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1.  Tyr-phosphorylation of PDP1 toggles recruitment between ACAT1 and SIRT3 to regulate pyruvate dehydrogenase complex 
Molecular cell  2014;53(4):534-548.
SUMMARY
Mitochondrial pyruvate dehydrogenase complex (PDC) is crucial for glucose homoeostasis in mammalian cells. The current understanding of PDC regulation involves inhibitory serine phosphorylation of pyruvate dehydrogenase (PDH) by PDH kinase (PDK), whereas dephosphorylation of PDH by PDH phosphatase (PDP) activates PDC. Here we report that lysine acetylation of PDHA1 and PDP1 is common in EGF-stimulated cells and diverse human cancer cells. K321 acetylation inhibits PDHA1 by recruiting PDK1 and K202 acetylation inhibits PDP1 by dissociating its substrate PDHA1, both of which are important to promote glycolysis in cancer cells and consequent tumor growth. Moreover, we identified mitochondrial ACAT1 and SIRT3 as the upstream acetyltransferase and deacetylase, respectively, of PDHA1 and PDP1, while knockdown of ACAT1 attenuates tumor growth. Furthermore, Y381 phosphorylation of PDP1 dissociates SIRT3 and recruits ACAT1 to PDC. Together, hierarchical, distinct post-translational modifications act in concert to control molecular composition of PDC and contribute to the Warburg effect.
doi:10.1016/j.molcel.2013.12.026
PMCID: PMC3943932  PMID: 24486017
2.  Bacteria that glide with helical tracks 
Current biology : CB  2014;24(4):R169-R173.
Many bacteria glide smoothly on surfaces, but with no discernable propulsive organelles on their surface. Recent experiments with Myxococcus xanthus and Flavobacterium johnsoniae show that both distantly related bacterial species glide utilizing proteins that move in helical tracks, albeit with significantly different motility mechanisms. Both species utilize proton motive force for movement. However, the motors that power gliding in M. xanthus have been identified, while the F. johnsoniae motors remain to be discovered.
doi:10.1016/j.cub.2013.12.034
PMCID: PMC3964879  PMID: 24556443
3.  CsrA impacts survival of Yersinia enterocolitica by affecting a myriad of physiological activities 
BMC Microbiology  2015;15:31.
Background
A previous study identified a Yersinia enterocolitica transposon mutant, GY448, that was unable to export the flagellar type three secretion system (T3SS)-dependent phospholipase, YplA. This strain was also deficient for motility and unable to form colonies on Lauria-Bertani agar medium. Preliminary analysis suggested it carried a mutation in csrA. CsrA in Escherichia coli is an RNA-binding protein that is involved in specific post-transcriptional regulation of a myriad of physiological activities. This study investigated how CsrA affects expression of the flagellar regulatory cascade that controls YplA export and motility. It also explored the effect of csrA mutation on Y. enterocolitica in response to conditions that cue physiological changes important for growth in environments found both in nature and the laboratory.
Results
The precise location of the transposon insertion in GMY448 was mapped within csrA. Genetic complementation restored disruptions in motility and the YplA export phenotype (Yex), which confirmed this mutation disrupted CsrA function. Mutation of csrA affected expression of yplA and flagellar genes involved in flagellar T3SS dependent export and motility by altering expression of the master regulators flhDC. Mutation of csrA also resulted in increased sensitivity of Y. enterocolitica to various osmolytes, temperatures and antibiotics.
Conclusions
The results of this study reveal unique aspects of how CsrA functions in Y. enterocolitica to control its physiology. This provides perspective on how the Csr system is susceptible to adaptation to particular environments and bacterial lifestyles.
doi:10.1186/s12866-015-0343-6
PMCID: PMC4336687
Yersinia; CsrA; Csr system; Motility; Salt sensitivity; Antibiotic sensitivity; Temperature sensitivity; Psychrotroph; Mutant selection
4.  Detection of Hepatitis B Virus Genotypic Resistance Mutations by Coamplification at Lower Denaturation Temperature-PCR Coupled with Sanger Sequencing 
Journal of Clinical Microbiology  2014;52(8):2933-2939.
Mutations in the reverse transcriptase (rt) region of the DNA polymerase gene are the primary cause of hepatitis B virus (HBV) drug resistance. In this study, we established a novel method that couples coamplification at lower denaturation temperature (COLD)-PCR and Sanger sequencing, and we applied it to the detection of known and unknown HBV mutations. Primers were designed based on the common mutations in the HBV rt sequence at positions 180 to 215. The critical denaturation temperature (Tc) was established as a denaturing temperature for both fast and full COLD-PCR procedures. For single mutations, when a melting temperature (Tm)-reducing mutation occurred (e.g., C-G→T-A), the sensitivities of fast and full COLD-PCR for mutant detection were 1% and 2%, respectively; when the mutation caused no change in Tm (e.g., C-G→G-C) or raised Tm (e.g., T-A→C-G), only full COLD-PCR improved the sensitivity for mutant detection (2%). For combination mutations, the sensitivities of both full and fast COLD-PCR were increased to 0.5%. The limits of detection for fast and full COLD-PCR were 50 IU/ml and 100 IU/ml, respectively. In 30 chronic hepatitis B (CHB) cases, no mutations were detected by conventional PCR, whereas 18 mutations were successfully detected by COLD-PCR, including low-prevalence mutations (<10%), as confirmed by ultradeep pyrosequencing. In conclusion, COLD-PCR provides a highly sensitive, simple, inexpensive, and practical tool for significantly improving amplification efficacy and detecting low-level mutations in clinical CHB cases.
