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1.  IL-17 response mediates acute lung injury induced by the 2009 Pandemic Influenza A (H1N1) Virus 
Cell Research  2011;22(3):528-538.
The 2009 flu pandemic involved the emergence of a new strain of a swine-origin H1N1 influenza virus (S-OIV H1N1) that infected almost every country in the world. Most infections resulted in respiratory illness and some severe cases resulted in acute lung injury. In this report, we are the first to describe a mouse model of S-OIV virus infection with acute lung injury and immune responses that reflect human clinical disease. The clinical efficacy of the antiviral oseltamivir (Tamiflu) administered in the early stages of S-OIV H1N1 infection was confirmed in the mouse model. Moreover, elevated levels of IL-17, Th-17 mediators and IL-17-responsive cytokines were found in serum samples of S-OIV-infected patients in Beijing. IL-17 deficiency or treatment with monoclonal antibodies against IL-17-ameliorated acute lung injury induced by the S-OIV H1N1 virus in mice. These results suggest that IL-17 plays an important role in S-OIV-induced acute lung injury and that monoclonal antibodies against IL-17 could be useful as a potential therapeutic remedy for future S-OIV H1N1 pandemics.
doi:10.1038/cr.2011.165
PMCID: PMC3292301  PMID: 22025253
cytokine; acute lung injury; S-OIV H1N1
3.  Dietary and inhalation exposure to polycyclic aromatic hydrocarbons and urinary excretion of monohydroxy metabolites – a controlled case study in Beijing, China 
Daily dietary and inhalation exposures to 16 parent polycyclic aromatic hydrocarbons (PAHs) and urinary excretion of 13 monohydroxy metabolites (OHPAHs) were monitored for 12 non-smoking university students in Beijing, China, during a controlled feeding experiment. The relationship between the urinary excretion of OHPAHs and the uptake of PAHs was investigated. The results suggest severe exposure of the subjects to PAHs via both dietary and inhalation pathways. Large increase of most urinary OHPAHs occurred after the ingestion of lamb kabob. Higher concentrations of OHPAHs were observed for female subjects, with the intakes of parent PAHs lower than those by males, likely due to the gender differences in metabolism. It appears that besides 1-PYR, metabolites of PHE could also be used as biomarkers to indicate the short-term dietary exposure to PAHs and urinary 3-BaA may serve as the biomarker for inhalation intake of high molecular weight PAHs.
doi:10.1016/j.envpol.2013.10.005
PMCID: PMC4299857  PMID: 24177434
Polycyclic aromatic hydrocarbons; dietary exposure; urinary excretion; biomarkers
4.  Effects of aging, CMV infection, and EBV infection on human B cell repertoires 
Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by cytomegalovirus (CMV) is implicated as a driver of clonal T cell proliferations in some aging humans, but whether CMV or Epstein-Barr virus (EBV) infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of immunoglobulin heavy chain (IGH) gene rearrangements to study the B cell receptor repertoires over two successive years in 27 individuals ranging in age from 20 to 89 years. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG immunoglobulin genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual's age: EBV infection correlates with the presence of persistent clonal B cell expansions, while CMV infection correlates with the proportion of highly mutated antibody genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires, and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.
doi:10.4049/jimmunol.1301384
PMCID: PMC3947124  PMID: 24337376
5.  Bystander-initiated CPR in an Asian metropolitan: Does the socioeconomic status matter?☆ 
Resuscitation  2013;85(1):53-58.
Objectives
To determine the association of neighborhood socioeconomic status (SES) with bystander-initiated cardiopulmonary resuscitation (CPR) and patient outcomes of out of hospital cardiac arrests (OHCAs) in an Asian metropolitan area.
Methods
We performed a retrospective study in a prospectively collected cohort from the Utstein registry of adult non-traumatic OHCAs in Taipei, Taiwan. Average real estate value was assessed as the first proxy of SES. Twelve administrative districts in Taipei City were categorized into low versus high SES areas to test the association. The primary outcome was bystander-initiated CPR, and the secondary outcome was patient survival status. Factors associated with bystander-initiated CPR were adjusted for in multivariate analysis. The mean household income was assessed as the second proxy of SES to validate the association.
Results
From January 1, 2008 to December 30, 2009, 3573 OHCAs received prehospital resuscitation in the community. Among these, 617 (17.3%) cases received bystander CPR. The proportion of bystander CPR in low-SES vs. high-SES areas was 14.5% vs. 19.6% (p < 0.01). Odds ratio of receiving bystander-initiated CPR in low-SES areas was 0.72 (95% confidence interval: [0.60–0.88]) after adjusting for age, gender, witnessed status, public collapse, and OHCA unrecognized by the online dispatcher. Survival to discharge rate was significantly lower in low-SES areas vs. high-SES areas (4.3% vs. 6.8%; p < 0.01). All results above remained consistent in the analyses by mean household income.
Conclusions
Patients who experienced an OHCA in low-SES areas were less likely to receive bystander-initiated CPR, and demonstrated worse survival outcomes.
doi:10.1016/j.resuscitation.2013.07.033
PMCID: PMC4023511  PMID: 24056397
Cardiopulmonary resuscitation (CPR); Emergency medical system (EMS); Education; Socioeconomic status (SES); Neighborhood; First responder
6.  Percutaneous Intramyocardial Delivery of Mesenchymal Stem Cells Induces Superior Improvement in Regional Left Ventricular Function Compared with Bone Marrow Mononuclear Cells in Porcine Myocardial Infarcted Heart 
Theranostics  2015;5(2):196-205.
