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1.  Inactivation of DAP12 in PMN Inhibits TREM1-Mediated Activation in Rheumatoid Arthritis 
PLoS ONE  2015;10(2):e0115116.
Rheumatoid arthritis (RA) is an autoimmune disease characterized by dysregulated and chronic systemic inflammatory responses that affect the synovium, bone, and cartilage causing damage to extra-articular tissue. Innate immunity is the first line of defense against invading pathogens and assists in the initiation of adaptive immune responses. Polymorphonuclear cells (PMNs), which include neutrophils, are the largest population of white blood cells in peripheral blood and functionally produce their inflammatory effect through phagocytosis, cytokine production and natural killer-like cytotoxic activity. TREM1 (triggering receptor expressed by myeloid cells) is an inflammatory receptor in PMNs that signals through the use of the intracellular activating adaptor DAP12 to induce downstream signaling. After TREM crosslinking, DAP12’s tyrosines in its ITAM motif get phosphorylated inducing the recruitment of Syk tyrosine kinases and eventual activation of PI3 kinases and ERK signaling pathways. While both TREM1 and DAP12 have been shown to be important activators of RA pathogenesis, their activity in PMNs or the importance of DAP12 as a possible therapeutic target have not been shown. Here we corroborate, using primary RA specimens, that isolated PMNs have an increased proportion of both TREM1 and DAP12 compared to normal healthy control isolated PMNs both at the protein and gene expression levels. This increased expression is highly functional with increased activation of ERK and MAPKs, secretion of IL-8 and RANTES and cytotoxicity of target cells. Importantly, based on our hypothesis of an imbalance of activating and inhibitory signaling in the pathogenesis of RA we demonstrate that inhibition of the DAP12 signaling pathway inactivates these important inflammatory cells.
PMCID: PMC4313943  PMID: 25642940
2.  Identifying cooperative transcription factors in yeast using multiple data sources 
BMC Systems Biology  2014;8(Suppl 5):S2.
Transcriptional regulation of gene expression is usually accomplished by multiple interactive transcription factors (TFs). Therefore, it is crucial to understand the precise cooperative interactions among TFs. Various kinds of experimental data including ChIP-chip, TF binding site (TFBS), gene expression, TF knockout and protein-protein interaction data have been used to identify cooperative TF pairs in existing methods. The nucleosome occupancy data is not yet used for this research topic despite that several researches have revealed the association between nucleosomes and TFBSs.
In this study, we developed a novel method to infer the cooperativity between two TFs by integrating the TF-gene documented regulation, TFBS and nucleosome occupancy data. TF-gene documented regulation and TFBS data were used to determine the target genes of a TF, and the genome-wide nucleosome occupancy data was used to assess the nucleosome occupancy on TFBSs. Our method identifies cooperative TF pairs based on two biologically plausible assumptions. If two TFs cooperate, then (i) they should have a significantly higher number of common target genes than random expectation and (ii) their binding sites (in the promoters of their common target genes) should tend to be co-depleted of nucleosomes in order to make these binding sites simultaneously accessible to TF binding. Each TF pair is given a cooperativity score by our method. The higher the score is, the more likely a TF pair has cooperativity. Finally, a list of 27 cooperative TF pairs has been predicted by our method. Among these 27 TF pairs, 19 pairs are also predicted by existing methods. The other 8 pairs are novel cooperative TF pairs predicted by our method. The biological relevance of these 8 novel cooperative TF pairs is justified by the existence of protein-protein interactions and co-annotation in the same MIPS functional categories. Moreover, we adopted three performance indices to compare our predictions with 11 existing methods' predictions. We show that our method performs better than these 11 existing methods in identifying cooperative TF pairs in yeast. Finally, the cooperative TF network constructed from the 27 predicted cooperative TF pairs shows that our method has the power to find cooperative TF pairs of different biological processes.
Our method is effective in identifying cooperative TF pairs in yeast. Many of our predictions are validated by the literature, and our method outperforms 11 existing methods. We believe that our study will help biologists to understand the mechanisms of transcriptional regulation in eukaryotic cells.
PMCID: PMC4305981  PMID: 25559499
transcription factor cooperativity; nucleosome; transcription factor binding site; yeast
3.  A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae 
BMC Systems Biology  2014;8(Suppl 5):S9.