doi:10.1128/JCM.01127-14
PMCID: PMC4136161  PMID: 24899029
5.  NVP-BEZ235 overcomes gefitinib-acquired resistance by down-regulating PI3K/AKT/mTOR phosphorylation 
OncoTargets and therapy  2015;8:269-277.
Background
Patients harboring activating mutations in epidermal growth factor receptors (EGFR) are particularly sensitive to EGFR tyrosine kinase inhibitors (TKIs). However, most patients develop an acquired resistance after a period of about 10 months. This study focuses on the therapeutic effect of NVP-BEZ235, a dual inhibitor of phosphatidylinositol-3-kinase/mammalian target of rapamycin (PI3K/mTOR), in gefitinib-resistant non-small cell lung cancer.
Methods
H1975 cell line was validated as a gefitinib-resistant cell model by the nucleotide-sequence analysis. We used the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay to detect the growth of H1975 cell line in vitro. H1975 cells’ migration was detected by the migration assay. Xenograft models were used to investigate the growth of gefitinib-resistant non-small cell lung cancer in vivo. Western blot and immunohistochemical analysis were used to investigate the level of PI3K/protein kinase B(AKT)/mTOR signaling pathway proteins.
Results
We show that NVP-BEZ235 effectively inhibited the growth of H1975 cells in vivo as well as in vitro. Similarly, H1975 cell migration was reduced by NVP-BEZ235. Further experiments revealed that NVP-BEZ235 attenuated the phosphorylation of PI3K/AKT/mTOR signaling pathway proteins.
Conclusion
Taken together, we suggest that NVP-BEZ235 inhibits gefitinib-resistant tumor growth by downregulating PI3K/AKT/mTOR phosphorylation.
doi:10.2147/OTT.S62128
PMCID: PMC4321659
gefitinib-acquired resistance; PI3K kinase; mTOR; NVP-BEZ235
6.  New substitute name for the genus Poliocoris Slater, 1994 (Hemiptera, Heteroptera, Rhyparochromidae) 
ZooKeys  2015;147-148.
Neopoliocoris nom. n., a new substitute name is proposed for Poliocoris Slater, 1994 (Hemiptera: Heteroptera: Rhyparochromidae), preoccupied by Poliocoris Kirkaldy, 1910 (Hemiptera: Heteroptera: Pentatomidae). A new combination, Neopoliocoris umbrosus (Slater, 1994), comb. n. is proposed for Poliocoris umbrosus Slater, 1994.
doi:10.3897/zookeys.478.9063
PMCID: PMC4319055
Hemiptera; Heteroptera; bugs; homonym; replacement name
7.  Liver Damage Associated with Polygonum multiflorum Thunb.: A Systematic Review of Case Reports and Case Series 
Objective. To summarize the characteristics and analysis of relevant factors and to give references for prevention and further study of liver damage associated with Polygonum multiflorum Thunb. (HSW), we provide a systematic review of case reports and case series about liver damage associated with HSW. Methods. An extensive search of 6 medical databases was performed up to June 2014. Case reports and case series involving liver damage associated with HSW were included. Results. This review covers a total of 450 cases in 76 articles. HSW types included raw and processed HSW decoction pieces and many Chinese patent medicines that contain HSW. Symptoms of liver damage occur mostly a month or so after taking the medicine, mainly including jaundice, fatigue, anorexia, and yellow or tawny urine. Of the 450 patients, two cases who received liver transplantation and seven who died, the remaining 441 cases recovered or had liver function improvement after discontinuing HSW products and conservative care. Conclusion. HSW causes liver toxicity and may cause liver damage in different degrees and even lead to death; most of them are much related to long-term and overdose of drugs. Liver damage associated with HSW is reversible, and, after active treatment, the majority can be cured. People should be alert to liver damage when taking HSW preparations.
doi:10.1155/2015/459749
PMCID: PMC4306360  PMID: 25648693
8.  Vav1 as a Central Regulator of Invadopodia Assembly 
Current biology : CB  2013;24(1):86-93.