Aim: To investigate the efficacy and feasibility of percutaneous intramyocardial injection of bone marrow mesenchymal stem cells (MSC) and autologous bone marrow-derived mononuclear cells (BMMNC) on cardiac functional improvement in porcine myocardial infarcted hearts. Methods and Results: Acute myocardial infarction (AMI) was induced in 22 minipigs by temporary balloon occlusion of the left anterior descending coronary artery for 60min.Two weeks post AMI, BMMNC (n = 7, 245 ± 98×106), MSC (n = 8, 56 ± 17×106), or phosphate buffered saline (PBS; n = 7) were injected intramyocardially. Cardiac function and myocardial perfusion were analyzed by echocardiography and gated single-photon emission computed tomography/computed tomography (SPECT/CT) at 1 week before AMI and 2 and 10 weeks after AMI. Cell engraftment, proliferation, vascular density, and cardiac fibrosis were evaluated by histology analysis. In all groups, the echocardiography revealed no significant change in the left ventricular ejection fraction (LVEF), left ventricular end-systolic volume (LVESV), or left ventricular end-diastolic volume (LVEDV) at 10 weeks after AMI compared with those at 2 weeks after AMI. However, the wall motion score index (WMSI) and left ventricular systolic wall thickening (WT%) were significantly improved at 10 weeks compared with those at 2 weeks after AMI in the MSC group (WMSI 1.55 ± 0.06 vs. 1.87 ± 0.10, WT 33.4 ± 2.3% vs.24.8 ± 2.7%,p < 0.05) but not in the BMMNC group. In addition, myocardial perfusion quantified by SPECT/CT was improved in both the MSC and BMMNC groups, whereas the MSC group showed a superior improvement in vascular density and collagen volume fraction (p < 0.05). Conclusion: This preclinically relevant study suggests that when delivered by percutaneous (transcatheter) intramyocardial injection, MSC might be more effective than BMMNC to improve ischemia and reperfusion after AMI.
doi:10.7150/thno.7976
PMCID: PMC4279004  PMID: 25553108
Angiogenesis; Imaging; Myocardial infarction; Remodeling; Stem cells.
7.  Induction of H2AX phosphorylation in tumor cells by gossypol acetic acid is mediated by phosphatidylinositol 3-kinase (PI3K) family 
Cancer Cell International  2014;14(1):141.
Background
H2AX is phosphorylated (γH2AX) by members of the phosphatidylinositol 3-kinase (PI3K) family, including Ataxia telangiectasia-mutated (ATM), ATM- and Rad3-related (ATR) and DNA-PK in response to DNA damage. Our study shows that gossypol acetic acid (GAA) alone can induce γH2AX in Human mucoepidermoid carcinoma cell line (MEC-1) in vitro. Thus, we further examined the possible mechanisms of GAA to induce γH2AX in tumor cells.
Materials and methods
The PI3K inhibitors caffeine and wortmannin were used in an effort to identify the kinase(s) responsible for GAA -induced γH2AX in MEC-1 cells. DNA dependent protein kinase (DNA-PK) - proficient and –deficient cells, human glioma cell lines M059K and M059J, were also used to evaluate the kinases responsible for GAA induced H2AX phosphorylation. γH2AX expression was detected by immunofluorescent microscopy. Flow cytometry assay was used to assay γH2AX and cell cycle.
Results
GAA induced H2AX phosphorylation in a cell cycle-dependent manner and a significant G0/G1 phase arrest in MEC-1 cells was shown. Caffeine and wortmannin significantly inhibited GAA-induced H2AX phosphorylation in MEC-1 cells. GAA induced H2AX phosphorylation in M059K, but not in M059J. Taken together, these data suggested that GAA treatment alone could induce H2AX phosphorylation in a cell cycle dependent manner in MEC-1 and M059K, but not in M059J cells. A significant G0/G1 phase arrest was shown in MEC-1.
Conclusions
The member of PI3K family, DNA-PK, ATM and ATR are involved in the H2AX phosphorylation of MEC-1 cells.
doi:10.1186/s12935-014-0141-5
PMCID: PMC4272777  PMID: 25530717
Gossypol acetic acid; H2AX phosphorylation; DNA-PK; ATM; ATR
8.  Frailty Attenuates the Impact of Metformin on Reducing Mortality in Older Adults with Type 2 Diabetes 
Objective
To determine whether the protective effect of metformin against death is modified by frailty status in older adults with type 2 diabetes.
Research Design and Methods
We conducted a cohort study during October 1, 1999–September 30, 2006 among veterans aged 65–89 years old with type 2 diabetes but without history of liver, renal diseases, or cancers, who had sulfonylureas or metformin as the sole antidiabetic drug for ≥180 days. The Cox proportional hazard model was used to compare hazard rates of all-cause mortality between the metformin and sulfonylurea users adjusting for the propensity score of metformin use and covariates: age, race/ethnicity, diabetes duration, Charlson comorbidity score, statin use, smoking status, BMI, LDL, and HbA1c.