Defining a measure for regulatory similarity (RS) of two genes is an important step toward identifying co-regulated genes. To date, transcription factor binding sites (TFBSs) have been widely used to measure the RS of two genes because transcription factors (TFs) binding to TFBSs in promoters is the most crucial and well understood step in gene regulation. However, existing TFBS-based RS measures consider the relation of a TFBS to a gene as a Boolean (either 'presence' or 'absence') without utilizing the information of TFBS locations in promoters.
Functional TFBSs of many TFs in yeast are known to have a strong positional preference to occur in a small region in the promoters. This biological knowledge prompts us to develop a novel RS measure that exploits the TFBS location information. The performances of different RS measures are evaluated by the fraction of gene pairs that are co-regulated (validated by literature evidence) by at least one common TF under different RS scores. The experimental results show that the proposed RS measure is the best co-regulation indicator among the six compared RS measures. In addition, the co-regulated genes identified by the proposed RS measure are also shown to be able to benefit three co-regulation-based applications: detecting gene co-function, gene co-expression and protein-protein interactions.
The proposed RS measure provides a good indicator for gene co-regulation. Besides, its good performance reveals the importance of the location information in TFBS-based RS measures.
PMCID: PMC4305988  PMID: 25560196
4.  Lenalidomide Induces Lipid Raft Assembly to Enhance Erythropoietin Receptor Signaling in Myelodysplastic Syndrome Progenitors 
PLoS ONE  2014;9(12):e114249.
Anemia remains the principal management challenge for patients with lower risk Myelodysplastic Syndromes (MDS). Despite appropriate cytokine production and cellular receptor display, erythropoietin receptor (EpoR) signaling is impaired. We reported that EpoR signaling is dependent upon receptor localization within lipid raft microdomains, and that disruption of raft integrity abolishes signaling capacity. Here, we show that MDS erythroid progenitors display markedly diminished raft assembly and smaller raft aggregates compared to normal controls (p = 0.005, raft number; p = 0.023, raft size). Because lenalidomide triggers raft coalescence in T-lymphocytes promoting immune synapse formation, we assessed effects of lenalidomide on raft assembly in MDS erythroid precursors and UT7 cells. Lenalidomide treatment rapidly induced lipid raft formation accompanied by EpoR recruitment into raft fractions together with STAT5, JAK2, and Lyn kinase. The JAK2 phosphatase, CD45, a key negative regulator of EpoR signaling, was displaced from raft fractions. Lenalidomide treatment prior to Epo stimulation enhanced both JAK2 and STAT5 phosphorylation in UT7 and primary MDS erythroid progenitors, accompanied by increased STAT5 DNA binding in UT7 cells, and increased erythroid colony forming capacity in both UT7 and primary cells. Raft induction was associated with F-actin polymerization, which was blocked by Rho kinase inhibition. These data indicate that deficient raft integrity impairs EpoR signaling, and provides a novel strategy to enhance EpoR signal fidelity in non-del(5q) MDS.
PMCID: PMC4254997  PMID: 25469886
5.  ALDH1A1 overexpression is associated with the progression and prognosis in gastric cancer 
BMC Cancer  2014;14(1):705.
Aldehyde dehydrogenase 1 family member A1 (ALDH1A1) is a cancer stem cell marker, and its expression correlates with prognosis in a number of malignancies. The aim of this study is to determine the relationship of ALDH1A1 expression with clinicopathological parameters and prognosis in gastric cancer.
ALDH1A1 and matrix metallopeptidase 9 (MMP-9) was evaluated by immunohistochemistry in 216 gastric carcinoma samples. The association between expression of ALDH1A1 and MMP-9, clinicopathological parameters, and prognosis of gastric cancer was examined.
ALDH1A1 protein expression was significantly associated with depth invasion, lymph node metastasis and stage of disease (all P < 0.05). Both univariate and multivariate analyses revealed that ALDH1A1 was an independent prognostic factor for both overall survival (OS) and recurrence-free survival (RFS) (both P < 0.001). Furthermore, ALDH1A1 overexpression was associated with poor prognosis in patients subgroups stratified by tumor size, depth invasion and lymph node metastasis. Moreover, ALDH1A1 was significantly correlated with MMP-9 among 216 gastric cancer tissues (P < 0.001). Patients who had ALDH1A1 overexpression, in which tumor cells displayed high invasiveness, had poor OS and shorter RFS.