Summary
Invadopodia are protrusive structures used by tumor cells for degradation of the extracellular matrix to promote invasion [1]. Invadopodia formation and function are regulated by cytoskeletal remodeling pathways and the oncogenic kinase Src. The guanine nucleotide exchange factor Vav1, which is an activator of Rho family GTPases, is ectopically expressed in many pancreatic cancers, where it promotes tumor cell survival and migration [2, 3]. We have now determined that Vav1 is also a potent regulator of matrix degradation by pancreatic tumor cells, as depletion of Vav1 by siRNA-mediated knockdown inhibits the formation of invadopodia. This requires the exchange function of Vav1 toward the GTPase Cdc42, which is required for invadopodia assembly [4, 5]. In addition, we have determined that Src-mediated phosphorylation and activation of Vav1 is both required for, and, unexpectedly, sufficient for, invadopodia formation. Expression of Vav1 Y174F, which mimics its activated state, is a potent inducer of invadopodia formation through Cdc42, even in the absence of Src activation and phosphorylation of other Src substrates, such as cortactin. Thus, these data identify a novel mechanism by which Vav1 can enhance the tumorigenicity and invasive potential of cancer cells. These data suggest that Vav1 promotes the matrix-degrading processes underlying tumor cell migration, and further, under conditions of ectopic Vav1 expression, that Vav1 is a central regulator and major driver of invasive matrix remodeling by pancreatic tumor cells.
doi:10.1016/j.cub.2013.11.013
PMCID: PMC3917499  PMID: 24332539
9.  Blood Pressure Responses to Dietary Sodium and Potassium Interventions and the Cold Pressor Test: The GenSalt Replication Study in Rural North China 
BACKGROUND
In the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) study, we observed that blood pressure (BP) responses to dietary sodium and potassium interventions and the cold pressor test (CPT) varied greatly among individuals. We conducted a replication study to confirm our previous findings among 695 study participants.
METHODS
The dietary intervention included a 7-day low sodium (51.3 mmol/day), a 7-day high sodium (307.8 mmol/day), and a 7-day high sodium with potassium supplementation (307.8 mmol sodium and 60 mmol potassium/day). BP measurements were obtained during the baseline and each intervention phase. During the CPT, BP was measured before and at 0, 1, 2, and 4 minutes after the participants immersed their right hand in ice water for 1 minute.
RESULTS
Systolic and diastolic BP responses (mean ± SD (range), mm Hg) were 8.1±8.4 (−39.1 to 18.2) and −3.5±5.1 (−25.1 to 11.1) to low sodium, 9.1±8.4 (−13.3 to 33.1) and 4.0±5.4 (−16.0 to 20.7) to high sodium, and −4.6±5.8 (−31.8 to 11.6) and −1.9±4.3 (−16.9 to 14.2) to potassium supplementation, respectively (all P < 0.0001 for comparison with each former phase). The mean maximum systolic and diastolic BP responses to the CPT were 16.5±10.5 (−15.3 to 63.3) and 7.6±6.1 (−8.7 to 39.3), respectively (all P < 0.0001).
CONCLUSIONS
Our study indicates that there are large variations in BP responses to dietary sodium and potassium interventions and to the CPT among individuals.
doi:10.1093/ajh/hpt163
PMCID: PMC3848630  PMID: 24004934
blood pressure; cold pressor test; dietary potassium; hypertension; salt sensitivity; sodium.
10.  Application of the Protection Motivation Theory in Predicting Cigarette Smoking Among Adolescents in China 
Addictive behaviors  2013;39(1):181-188.
Reducing tobacco use among adolescents in China represents a significant challenge for global tobacco control. Existing behavioral theories developed in the West – such as the Protection Motivation Theory (PMT) – may be useful tools to help tackle this challenge. We examined the relationships between PMT factors and self-reported cigarette smoking behavior and intention among a random sample of vocational high school students (N = 553) in Wuhan, China. Tobacco-related perceptions were assessed using the PMT Scale for Adolescent Smoking. Among the total sample, 45% had initiated cigarette smoking, and 25% smoked in the past month. Among those who never smoked, 15% indicated being likely or very likely to smoke in a year. Multiple regression modeling analysis indicated the significance of the seven PMT constructs, the four PMT perceptions and the two PMT pathways in predicting intention to smoke and actual smoking behavior. Overall, perceived rewards of smoking, especially intrinsic rewards, were consistently positively related to smoking intentions and behavior, and self-efficacy to avoid smoking was negatively related to smoking. The current study suggests the utility of PMT for further research examining adolescent smoking. PMT-based smoking prevention and clinical smoking cessation intervention programs should focus more on adolescents’ perceived rewards from smoking and perceived efficacy of not smoking to reduce their intention to and actual use of tobacco.
doi:10.1016/j.addbeh.2013.09.027
PMCID: PMC3966196  PMID: 24157424
Protection Motivation Theory; Adolescents; Cigarette smoking; China
11.  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
12.  Genome-Wide Association Study Identifies Eight Novel Loci Associated with Blood Pressure Responses to Interventions in Han Chinese 
Background
Blood pressure (BP) responses to dietary sodium and potassium intervention and cold pressor test (CPT) vary considerably among individuals. We aimed to identify novel genetic variants influencing individuals’ BP responses to dietary intervention and CPT.