Results
In this cohort of 2,415 veterans, 307 (12.7%) were metformin users, 2,108 (87.3%) were sulfonylurea users, the mean age was 73.7±5.2 years, the mean study period was 5.6±2.3 years, the mean HbA1c at baseline was 6.7±1.0%, 23% had diabetes for ≥10 years, and 43.6% (N=1,048) died during the study period. For patients with and without frailty, the adjusted hazard ratio (HR) of death for metformin vs. sulfonylurea use were 0.92 (95% CI=0.90–1.31, p-value=0.19) and 0.69 (95% CI = 0.60–0.79, p-value<0.001), respectively. Logistic regression analyses showed that metformin (vs. sulfonylurea) was significantly associated with a decreased odds of frailty (OR: 0.66, 95% CI: 0.61–0.71, p-value <.0001)
Conclusion
Our study suggests that metformin could potentially promote longevity via preventing frailty in older adults with type 2 diabetes.
PMCID: PMC4264048  PMID: 25506599
Metformin; Frailty; Mortality; Type 2 diabetes
9.  Differentiating Amino Acid Residues and Side Chain Orientations in Peptides Using Scanning Tunneling Microscopy 
Journal of the American Chemical Society  2013;135(49):18528-18535.
Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structure at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer’s and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.
doi:10.1021/ja408550a
PMCID: PMC4117194  PMID: 24219245
Single molecule; protein structure; scanning tunneling microscopy; amyloid; atomic force microscopy; peptide structure
10.  Sevoflurane Postconditioning Protects Rat Hearts against Ischemia-Reperfusion Injury via the Activation of PI3K/AKT/mTOR Signaling 
Scientific Reports  2014;4:7317.
Phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway plays a key role in myocardial ischemia-reperfusion (I/R) injury. Mammalian target of rapamycin (mTOR), a downstream target of PI3K/AKT signaling, is necessary and sufficient to protect the heart from I/R injury. Inhaled anesthetic sevoflurane is widely used in cardiac surgeries because its induction and recovery are faster and smoother than other inhaled anesthetics. Sevoflurane proved capable of inducing postconditioning effects in the myocardium. However, the underlying molecular mechanisms for sevoflurane-induced postconditioning (SPC) were largely unclear. In the present study, we demonstrated that SPC protects myocardium from I/R injury with narrowed cardiac infarct focus, increased ATP content, and decreased cardiomyocyte apoptosis, which are mainly due to the activation of PI3K/AKT/mTOR signaling and the protection of mitochondrial energy metabolism. Application of dactolisib (BEZ235), a PI3K/mTOR dual inhibitor, abolishes the up-regulation of pho-AKT, pho-GSK, pho-mTOR, and pho-p70s6k induced by SPC, hence abrogating the anti-apoptotic effect of sevoflurane and reducing SPC-mediated protection of heart from I/R injury. As such, this study proved that PI3K/AKT/mTOR pathway plays an important role in SPC induced cardiac protection against I/R injury.
doi:10.1038/srep07317
PMCID: PMC4255182  PMID: 25471136
12.  Temporal trends in new exposure to antiepileptic drug monotherapy and suicide-related behavior 
Neurology  2013;81(22):1900-1906.
Objective:
Because some recent studies suggest increased risk for suicide-related behavior (SRB; ideation, attempts) among those receiving antiepileptic drugs (AEDs), we examined the temporal relationship between new AED exposure and SRB in a cohort of older veterans.
Methods:
We used national Veterans Health Administration databases to identify veterans aged ≥65 years who received a new AED prescription in 2004–2006. All instances of SRB were identified using ICD-9-CM codes 1 year before and after the AED exposure (index) date. We also identified comorbid conditions and medication associated with SRB in prior research. We used generalized estimating equations with a logit link to examine the association between new AED exposure and SRB during 30-day intervals during the year before and after the index date, controlling for potential confounders.
Results:
In this cohort of 90,263 older veterans, the likelihood of SRB the month prior to AED exposure was significantly higher than in other time periods even after adjusting for potential confounders. Although there were 87 SRB events (74 individuals) the year before and 106 SRB events (92 individuals) after, approximately 22% (n = 16) of those also had SRB before the index date. Moreover, the rate of SRB after AED start was gradually reduced over time.
Conclusions:
The temporal pattern of AED exposure and SRB suggests that, in clinical practice, the peak in SRB is prior to exposure. While speculative, the rate of gradual reduction in SRB thereafter suggests that symptoms may prompt AED prescription.
doi:10.1212/01.wnl.0000436614.51081.2e
PMCID: PMC3843385  PMID: 24174583
13.  A huge adenosquamous carcinoma of the pancreas with sarcomatoid change: An unusual case report 
World Journal of Gastroenterology : WJG  2014;20(43):16381-16386.