ALDH1A1 plays an important role in tumor aggressiveness and prognosis, and may act as a promising target for prognostic prediction.
PMCID: PMC4180139  PMID: 25253129
6.  Heat Shock Protein 60 Overexpression Is Associated with the Progression and Prognosis in Gastric Cancer 
PLoS ONE  2014;9(9):e107507.
Heat shock protein 60 (HSP60) is a chaperonin with essential functions for cell physiology and survival, and its expression correlates with prognosis in a number of malignancies. The aim of this study is to determine the relationship of HSP60 status with clinicopathological parameters and prognosis in gastric cancer.
The levels of HSP60 and matrix metallopeptidase 9 (MMP-9) antigen was evaluated by immunohistochemistry in 223 gastric carcinoma samples. The association between HSP60 and MMP-9, clinicopathological parameters, and prognosis of gastric cancer was examined.
The level of HSP60 protein was significantly associated with depth invasion, lymph node metastasis and stage of disease (all P<0.05). Both univariate and multivariate analyses revealed that HSP60 was an independent prognostic factor for both overall survival (OS) and recurrence-free survival (RFS) (both P<0.05). Furthermore, HSP60 overexpression was associated with a poor prognosis in patients with advanced gastric cancer in different risk groups. Moreover, HSP60 was significantly correlated with MMP-9 among 223 gastric cancer tissues (P<0.001). Patients who had HSP60 overexpression, in which tumor cells displayed high invasiveness, had poor OS and shorter RFS.
HSP60 plays an important role on tumor aggressiveness and prognosis, and may act as a promising target for prognostic prediction.
PMCID: PMC4160299  PMID: 25207654
7.  The Diagnosis Accuracy of PLA2R-AB in the Diagnosis of Idiopathic Membranous Nephropathy: A Meta-Analysis 
PLoS ONE  2014;9(8):e104936.
The presence of antibodies against the M-type phospholipase A2 receptor (PLA2R-AB) is considered to be a promising serological diagnostic biomarker of idiopathic membranous nephropathy (iMN). However, controversy remains about the diagnostic accuracy of serum PLA2R-AB testing. Here, we performed a comprehensive meta-analysis to assess the overall diagnostic value of serum PLA2R-AB testing in iMN detection.
PubMed, Embase, and CNKI (Chinese National Knowledge Infrastructure) were searched for relevant original articles through January 31, 2014. The summary sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio (DOR) were estimated using the bivariate model. The heterogeneity among studies was explored by subgroup and meta-regression analysis.
9 articles, including 15 studies, were eventually identified with a total of 2212 patients. The summary sensitivity of all studies is 78% (95% CI: 66% to 87%) and the specificity is 99% (95% CI: 96% to 100%). The summary positive and negative likelihood ratios are 96.1 (95% CI, 19.5 to 472.1) and 0.22 (95% CI: 0.14 to 0.35), respectively. The DOR is 437 (95%CI, 74 to 2592). The subgroup analysis and meta-regression suggest the test interval is the main source of heterogeneity.
Serum PLA2R-AB testing is a useful tool to detect iMN. In addition, considering the high heterogeneity and potential publication bias, further high quality studies are needed in the future.
PMCID: PMC4138154  PMID: 25136841
8.  HPV seropositivity joints with susceptibility loci identified in GWASs at apoptosis associated genes to increase the risk of Esophageal Squamous Cell Carcinoma (ESCC) 
BMC Cancer  2014;14:501.
We previously showed that human papillomavirus (HPV) serostatus was not an independent risk factor for esophageal squamous cell carcinoma(ESCC) in nonsmokers and nondrinkers; however, HPV increased the risk in smokers.