Methods and Results
We conducted a genome-wide association study of BP responses in 1,881 Han Chinese and de novo genotyped top findings in 698 Han Chinese. Diet-feeding study included a 7-day low-sodium (51.3 mmol/day), a 7-day high-sodium (307.8 mmol/day), and a 7-day high-sodium plus potassium-supplementation (60 mmol/day). Nine BP measurements were obtained during baseline observation and each intervention period. The meta-analyses identified eight novel loci for BP phenotypes, which physically mapped in or near PRMT6 (P=7.29×10−9), CDCA7 (P=3.57×10−8), PIBF1 (P=1.78×10−9), ARL4C (P=1.86×10−8), IRAK1BP1 (P=1.44×10−10), SALL1 (P=7.01×10−13), TRPM8 (P=2.68×10−8), and FBXL13 (P=3.74×10−9). There was a strong dose-response relationship between the number of risk alleles of these independent SNPs and the risk of developing hypertension over 7.5-year follow-up in the study participants. Compared to those in the lowest quartile of risk alleles, odds ratios (95% confidence intervals) for those in the second, third and fourth quartiles were 1.39 (0.97, 1.99), 1.72 (1.19, 2.47), and 1.84 (1.29, 2.62), respectively (P=0.0003 for trend).
Conclusions
Our study identified 8 novel loci for BP responses to dietary sodium and potassium intervention and CPT. The effect size of these novel loci on BP phenotypes are much larger than those reported by the previously published studies. Furthermore, these variants predict the risk of developing hypertension among individuals with normal BP at baseline.
doi:10.1161/CIRCGENETICS.113.000307
PMCID: PMC3952335  PMID: 24165912
blood pressure; genomics; sodium; potassium
13.  A non-invasive screening technique for type 1 autoimmune pancreatitis 
Introduction
Type 1 autoimmune pancreatitis (AIP) is the pancreatic manifestation of a systemic fibroinflammatory IgG4-related disease. Accurate diagnosis of AIP can avoid major hepatobiliary and pancreatic surgery as it respond dramatically to corticosteroid therapy.
Aim
This research investigated the feasibility of using peripheral blood cell immunohistochemistry, serum IgG4, T-cell receptor (TCR) and serum isoelectric focusing electrophoresis in the screening of type 1 autoimmune pancreatitis (AIP).
Material and methods
The peripheral blood from 3 type 1 AIP patients, 10 pancreatic cancer patients and 40 normal controls was collected. Sediment smears were jointly incubated with anti-IgG4 and anti-IgG. The percentage of IgG4/IgG positive cells was counted and serum TCR and IgG4 were detected through the whole process. After serum isoelectric focusing electrophoresis, anti-IgG4 and anti-IgG were used to confirm the components of serum.
Results
In the serum isoelectric focusing electrophoresis, IgG4 and IgG strips showed mirrored distribution in type 1 AIP patients, while there were no strips in the normal controls and pancreatic cancer. Compared with pancreatic tumor patients and healthy controls, serum TCR was significant increased in AIP. The percentage of IgG4/IgG positive cells of peripheral blood cell immunohistochemistry was related to serum IgG4 and hormone therapy reactions.
Conclusions
Peripheral blood cell immunohistochemistry, serum IgG4, TCR and serum isoelectric focusing electrophoresis is suitable for the screening of type 1 AIP and monitoring its response assessment.
doi:10.5114/wiitm.2014.44290
PMCID: PMC4280412  PMID: 25561988
type 1 autoimmune pancreatitis; peripheral blood cell immunohistochemistry; serum IgG4; TCR; serum isoelectric focusing electrophoresis
14.  A Comparative Study of Sodium Houttuyfonate and 2-Undecanone for Their in Vitro and in Vivo Anti-Inflammatory Activities and Stabilities 
Houttuynia cordata Thunb. (H. cordata) is an anti-inflammatory herbal drug that is clinically used in Asia. The essential oil obtained from H. cordata is known to contain 2-undecanone (2-methyl nonyl ketone). In addition, sodium houttuyfonate is a compound that can be derived from H. cordata and has important clinical uses as an anti-inflammatory agent. Sodium houttuyfonate can be converted to decanoyl acetaldehyde (houttuynin) and then to 2-undecanone. Therefore, the experiments described here explore the comparative anti-inflammatory activities of these compounds. Sodium houttuyfonate showed more potent anti-inflammatory activities than that of 2-undecanone at the same dosage, both in vitro and in vivo, although both compounds significantly inhibited the production of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and the expression of toll-like receptor 4 (TLR4), but increased the secretion of interleukin-10 (IL-10) in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. In addition, both compounds showed dose-dependent inhibitory effects on xylene-induced mouse ear edema. In a previous study, we found sodium houttuyfonate to be transformed to 2-undecanone during steam distillation (SD). Optimum therapeutic effects are related to the stability and pharmacological activity of the drugs. Consequently, we studied the stability of sodium houttuyfonate under a simulated gastrointestinal environment with the main influencing factors being solvent, temperature and pH effects. For the first time, sodium houttuyfonate and 2-undecanone were detected simultaneously in the mouse serum and the gastrointestinal tissue after oral administration. Sodium houttuyfonate is detected within a short period of time in the systemic circulation and tissues without conversion to 2-undecanone.