Adenosquamous carcinoma rarely occurs in the pancreas, and is characterized by the presence of cellular components from both duct adenocarcinoma and squamous carcinoma. Here, we describe a rare case of pancreatic adenosquamous carcinoma with sarcomatous change. Immunohistochemistry showed that the sarcomatous lesion lost the epithelial marker and aberrantly expressed of acquired mesenchymal markers, which indicated that this special histological phenotype may be attributed to epithelial-mesenchymal transition. This case also indicated that a routine radical surgery without aggressive treatment strategies was still appropriate for adenosquamous carcinoma of the pancreas with sarcomatoid change.
doi:10.3748/wjg.v20.i43.16381
PMCID: PMC4239535  PMID: 25473201
Adenosquamous carcinoma; Sarcomatoid change; Pancreatic tumors; Histopathological types; Epithelial-mesenchymal transition
14.  A Kullback-Leibler Divergence for Bayesian Model Diagnostics 
Open journal of statistics  2011;1(3):172-184.
This paper considers a Kullback-Leibler distance (KLD) which is asymptotically equivalent to the KLD by Goutis and Robert [1] when the reference model (in comparison to a competing fitted model) is correctly specified and that certain regularity conditions hold true (ref. Akaike [2]). We derive the asymptotic property of this Goutis-Robert-Akaike KLD under certain regularity conditions. We also examine the impact of this asymptotic property when the regularity conditions are partially satisfied. Furthermore, the connection between the Goutis-Robert-Akaike KLD and a weighted posterior predictive p-value (WPPP) is established. Finally, both the Goutis-Robert-Akaike KLD and WPPP are applied to compare models using various simulated examples as well as two cohort studies of diabetes.
doi:10.4236/ojs.2011.13021
PMCID: PMC4235748  PMID: 25414801
Kullback-Leibler Distance; Model Diagnostic; Weighted Posterior Predictive p-Value
15.  Change-point diagnostics in competing risks models: Two posterior predictive p-value approaches 
Test (Madrid, Spain)  2007;16(1):145-171.
This paper presents a Bayesian diagnostic procedure for examining change-point assumption in the competing risks model framework. It considers the family of distributions arising from the cause-specific model as reported by Chiang (Introduction to stochastic processes in biostatistics. Wiley, New York, 1968) upon which change-points are added to accommodate possible distributional heterogeneity. Model departure, due to misspecification of change-points associated with either the overall survival distribution or cause-specific probabilities, is quantified in terms of a sequence of cumulative-sum statistics between each pair of adjacent change-points assumed. When assessing the asymptotic behavior of each sequence of cumulative-sum statistics using its posterior predictive p-values, see Rubin (Ann Stat 12:1151–1172, 1984) and partial posterior predictive p-values as reported by Bayarri and Berger (J Am Stat Assoc 95:1127–1142, 2000), we show that both types of p-values attain their greatest departure from 0.5 at the change-point that is missed in the assumed model, from which a diagnostic procedure is formalized. Statistical power of these two types of p-values is discussed.
doi:10.1007/s11749-006-0006-x
PMCID: PMC4226243  PMID: 25392679
Change-point; Competing risks; Posterior predictive p-values
16.  B-RAF kinase drives developmental axon growth and promotes axon regeneration in the injured mature CNS 
Intraneuronal activation of B-RAF kinase is sufficient to drive the growth of peripheral axon projections and enables robust regenerative axon growth in the injured optic nerve.
Activation of intrinsic growth programs that promote developmental axon growth may also facilitate axon regeneration in injured adult neurons. Here, we demonstrate that conditional activation of B-RAF kinase alone in mouse embryonic neurons is sufficient to drive the growth of long-range peripheral sensory axon projections in vivo in the absence of upstream neurotrophin signaling. We further show that activated B-RAF signaling enables robust regenerative growth of sensory axons into the spinal cord after a dorsal root crush as well as substantial axon regrowth in the crush-lesioned optic nerve. Finally, the combination of B-RAF gain-of-function and PTEN loss-of-function promotes optic nerve axon extension beyond what would be predicted for a simple additive effect. We conclude that cell-intrinsic RAF signaling is a crucial pathway promoting developmental and regenerative axon growth in the peripheral and central nervous systems.
doi:10.1084/jem.20131780
PMCID: PMC4010899  PMID: 24733831
17.  The efficacy of a thrombin-based hemostatic agent in primary total knee arthroplasty: a meta-analysis 
Purpose
Total knee arthroplasty (TKA) is a popular procedure in severe osteoarthritis. But perioperative bleeding remains a problem. Floseal® is a mixture of thrombin and bovine gelatin which can benefit a lot on reducing intraoperative and postoperative bleeding. However, there is no enough evidence judging its safety and efficiency. So a meta-analysis is conducted by us to evaluate the efficacy and safety of a thrombin-based hemostatic agent compared with conventional methods in TKA.
Method
Two independent reviewers selected literatures published before August 2014 from MEDLINE, Embase, and The Cochrane Central Register of Controlled Trials. Other internet databases were also performed to identify trials according to the Cochrane Collaboration guidelines. High-quality randomized controlled trials (RCTs), prospective control trials (PCTs), and case controlled trials (CCTs) were selected. The meta-analysis was undertaken using RevMan 5.1 for Windows.
Results
Three RCTs, one PCT, and one CCT met the inclusion criteria. There were significant differences in hemoglobin decline and calculated total blood loss between the Floseal® group and control group. There were no significant differences in postoperative drainage volume, rate of transfusion requirement, incidence of wound infection, deep vein thrombosis (DVT), and pulmonary embolism (PE) between treatment and control groups.