Here we investigated possible interactions between HPV16 serostatus and three susceptibility loci identified in GWASs at apoptosis associated genes with regard to risk of ESCC in a case–control study of 313 patients with ESCC and 314 healthy controls. The loci (CHK2 rs738722, C12orf51 rs2074356, and PLCE1 rs2274223) were genotyped, and the presence or absence of HPV16 in serum was measured by ELISA. Multivariable logistic regression was used to evaluate possible interactions of HPV16 serostatus and the three loci on the risk of ESCC.
A significant interaction was found between HPV16 serology and rs2074356 (P = 0.005, odds ratio [OR] 1.40, 95% confidence interval [CI] 1.11–1.77) or rs2274223 (P < 0.001, OR 1.53, 95% CI 1.23–1.91), but not for rs738722. For rs2074356, risk of ESCC was increased substantially in smokers (P < 0.001, OR 8.25, 95% CI 3.84–17.71) and drinkers (OR4.04, P = 0.001, 95% CI 1.79–9.10) who carried risk alleles (TT or TC genotype) and were HPV16-seropositive. Similar results were observed for rs2274223 in smokers (P < 0.001, OR6.06, 95% CI 2.85–12.88) and drinkers (P < 0.001, OR 5.43, 95% CI 2.51–11.76), but not for rs738722.
Consistent with the previous study, loci at rs2074356 and rs2274223 could increase the risk of ESCC, furthermore, there were significant interactions between HPV sero-status and the susceptibility loci on the risk of ESCC. This effect could be modified obviously by smoking and drinking.
PMCID: PMC4227071  PMID: 25008389
Esophageal squamous cell carcinoma; Apoptosis; Genome-wide association study; HPV16; Single nucleotide polymorphism; Smoking; Drinking
9.  The High Diagnostic Accuracy of Combined Test of Thyroid Transcription Factor 1 and Napsin A to Distinguish between Lung Adenocarcinoma and Squamous Cell Carcinoma: A Meta-Analysis 
PLoS ONE  2014;9(7):e100837.
Accurate classification of non-small cell lung cancer (NSCLC) using morphological features has several limitations. However, the use of thyroid transcription factor 1 (TTF-1) and Napsin A as markers for the identification of various subtypes of NSCLC has shown promise. This meta-analysis was designed to evaluate the diagnostic value of combined TTF-1 and Napsin A test to distinguish lung adenocarcinoma from squamous cell carcinoma.
The Medline, EMBASE and Web of Science databases were searched, along with the reference lists of relevant articles (up to May 4, 2014). Ten studies containing 1,446 subjects were identified. The sensitivity, specificity, diagnostic odds ratio (DOR) and area under the summary receiver operating characteristics curve (AUC) were calculated to estimate the combined diagnostic value of TTF-1 and Napsin A.
The pooled sensitivity and specificity were 0.76 (95% CI: 0.69–0.83) and 1.00 (95% CI: 0.92–1.00), respectively. The positive and negative likelihood ratios were 877.60 (95% CI: 8.40–91533.40) and 0.24 (95% CI: 0.18–0.32). The DOR was 3719 (95% CI: 33–414884). The AUC was 0.92 (95%CI: 0.89–0.94). The patient's location was a source of heterogeneity for sensitivity. The patient's location, the study's sample size and the threshold used to determine positive staining were consistently found to be sources of heterogeneity for specificity in subgroup analyses and meta-regression.
The combined test of TTF-1 and Napsin A presents a promising alternative method, useful to distinguish between lung adenocarcinoma and squamous cell carcinoma.
PMCID: PMC4086931  PMID: 25003505
10.  Resident intruder paradigm-induced aggression relieves depressive-like behaviors in male rats subjected to chronic mild stress 
Accumulating epidemiological evidence shows that life event stressors are major vulnerability factors for psychiatric diseases such as major depression. It is also well known that the resident intruder paradigm (RIP) results in aggressive behavior in male rats. However, it is not known how resident intruder paradigm-induced aggression affects depressive-like behavior in isolated male rats subjected to chronic mild stress (CMS), which is an animal model of depression.
Male Wistar rats were divided into 3 groups: non-stressed controls, isolated rats subjected to the CMS protocol, and resident intruder paradigm-exposed rats subjected to the CMS protocol.