doi:10.3390/ijms151222978
PMCID: PMC4284749  PMID: 25514406
sodium houttuyfonate; 2-undecanone; anti-inflammatory activity; stability; bioavailability; gas chromatography-mass spectrometry (GC-MS)
15.  An Improved Performance Frequency Estimation Algorithm for Passive Wireless SAW Resonant Sensors 
Sensors (Basel, Switzerland)  2014;14(12):22261-22273.
Passive wireless surface acoustic wave (SAW) resonant sensors are suitable for applications in harsh environments. The traditional SAW resonant sensor system requires, however, Fourier transformation (FT) which has a resolution restriction and decreases the accuracy. In order to improve the accuracy and resolution of the measurement, the singular value decomposition (SVD)-based frequency estimation algorithm is applied for wireless SAW resonant sensor responses, which is a combination of a single tone undamped and damped sinusoid signal with the same frequency. Compared with the FT algorithm, the accuracy and the resolution of the method used in the self-developed wireless SAW resonant sensor system are validated.
doi:10.3390/s141222261
PMCID: PMC4299012  PMID: 25429410
wireless SAW sensors; singular value decomposition; frequency estimation
16.  Long non-coding RNAs in non-small cell lung cancer as biomarkers and therapeutic targets 
Lung cancer-associated mortality is the most common cause of cancer death worldwide. Non-coding RNAs (ncRNAs), with no protein-coding ability, have multiple biological roles. Long non-coding RNAs (lncRNAs) are a recently characterized class of ncRNAs that are over 200 nucleotides in length. Many lncRNAs have the ability of facilitating or inhibiting the development and progression of tumours, including non-small cell lung cancer (NSCLC). Because of their fundamental roles in regulating gene expression, along with their involvement in the biological mechanisms underlying tumourigenesis, they are a promising class of tissue- and/or blood-based cancer biomarkers. In this review, we highlight the emerging roles of lncRNAs in NSCLC, and discuss their potential clinical applications as diagnostic and prognostic markers and as therapeutic targets.
doi:10.1111/jcmm.12431
PMCID: PMC4302648  PMID: 25297942
long non-coding RNA; non-small cell lung cancer; biomarker; molecular target
17.  Glycoproteomic Analysis of Bronchoalveolar Lavage (BAL) Fluid Identifies Tumor-associated Glycoproteins from Lung Adenocarcinoma 
Journal of proteome research  2013;12(8):3689-3696.
Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in 8 cases of BAL fluid, as well as 8 lung adenocarcinoma tissues and 8 tumor-matched normal lung tissues, were analyzed using the solid-phase extraction of N-glycoprotein (SPEG), iTRAQ labeling and liquid chromatography tandem mass spectrometry (LC-MS/MS). Of 80 glycoproteins found in BAL specimens, 32 were identified in both cancer BAL and cancer tissues with levels of 25 glycoproteins showing at least a 2-fold difference between cancer and benign BAL. Among them, 8 glycoproteins showed greater than 2-fold elevations in cancer BAL, including Neutrophil elastase (NE), Integrin alpha-M, Cullin-4B, Napsin A, Lysosome-associaed membrane protein 2 (LAMP2), Cathepsin D, BPI fold-containing family B member 2, and Neutrophil gelatinase-associated lipocalin. The levels of Napsin A in cancer BAL were further verified in an independently collected 39 BAL specimens using an ELISA assay. Our study demonstrates that potential protein biomarkers in BAL fluid can be detected and quantified.
doi:10.1021/pr400274w
PMCID: PMC4238415  PMID: 23802180
glycoproteomics; bronchoalveolar lavage (BAL); glycoproteins; lung adenocarcinoma; non-small cell lung cancer (NSCLC)
18.  Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway 
PLoS Pathogens  2014;10(11):e1004522.
Enteropathogenic E. coli (EPEC) and related enterobacteria rely on a type III secretion system (T3SS) effector NleE to block host NF-κB signaling. NleE is a first in class, novel S-adenosyl-L-methionine (SAM)-dependent methyltransferase that methylates a zinc-coordinating cysteine in the Npl4-like Zinc Finger (NZF) domains in TAB2/3 adaptors in the NF-κB pathway, but its mechanism of action and other human substrates are unknown. Here we solve crystal structure of NleE-SAM complex, which reveals a methyltransferase fold different from those of known ones. The SAM, cradled snugly at the bottom of a deep and narrow cavity, adopts a unique conformation ready for nucleophilic attack by the methyl acceptor. The substrate NZF domain can be well docked into the cavity, and molecular dynamic simulation indicates that Cys673 in TAB2-NZF is spatially and energetically favorable for attacking the SAM. We further identify a new NleE substrate, ZRANB3, that functions in PCNA binding and remodeling of stalled replication forks at the DNA damage sites. Specific inactivation of the NZF domain in ZRANB3 by NleE offers a unique opportunity to suggest that ZRANB3-NZF domain functions in DNA repair processes other than ZRANB3 recruitment to DNA damage sites. Our analyses suggest a novel and unexpected link between EPEC infection, virulence proteins and genome integrity.