Conclusions
The present meta-analysis indicates that a thrombin-based hemostatic agent can reduce hemoglobin decline and calculated total blood loss after TKA and is not related to adverse reactions or complications such as wound infection, DVT, and PE.
doi:10.1186/s13018-014-0090-7
PMCID: PMC4212119  PMID: 25316253
Floseal®; Thrombin; Arthroplasty; Meta-analysis
18.  A designed peptide targeting CXCR4 displays anti-acute myelocytic leukemia activity in vitro and in vivo 
Scientific Reports  2014;4:6610.
Leukemia cells highly expressing chemokine receptor CXCR4 can actively response to stroma derived factor 1α (CXCL12), trafficking and homing to the marrow microenvironment, which causes poor prognosis and relapse. Here we demonstrate that a novel designed peptide (E5) targeting CXCR4 inhibits CXCL12- and stroma-induced activation in multiple acute myelocytic leukemia (AML) cell lines and displays anti-AML activity. We show that E5 has high affinity to multiple AML cells with high CXCR4 level in a concentration dependent manner. E5 significantly inhibits CXCL12- or murine stromal cell (MS-5)-induced migration of leukemia cells and prevents the cells from adhering to stromal cells. Mechanistic studies demonstrate that E5 down-regulates CXCL12-induced phosphorylation of Akt, Erk, and p38, which affects the cytoskeleton F-actin organization and ultimately results in the inhibition of CXCL12- and stroma-mediated leukemia cell responses. E5 can induce concentration-dependent apoptosis in the four AML cell lines tested while did not affect the viability of MS-5 or human umbilical vein cell (ea.hy926) even at 80 µM, both of which have a low level of CXCR4. In vivo experimental results show that immunocompromised mice transplanted with HL-60 cells survived longer when treated with E5 twice a week in comparison to those treated with cyclophosphamide.
doi:10.1038/srep06610
PMCID: PMC4196105  PMID: 25312253
19.  Lin28a Protects against Hypoxia/Reoxygenation Induced Cardiomyocytes Apoptosis by Alleviating Mitochondrial Dysfunction under High Glucose/High Fat Conditions 
PLoS ONE  2014;9(10):e110580.
Aim
The aim of the present study was to investigate the role of Lin28a in protecting against hypoxia/reoxygenation (H/R)-induced cardiomyocytes apoptosis under high glucose/high fat (HG/HF) conditions.
Methods
Primary cardiomyocytes which were isolated from neonatal mouse were randomized to be treated with lentivirus carrying Lin28a siRNA, Lin28acDNA 72 h before H/R (9 h/2 h). Cardiomyocytes biomarkers release (LDH and CK), cardiomyocytes apoptosis, mitochondria biogenesis and morphology, intracellular reactive oxygen species (ROS) production, ATP content and inflammatory cytokines levels after H/R injury in high glucose/high fat conditions were compared between groups. The target proteins of Lin28a were examined by western blot analysis.
Results
Our results revealed that Lin28a cDNA transfection (overexpression) significantly inhibited cardiomyocyte apoptotic index, improved mitochondria biogenesis, increased ATP production and reduced ROS production as compared with the H/R group in HG/HF conditions. Lin28a siRNA transfection (knockdown) rendered the cardiomyocytes more susceptible to H/R injury as evidenced by increased apoptotic index, impaired mitochondrial biogenesis, decreased ATP production and increased ROS level. Interestingly, these effects of Lin28a were blocked by pretreatment with the PI3K inhibitor wortmannin. Lin28a overexpression increased, while Lin28a knockdown inhibited IGF1R, Nrf-1, Tfam, p-IRS-1, p-Akt, p-mTOR, p-p70s6k, p-AMPK expression levels after H/R injury in HG/HF conditions. Moreover, pretreatment with wortmannin abolished the effects of Lin28a on the expression levels of p-AKT, p-mTOR, p-p70s6k, p-AMPK.
Conclusions
The present results suggest that Lin28a inhibits cardiomyocytes apoptosis by enhancing mitochondrial biogenesis and function under high glucose/high fat conditions. The mechanism responsible for the effects of Lin28a is associated with the PI3K/Akt dependent pathway.
doi:10.1371/journal.pone.0110580
PMCID: PMC4196990  PMID: 25313561
20.  H2B Mono-ubiquitylation Facilitates Fork Stalling and Recovery during Replication Stress by Coordinating Rad53 Activation and Chromatin Assembly 
PLoS Genetics  2014;10(10):e1004667.
The influence of mono-ubiquitylation of histone H2B (H2Bub) on transcription via nucleosome reassembly has been widely documented. Recently, it has also been shown that H2Bub promotes recovery from replication stress; however, the underling molecular mechanism remains unclear. Here, we show that H2B ubiquitylation coordinates activation of the intra-S replication checkpoint and chromatin re-assembly, in order to limit fork progression and DNA damage in the presence of replication stress. In particular, we show that the absence of H2Bub affects replication dynamics (enhanced fork progression and reduced origin firing), leading to γH2A accumulation and increased hydroxyurea sensitivity. Further genetic analysis indicates a role for H2Bub in transducing Rad53 phosphorylation. Concomitantly, we found that a change in replication dynamics is not due to a change in dNTP level, but is mediated by reduced Rad53 activation and destabilization of the RecQ helicase Sgs1 at the fork. Furthermore, we demonstrate that H2Bub facilitates the dissociation of the histone chaperone Asf1 from Rad53, and nucleosome reassembly behind the fork is compromised in cells lacking H2Bub. Taken together, these results indicate that the regulation of H2B ubiquitylation is a key event in the maintenance of genome stability, through coordination of intra-S checkpoint activation, chromatin assembly and replication fork progression.
