMID: 22004930
23.  Common Variants on 8p12 and 1q24.2 Confer Risk of Schizophrenia 
Nature genetics  2011;43(12):1224-1227.
Schizophrenia is a severe mental disorder affecting ~1% of the world population, with heritability of up to 80%. To identify new common genetic risk factors, we performed a genome-wide association study (GWAS) in the Han Chinese population. The discovery sample set consisted of 3,750 patients and 6,468 healthy controls (1,578 cases and 1,592 controls from the Northern Han; 1,238 cases and 2,856 controls from the Central Han; 934 cases and 2,020 controls from the Southern Han); and we followed up the top association signals in an additional independent cohort of 4,383 cases and 4,539 controls from the Han Chinese. Meta-analysis identified genome-wide significant association of common SNPs with schizophrenia on chromosome 8p12 (rs16887244, P=1.27×10−10) and 1q24.2 (rs10489202, P=9.50×10−9). Our findings provide new insights into the pathogenesis of schizophrenia.
doi:10.1038/ng.980
PMCID: PMC3773910  PMID: 22037555
24.  Microbial Products Induce Claudin-2 to Compromise Gut Epithelial Barrier Function 
PLoS ONE  2013;8(8):e68547.
The epithelial barrier dysfunction is an important pathogenic feature in a number of diseases. The underlying mechanism is to be further investigated. The present study aims to investigate the role of tight junction protein claudin-2 (Cldn2) in the compromising epithelial barrier function. In this study, the expression of Cldn2 in the epithelial layer of mice and patients with food allergy was observed by immunohistochemistry. The induction of Cldn2 was carried out with a cell culture model. The Cldn2-facilitated antigen internalization was observed by confocal microscopy. The epithelial barrier function in the gut epithelial monolayer was assessed by recording the transepithelial resistance and assessing the permeability to a macromolecular tracer. The results showed that the positive immune staining of Cldn2 was observed in the epithelial layer of the small intestine that was weakly stained in naïve control mice, and strongly stained in sensitized mice as well as patients with food allergy. Exposure to cholera toxin or Staphylococcal enterotoxin B induced the expression of Cldn2 in HT-29 or T84 cells. Cldn2 could bind protein antigen to form complexes to facilitate the antigen transport across the epithelial barrier. Blocking Cldn2 prevented the allergen-related hypersensitivity the intestine. We conclude that the tight junction protein Cldn2 is involved in the epithelial barrier dysfunction.
doi:10.1371/journal.pone.0068547
PMCID: PMC3749177  PMID: 23990874
25.  Comparison of the GnRH agonist and antagonist protocol on the same patients in assisted reproduction during controlled ovarian stimulation cycles 
Despite the fact that both gonadotropin-releasing hormone (GnRH) agonist and antagonist protocol are effective in suppressing the incidence of premature luteinizing hormone (LH) surges through reversibly blocking the secretion of pituitary gonadotropins, the exact impact of these two distinctive protocols on the clinical setting of patients for in vitro fertilization and embryo transfer (IVF-ET) treatment, however, remained controversial. We thus in the present report conducted a retrospective study to compare the impact of GnRH agonist and antagonist protocol on the same patients during controlled ovarian stimulation cycles. A total of 81 patients undergoing 105 agonist and 88 antagonist protocol were analyzed. We failed to detect a significant difference between two protocols for the difference in duration of ovarian stimulation, number of recombinant FSH (Gonal-F) ampoules used, number of oocytes retrieved, serum levels for estradiol (E2) and progestone (P), thickness of endometrium, and the zygote- and blastocyst-development rate. It is seemly that high quality embryo rate was higher in the antagonist protocol, but the data did not reach a statistical significance. Nevertheless, Implantation rate and clinical pregnancy rate were significantly higher in the antagonist protocol (10.64% and 30.26%, respectively) than that of the agonist protocol (5.26% and 15.82%, respectively). Our data also suggest that the GnRH antagonist protocol is likely to have the advantage for improving the outcome of pregnancy in those patients with a history of multiple failures for the IVF-ET treatment.
PMCID: PMC3759499  PMID: 24040457
Gonadotropin-releasing hormone (GnRH); agonist; antagonist; in vitro fertilization; embryo transfer; assisted reproduction; controlled ovarian stimulation cycles

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