Author Summary
Pathogens often manipulate host functions by posttranslational modifications such as ubiquitination and methylation. The NF-κB pathway is most critical for immune defense against infection, thereby frequently targeted by bacterial virulence factors. NleE, a virulence effector from EPEC, is a SAM-dependent methyltransferase that modifies a zinc-finger cysteine in TAB2/3 in the NF-κB pathway. NleE is not homologous to any known methyltransferases. We present the crystal structure of SAM-bound NleE that shows a novel methyltransferase fold with a unique SAM-binding mode. Computational docking and molecular dynamics simulation illustrate a structural and chemical mechanism underlying NleE recognition of the NZF and catalyzing site-specific cysteine methylation. Subsequent substrate specificity analyses identify an N-terminal region in TAB3 required for efficient NleE recognition as well as another NZF protein ZRANB3 being a new substrate of NleE. NleE-catalyzed cysteine methylation also disrupts the ubiquitin chain-binding of ZRANB3-NZF domain, providing new insights into ZRANB3-NZF functioning in DNA damage repair. These results reinforce the idea of harnessing bacterial effectors as a tool for dissecting eukaryotic functions.
doi:10.1371/journal.ppat.1004522
PMCID: PMC4239114  PMID: 25412445
19.  Solid Phase Extraction of N-linked Glycopeptides Using Hydrazide Tip 
Analytical chemistry  2013;85(22):10670-10674.
Glycoproteome contains valuable information where biomarkers may be discovered for disease diagnosis and monitoring. Nowadays, with the ever increasing performances of mass spectrometers, the emphasis is shifting to the sample preparation for better throughput and reproducibility. Therefore, to facilitate high throughput N-linked glycopeptide isolation, in this study, a novel hydrazide tip was devised and an integrated workflow of N-linked glycopeptide isolation using hydrazide tips was presented. Using bovine fetuin as a standard glycoprotein, the incubation time was determined for each major step of glycopeptide isolation. Using commercially available human serum, multiple parallel isolations of glycopeptides were performed using hydrazide tips with a liquid handling robotic system. We demonstrated that, with the hydrazide tips, the processing time was significantly decreased from 3–4 days to less than 8 h with excellent reproducibility. The hydrazide pipette tips have great potential in achieving automation of N-linked glycopeptide isolation for high throughput sample preparation when used in combination with liquid handling robotic systems.
doi:10.1021/ac401812b
PMCID: PMC4082910  PMID: 24079330
Proteomics; glycopeptides; pipette tip; solid phase extraction; hydrazide
20.  A phylogenetic study of Drosophila splicing assembly chaperone RNP-4F associated U4-/U6-snRNA secondary structure 
The rnp-4f gene in Drosophila melanogaster encodes nuclear protein RNP-4F. This encoded protein is represented by homologs in other eukaryotic species, where it has been shown to function as an intron splicing assembly factor. Here, RNP-4F is believed to initially bind to a recognition sequence on U6-snRNA, serving as a chaperone to facilitate its association with U4-snRNA by intermolecular hydrogen bonding. RNA conformations are a key factor in spliceosome function, so that elucidation of changing secondary structures for interacting snRNAs is a subject of considerable interest and importance. Among the five snRNAs which participate in removal of spliceosomal introns, there is a growing consensus that U6-snRNA is the most structurally dynamic and may constitute the catalytic core. Previous studies by others have generated potential secondary structures for free U4- and U6-snRNAs, including the Y-shaped U4-/U6-snRNA model. These models were based on study of RNAs from relatively few species, and the popular Y-shaped model remains to be systematically re-examined with reference to the many new sequences generated by recent genomic sequencing projects. We have utilized a comparative phylogenetic approach on 60 diverse eukaryotic species, which resulted in a revised and improved U4-/U6-snRNA secondary structure. This general model is supported by observation of abundant compensatory base mutations in every stem, and incorporates more of the nucleotides into base-paired associations than in previous models, thus being more energetically stable. We have extensively sampled the eukaryotic phylogenetic tree to its deepest roots, but did not find genes potentially encoding either U4- or U6-snRNA in the Giardia and Trichomonas data-bases. Our results support the hypothesis that nuclear introns in these most deeply rooted eukaryotes may represent evolutionary intermediates, sharing characteristics of both group II and spliceosomal introns. An unexpected result of this study was discovery of a potential competitive binding site for Drosophila splicing assembly factor RNP-4F to a 5’-UTR regulatory region within its own premRNA, which may play a role in negative feedback control.
doi:10.4236/ojas.2013.34A2005
PMCID: PMC4237228  PMID: 25419488
RNP-4F; snRNA Secondary Structure; U4-/U6-snRNA Phylogeny; Spliceosome Evolution
21.  Low Serum Cartonectin/CTRP3 Concentrations in Newly Diagnosed Type 2 Diabetes Mellitus: In Vivo Regulation of Cartonectin by Glucose 
PLoS ONE  2014;9(11):e112931.