Author Summary
Eukaryotic DNA is organized into nucleosomes, which are the fundamental repeating units of chromatin. Coordination of chromatin structure is required for efficient and accurate DNA replication. Aberrant DNA replication results in mutations and chromosome rearrangements that may be associated with human disorders. Therefore, cellular surveillance mechanisms have evolved to counteract potential threats to DNA replication. These mechanisms include checkpoints and specialized enzymatic activities that prevent the replication and segregation of defective DNA molecules. We employed a genome-wide approach to investigate how chromatin structure affects DNA replication under stress. We report that coordination of chromatin assembly and checkpoint activity by a histone modification, H2B ubiquitylation (H2Bub), is critical for the cell response to HU-induced replication stress. In cells with a mutation that abolishes H2Bub, replication progression is enhanced, and the forks are more susceptible to damage by environmental insults. The replication proteins on replicating DNA are akin to a train on the tracks, and movement of this train is carefully controlled. Our data indicate that H2Bub helps organize DNA in the nuclei during DNA replication; this process plays a similar role to the brakes on a train, serving to slow down replication, and maintaining stable progression of replication under environmental stress.
doi:10.1371/journal.pgen.1004667
PMCID: PMC4183429  PMID: 25275495
21.  Large-Scale Evaluation of Common Variation in Regulatory T Cell-Related Genes and Ovarian Cancer Outcome 
Charbonneau, Bridget | Moysich, Kirsten B. | Kalli, Kimberly R. | Oberg, Ann L. | Vierkant, Robert A. | Fogarty, Zachary C. | Block, Matthew S. | Maurer, Matthew J. | Goergen, Krista M. | Fridley, Brooke L. | Cunningham, Julie M. | Rider, David N. | Preston, Claudia | Hartmann, Lynn C. | Lawrenson, Kate | Wang, Chen | Tyrer, Jonathan | Song, Honglin | deFazio, Anna | Johnatty, Sharon E. | Doherty, Jennifer A. | Phelan, Catherine M. | Sellers, Thomas A. | Ramirez, Starr M. | Vitonis, Allison F. | Terry, Kathryn L. | Van Den Berg, David | Pike, Malcolm C. | Wu, Anna H. | Berchuck, Andrew | Gentry-Maharaj, Aleksandra | Ramus, Susan J. | Diergaarde, Brenda | Shen, Howard | Jensen, Allan | Menkiszak, Janusz | Cybulski, Cezary | Lubiński, Jan | Ziogas, Argyrios | Rothstein, Joseph H. | McGuire, Valerie | Sieh, Weiva | Lester, Jenny | Walsh, Christine | Vergote, Ignace | Lambrechts, Sandrina | Despierre, Evelyn | Garcia-Closas, Montserrat | Yang, Hannah | Brinton, Louise A. | Spiewankiewicz, Beata | Rzepecka, Iwona K. | Dansonka-Mieszkowska, Agnieszka | Seibold, Petra | Rudolph, Anja | Paddock, Lisa E. | Orlow, Irene | Lundvall, Lene | Olson, Sara H. | Hogdall, Claus K. | Schwaab, Ira | du Bois, Andreas | Harter, Philipp | Flanagan, James M. | Brown, Robert | Paul, James | Ekici, Arif B. | Beckmann, Matthias W. | Hein, Alexander | Eccles, Diana | Lurie, Galina | Hays, Laura E. | Bean, Yukie T. | Pejovic, Tanja | Goodman, Marc T. | Campbell, Ian | Fasching, Peter A. | Konecny, Gottfried | Kaye, Stanley B. | Heitz, Florian | Hogdall, Estrid | Bandera, Elisa V. | Chang-Claude, Jenny | Kupryjanczyk, Jolanta | Wentzensen, Nicolas | Lambrechts, Diether | Karlan, Beth Y. | Whittemore, Alice S. | Culver, Hoda Anton | Gronwald, Jacek | Levine, Douglas A. | Kjaer, Susanne K. | Menon, Usha | Schildkraut, Joellen M. | Pearce, Celeste Leigh | Cramer, Daniel W. | Rossing, Mary Anne | Chenevix-Trench, Georgia | Pharoah, Paul D.P. | Gayther, Simon A. | Ness, Roberta B. | Odunsi, Kunle | Sucheston, Lara E. | Knutson, Keith L. | Goode, Ellen L.
Cancer immunology research  2014;2(4):332-340.
The presence of regulatory T cells (Tregs) in solid tumors is known to play a role in patient survival in ovarian cancer and other malignancies. We assessed inherited genetic variations via 749 tag SNPs in 25 Treg-associated genes (CD28, CTLA4, FOXP3, IDO1, IL10, IL10RA, IL15, 1L17RA, IL23A, IL23R, IL2RA, IL6, IL6R, IL8, LGALS1, LGALS9, MAP3K8, STAT5A, STAT5B, TGFB1, TGFB2, TGFB3, TGFBR1, TGRBR2, and TGFBR3) in relation to ovarian cancer survival. We analyzed genotype and overall survival in 10,084 women with invasive epithelial ovarian cancer, including 5,248 high-grade serous, 1,452 endometrioid, 795 clear cell, and 661 mucinous carcinoma cases of European descent across 28 studies from the Ovarian Cancer Association Consortium (OCAC). The strongest associations were found for endometrioid carcinoma and IL2RA SNPs rs11256497 [HR=1.42, 95% CI: 1.22-1.64; p=5.7 × 10−6], rs791587 [HR=1.36, 95% CI:1.17-1.57; p=6.2 × 10−5], rs2476491 [HR=1.40, 95% CI: 1.19-1.64; p=5.6 × 10−5], and rs10795763 [HR=1.35, 95% CI: 1.17-1.57; p=7.9 × 10−5], and for clear cell carcinoma and CTLA4 SNP rs231775 [HR=0.67, 95% CI: 0.54-0.82; p=9.3 × 10−5] after adjustment for age, study site, population stratification, stage, grade, and oral contraceptive use. The rs231775 allele associated with improved survival in our study also results in an amino acid change in CTLA4 and previously has been reported to be associated with autoimmune conditions. Thus, we found evidence that SNPs in genes related to Tregs appear to play a role in ovarian cancer survival, particularly in patients with clear cell and endometrioid EOC.
doi:10.1158/2326-6066.CIR-13-0136
PMCID: PMC4000890  PMID: 24764580
clear cell; endometrioid; gynecologic neoplasms; single nucleotide polymorphism
22.  Large-Scale Evaluation of Common Variation in Regulatory T Cell-Related Genes and Ovarian Cancer Outcome 
Charbonneau, Bridget | Moysich, Kirsten B. | Kalli, Kimberly R. | Oberg, Ann L. | Vierkant, Robert A. | Fogarty, Zachary C. | Block, Matthew S. | Maurer, Matthew J. | Goergen, Krista M. | Fridley, Brooke L. | Cunningham, Julie M. | Rider, David N. | Preston, Claudia | Hartmann, Lynn C. | Lawrenson, Kate | Wang, Chen | Tyrer, Jonathan | Song, Honglin | deFazio, Anna | Johnatty, Sharon E. | Doherty, Jennifer A. | Phelan, Catherine M. | Sellers, Thomas A. | Ramirez, Starr M. | Vitonis, Allison F. | Terry, Kathryn L. | Van Den Berg, David | Pike, Malcolm C. | Wu, Anna H. | Berchuck, Andrew | Gentry-Maharaj, Aleksandra | Ramus, Susan J. | Diergaarde, Brenda | Shen, Howard | Jensen, Allan | Menkiszak, Janusz | Cybulski, Cezary | Lubiński, Jan | Ziogas, Argyrios | Rothstein, Joseph H. | McGuire, Valerie | Sieh, Weiva | Lester, Jenny | Walsh, Christine | Vergote, Ignace | Lambrechts, Sandrina | Despierre, Evelyn | Garcia-Closas, Montserrat | Yang, Hannah | Brinton, Louise A. | Spiewankiewicz, Beata | Rzepecka, Iwona K. | Dansonka-Mieszkowska, Agnieszka | Seibold, Petra | Rudolph, Anja | Paddock, Lisa E. | Orlow, Irene | Lundvall, Lene | Olson, Sara H. | Hogdall, Claus K. | Schwaab, Ira | du Bois, Andreas | Harter, Philipp | Flanagan, James M. | Brown, Robert | Paul, James | Ekici, Arif B. | Beckmann, Matthias W. | Hein, Alexander | Eccles, Diana | Lurie, Galina | Hays, Laura E. | Bean, Yukie T. | Pejovic, Tanja | Goodman, Marc T. | Campbell, Ian | Fasching, Peter A. | Konecny, Gottfried | Kaye, Stanley B. | Heitz, Florian | Hogdall, Estrid | Bandera, Elisa V. | Chang-Claude, Jenny | Kupryjanczyk, Jolanta | Wentzensen, Nicolas | Lambrechts, Diether | Karlan, Beth Y. | Whittemore, Alice S. | Culver, Hoda Anton | Gronwald, Jacek | Levine, Douglas A. | Kjaer, Susanne K. | Menon, Usha | Schildkraut, Joellen M. | Pearce, Celeste Leigh | Cramer, Daniel W. | Rossing, Mary Anne | Chenevix-Trench, Georgia | Pharoah, Paul D.P. | Gayther, Simon A. | Ness, Roberta B. | Odunsi, Kunle | Sucheston, Lara E. | Knutson, Keith L. | Goode, Ellen L.
Cancer immunology research  2014;2(4):332-340.