Objectives
Cartonectin is a novel adipokine of the C1q complement/TNF-related protein (CTRP) superfamily, with glucose lowering effects, anti-inflammatory and cardio-protective properties. We sought to investigate circulating cartonectin concentrations in subjects with type 2 diabetes mellitus (T2DM) as well as age and BMI matched control subjects. We also examined the effects of a 2 hour 75 g oral glucose tolerance test (OGTT) on serum cartonectin concentrations in T2DM subjects.
Design
Cross-sectional study [newly diagnosed (first discovery, not on any treatments) T2DM (n = 47) and control (n = 63) subjects]. Serum cartonectin was measured by ELISA.
Results
Serum cartonectin concentrations were significantly lower in patients with T2DM compared to controls (P<0.05). Furthermore, serum cartonectin was significantly negatively correlated with glucose and CRP, and significantly positively correlated with leptin, in all subjects (n = 110). When subjected to multiple regression analysis, none of these variables were predictive of serum cartonectin (P>0.05). There were no significant correlations in T2DM subjects (n = 47). In control subjects (n = 63), serum cartonectin was significantly negatively correlated with CRP, and significantly positively correlated with insulin, HOMA-IR and leptin. However, when subjected to multiple regression analysis, none of these variables were predictive of serum cartonectin (P>0.05). Finally, serum cartonectin concentrations were significantly lower in T2DM subjects after a 2 hour 75 g OGTT (P<0.01).
Conclusions
Cartonectin may serve as a novel biomarker for the prediction and early diagnosis of T2DM patients. Furthermore, cartonectin and/or pharmacological agents that increase circulating cartonectin levels can represent a new therapeutic field in the treatment of T2DM patients. Further research is needed to clarify these points.
doi:10.1371/journal.pone.0112931
PMCID: PMC4237345  PMID: 25409499
22.  Identification, prioritization and evaluation of glycoproteins for aggressive prostate cancer using quantitative glycoproteomics and antibody-based assays on tissue specimens 
Proteomics  2013;13(15):2268-2277.
Prostate cancer is highly heterogeneous in nature; while the majority of cases are clinically insignificant, some cases are lethal. Currently, there are no reliable screening methods for aggressive prostate cancer. Since most established serum and urine biomarkers are glycoproteins secreted or leaked from the diseased tissue, the current study seeks to identify glycoprotein markers specific to aggressive prostate cancer using tissue specimens. With LC-MS/MS glycoproteomic analysis, we identified 350 glycopeptides with 17 being altered in aggressive prostate cancer. ELISA assays were developed/purchased to evaluate 4 candidates, i.e. cartilage oligomeric matrix protein (COMP), periostin, membrane primary amine oxidase (VAP-1) and cathepsin L, in independent tissue sets. In agreement with the proteomic analysis, we found that COMP and periostin expressions were significantly increased in aggressive prostate tumors while VAP-1 expression was significantly decreased in aggressive tumor. In addition, the expression of these proteins in prostate metastases also follows the same pattern observed in the proteomic analysis. This study provides a workflow for biomarker discovery, prioritization and evaluation of aggressive prostate cancer markers using tissue specimens. Our data suggest increase in COMP and periostin and decrease in VAP-1 expression in the prostate may be associated with aggressive prostate cancer.
doi:10.1002/pmic.201200541
PMCID: PMC4235679  PMID: 23716368
aggressive; prostate cancer; biomarker; glycoproteomics; OCT
23.  A Novel Contrast-Induced Acute Kidney Injury Model Based on the 5/6-Nephrectomy Rat and Nephrotoxicological Evaluation of Iohexol and Iodixanol In Vivo 
Contrast-induced acute kidney injury (CI-AKI) is a serious complication in patients after administration of iodinated contrast media. Proper animal models of CI-AKI can help understand the mechanisms involved and prevent the disorder. We used the 5/6-nephrectomized (NE) rat to develop a CI-AKI model and to evaluate differences in the toxic effects on the kidney between iohexol and iodixanol. We found that six weeks after ablative surgery was the preferred time to induce CI-AKI. We compared multiple pretreatment plans and found that dehydration for 48 hours before iodixanol (320, 10 mL/kg) administration was optimal to induce CI-AKI in the 5/6 NE rats. Compared with iodixanol, iohexol induced a significantly greater reduction in renal function, severe renal tissue damage, intrarenal hypoxia, and apoptotic tubular cells. Iohexol and iodixanol resulted in similarly marked increases in levels of inflammation and oxidative stress. In summary, the 5/6 NE rat combined with dehydration for 48 hours is a useful pretreatment to establish a novel and reliable CI-AKI model. Iohexol induced more severe CI-AKI than iodixanol in this model.
doi:10.1155/2014/427560
PMCID: PMC4244948  PMID: 25478060
24.  Blocking and reversing hepatic fibrosis in patients with chronic hepatitis B treated by traditional Chinese medicine (tablets of biejia ruangan or RGT): study protocol for a randomized controlled trial 
Trials  2014;15(1):438.
Background
Chronic hepatitis B (CHB) can progress to cirrhosis, hepatocellular carcinoma (HCC) and ultimately liver-related death. Although oral antiviral therapy for patients with CHB reduces the risk of such complications, once cirrhosis is established, the benefits of antiviral therapy are not robustly demonstrated. According to traditional Chinese medicine (TCM), some Chinese herbal medicines promote blood circulation and soften hard masses, and therefore they may block and reverse hepatic fibrosis. The aim of this study is to evaluate the effects of TCM tablets of the compound biejia ruangan (RGT) administered for fibrosis, and entecavir (ETV), on the development of HCC in patients with CHB or hepatitis B virus (HBV)-related compensated cirrhosis.
Methods/design
This multicenter, centrally randomized, double-blind, placebo-controlled, parallel-group study is planned to complete within 5 years. For the study, 1,000 with CHB or HBV-related compensated cirrhosis are randomly assigned in a 1:1 ratio to a treatment group (0.5 mg ETV once daily; 2 g RGT three times daily) or a control group (0.5 mg ETV once daily; 2 g RGT dummy agent three times daily). The primary end points are the development of HCC and liver-related death. Secondary end points include disease progression and overall survival.
Discussion
Although antiviral therapy can achieve sustained suppression of HBV replication, thereby preventing cirrhosis, patients with CHB treated with nucleos(t)ide analogs (NUCs) retain a higher risk for HCC compared with patients with inactive disease. Although previous clinical trials with RGT have confirmed the efficacy of blocking and reversing hepatic fibrosis in patients with CHB or compensated cirrhosis, the long-term risk for HCC or disease progression in these patients treated with combination of RGT and NUCs compared with NUCs alone is unclear. Therefore, it is necessary to investigate the effects of the RGT blockade and reversal of hepatic fibrosis on the development of HCC in patients with CHB or HBV-related compensated cirrhosis in large, prospective, multicenter, double-blind, randomized, controlled trials in China.
Trial registration
ClinicalTrials.gov Identifier: NCT01965418. Date registered: 17 October 2013
doi:10.1186/1745-6215-15-438
PMCID: PMC4234899  PMID: 25381721
Compound biejia ruangan tablet; multicenter randomized controlled trial; chronic hepatitis B; hepatocellular carcinoma; hepatic fibrosis
25.  A Comparison between the EQ-5D and the SF-6D in Patients with Chronic Obstructive Pulmonary Disease (COPD) 
PLoS ONE  2014;9(11):e112389.
Background
The appropriate use of generic preference-based measures determines the accuracy of disease assessment and further decision on healthcare policy using quality adjusted life years. The discriminative capacity of different instruments would differ across disease groups. Our study was to examine the difference in utility scores for COPD patients measured by EQ-5D and SF-6D and to assist the choice of a proper instrument in this disease group.
Methods
Differences of mean utility scores of EQ-5D and SF-6D in groups defined by socio-demographic characteristics, comorbidities, health service utilisation and severity of illness were tested using Mann-Whitney test, t-test, Kruskal-Wallis test, Pearson’s correlation coefficient and ANOVA, as appropriate. The discriminative properties of the two instruments were compared against indicators of quality of life using receiver operating characteristic curves. The statistical significance of the area under the curves (AUC) was tested by ANOVA and F-statistics used to compare the efficiency with which each instrument discriminated between disease severity groups.
Results
Mean utility scores of EQ-5D and SF-6D were 0.644 and 0.629 respectively in the 154 subjects included in the analysis. EQ-5D scores were significantly higher than SF-6D in groups less severe and these differences corresponded to a minimally important difference of greater than 0.03 (p<0.001). EQ-5D and SF-6D scores were strongly correlated across the whole sample (r = 0.677, p<0.001) and in pre-defined groups (r>0.5 and p<0.05 for all correlation coefficients). AUCs were above 0.5 against the indicators of health-related quality of life for both instruments. F-ratios suggested SF-6D was more efficient in discriminating cases of different disease severity than EQ-5D.
Conclusions
Both EQ-5D and SF-6D appeared to be valid preference-based measures in Chinese COPD patients. SF-6D was more efficient in detecting differences among subgroups with differing health status. EQ-5D and SF-6D measured different things and might not be used interchangeably in COPD patients.
doi:10.1371/journal.pone.0112389
PMCID: PMC4224433  PMID: 25379673

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