The presence of regulatory T cells (Tregs) in solid tumors is known to play a role in patient survival in ovarian cancer and other malignancies. We assessed inherited genetic variations via 749 tag SNPs in 25 Treg-associated genes (CD28, CTLA4, FOXP3, IDO1, IL10, IL10RA, IL15, 1L17RA, IL23A, IL23R, IL2RA, IL6, IL6R, IL8, LGALS1, LGALS9, MAP3K8, STAT5A, STAT5B, TGFB1, TGFB2, TGFB3, TGFBR1, TGRBR2, and TGFBR3) in relation to ovarian cancer survival. We analyzed genotype and overall survival in 10,084 women with invasive epithelial ovarian cancer, including 5,248 high-grade serous, 1,452 endometrioid, 795 clear cell, and 661 mucinous carcinoma cases of European descent across 28 studies from the Ovarian Cancer Association Consortium (OCAC). The strongest associations were found for endometrioid carcinoma and IL2RA SNPs rs11256497 [HR=1.42, 95% CI: 1.22–1.64; p=5.7 × 10−6], rs791587 [HR=1.36, 95% CI:1.17–1.57; p=6.2 × 10−5], rs2476491 [HR=1.40, 95% CI: 1.191.64; p=5.6 × 10−5], and rs10795763 [HR=1.35, 95% CI: 1.17–1.57; p=7.9 × 10−5], and for clear cell carcinoma and CTLA4 SNP rs231775 [HR=0.67, 95% CI: 0.54–0.82; p=9.3 × 10−5] after adjustment for age, study site, population stratification, stage, grade, and oral contraceptive use. The rs231775 allele associated with improved survival in our study also results in an amino acid change in CTLA4 and previously has been reported to be associated with autoimmune conditions. Thus, we found evidence that SNPs in genes related to Tregs appear to play a role in ovarian cancer survival, particularly in patients with clear cell and endometrioid EOC.
doi:10.1158/2326-6066.CIR-13-0136
PMCID: PMC4000890  PMID: 24764580
clear cell; endometrioid; gynecologic neoplasms; single nucleotide polymorphism
23.  MACE: model based analysis of ChIP-exo 
Nucleic Acids Research  2014;42(20):e156.
Understanding the role of a given transcription factor (TF) in regulating gene expression requires precise mapping of its binding sites in the genome. Chromatin immunoprecipitation-exo, an emerging technique using λ exonuclease to digest TF unbound DNA after ChIP, is designed to reveal transcription factor binding site (TFBS) boundaries with near-single nucleotide resolution. Although ChIP-exo promises deeper insights into transcription regulation, no dedicated bioinformatics tool exists to leverage its advantages. Most ChIP-seq and ChIP-chip analytic methods are not tailored for ChIP-exo, and thus cannot take full advantage of high-resolution ChIP-exo data. Here we describe a novel analysis framework, termed MACE (model-based analysis of ChIP-exo) dedicated to ChIP-exo data analysis. The MACE workflow consists of four steps: (i) sequencing data normalization and bias correction; (ii) signal consolidation and noise reduction; (iii) single-nucleotide resolution border peak detection using the Chebyshev Inequality and (iv) border matching using the Gale-Shapley stable matching algorithm. When applied to published human CTCF, yeast Reb1 and our own mouse ONECUT1/HNF6 ChIP-exo data, MACE is able to define TFBSs with high sensitivity, specificity and spatial resolution, as evidenced by multiple criteria including motif enrichment, sequence conservation, direct sequence pileup, nucleosome positioning and open chromatin states. In addition, we show that the fundamental advance of MACE is the identification of two boundaries of a TFBS with high resolution, whereas other methods only report a single location of the same event. The two boundaries help elucidate the in vivo binding structure of a given TF, e.g. whether the TF may bind as dimers or in a complex with other co-factors.
doi:10.1093/nar/gku846
PMCID: PMC4227761  PMID: 25249628
24.  Mechanism of the C5 Stereoinversion Reaction in the Biosynthesis of Carbapenem Antibiotics† 
Science (New York, N.Y.)  2014;343(6175):1140-1144.
The bicyclic β-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by β-lactam ring closure. Carbapenem synthase (CarC), an Fe(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H•) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H• to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H•-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.
doi:10.1126/science.1248000
PMCID: PMC4160820  PMID: 24604200
25.  Evidence that the Fosfomycin-producing Epoxidase, HppE, is a Non-heme-iron Peroxidase⊥ 
Science (New York, N.Y.)  2013;342(6161):991-995.
The iron-dependent epoxidase, HppE, converts (S)-2-hydroxypropyl-1-phosphonate (S-HPP) to the antibiotic, fosfomycin [(1R, 2S)-epoxypropylphosphonate], in an unusual 1,3-dehydrogenation of a secondary alcohol to an epoxide. HppE has been classified as an oxidase, with proposed mechanisms differing primarily in the identity of the O2-derived iron complex that abstracts hydrogen (H•) from C1 of S-HPP to initiate epoxide ring closure. We show here that the preferred co-substrate is actually H2O2 and that HppE therefore almost certainly employs an iron(IV)-oxo complex as the H• abstractor. Reaction with H2O2 is accelerated by bound substrate and produces fosfomycin catalytically with a stoichiometry of unity. The ability of catalase to suppress the HppE activity previously attributed to its direct utilization of O2 implies that reduction of O2 and utilization of the resultant H2O2 were actually operant.
doi:10.1126/science.1240373
PMCID: PMC4160821  PMID: 24114783

Results 1-25 (279)