In the sucrose intake test, ingestion of a 1% sucrose solution by rats in the CMS group was significantly lower than in control and CMS+RIP rats after 3 weeks of stress. In the open-field test, CMS rats had significantly lower open-field scores compared to control rats. Furthermore, the total scores given the CMS group were significantly lower than in the CMS+RIP rats. In the forced swimming test (FST), the immobility times of CMS rats were significantly longer than those of the control or CMS+RIP rats. However, no differences were observed between controls and CMS+RIP rats.
Our data show that aggressive behavior evoked by the resident intruder paradigm could relieve broad-spectrum depressive-like behaviors in isolated adult male rats subjected to CMS.
PMCID: PMC4067422  PMID: 24911067
Resident Intruder Paradigm; Aggression; Depressive-Like Behaviors; Chronic Mild Stress
11.  Application of a New Hybrid Model with Seasonal Auto-Regressive Integrated Moving Average (ARIMA) and Nonlinear Auto-Regressive Neural Network (NARNN) in Forecasting Incidence Cases of HFMD in Shenzhen, China 
PLoS ONE  2014;9(6):e98241.
Outbreaks of hand-foot-mouth disease (HFMD) have been reported for many times in Asia during the last decades. This emerging disease has drawn worldwide attention and vigilance. Nowadays, the prevention and control of HFMD has become an imperative issue in China. Early detection and response will be helpful before it happening, using modern information technology during the epidemic.
In this paper, a hybrid model combining seasonal auto-regressive integrated moving average (ARIMA) model and nonlinear auto-regressive neural network (NARNN) is proposed to predict the expected incidence cases from December 2012 to May 2013, using the retrospective observations obtained from China Information System for Disease Control and Prevention from January 2008 to November 2012.
The best-fitted hybrid model was combined with seasonal ARIMA and NARNN with 15 hidden units and 5 delays. The hybrid model makes the good forecasting performance and estimates the expected incidence cases from December 2012 to May 2013, which are respectively −965.03, −1879.58, 4138.26, 1858.17, 4061.86 and 6163.16 with an obviously increasing trend.
The model proposed in this paper can predict the incidence trend of HFMD effectively, which could be helpful to policy makers. The usefulness of expected cases of HFMD perform not only in detecting outbreaks or providing probability statements, but also in providing decision makers with a probable trend of the variability of future observations that contains both historical and recent information.
PMCID: PMC4043537  PMID: 24893000
12.  Acrolein- and 4-Aminobiphenyl-DNA adducts in human bladder mucosa and tumor tissue and their mutagenicity in human urothelial cells 
Oncotarget  2014;5(11):3526-3540.
Tobacco smoke (TS) is a major cause of human bladder cancer (BC). Two components in TS, 4-aminobiphenyl (4-ABP) and acrolein, which also are environmental contaminants, can cause bladder tumor in rat models. Their role in TS related BC has not been forthcoming. To establish the relationship between acrolein and 4-ABP exposure and BC, we analyzed acrolein-deoxyguanosine (dG) and 4-ABP-DNA adducts in normal human urothelial mucosa (NHUM) and bladder tumor tissues (BTT), and measured their mutagenicity in human urothelial cells. We found that the acrolein-dG levels in NHUM and BTT are 10-30 fold higher than 4-ABP-DNA adduct levels and that the acrolein-dG levels in BTT are 2 fold higher than in NHUM. Both acrolein-dG and 4-ABP-DNA adducts are mutagenic; however, the former are 5 fold more mutagenic than the latter. These two types of DNA adducts induce different mutational signatures and spectra. We found that acrolein inhibits nucleotide excision and base excision repair and induces repair protein degradation in urothelial cells. Since acrolein is abundant in TS, inhaled acrolein is excreted into urine and accumulates in the bladder and because acrolein inhibits DNA repair and acrolein-dG DNA adducts are mutagenic, we propose that acrolein is a major bladder carcinogen in TS.
PMCID: PMC4116500  PMID: 24939871
Bladder cancer; 4-aminobiphenyl; Acrolein; DNA repair; Mutagenesis
13.  Does Chronic Obstructive Pulmonary Disease with or without Type 2 Diabetes Mellitus Influence the Risk of Lung Cancer? Result from a Population-Based Cohort Study 
PLoS ONE  2014;9(5):e98290.
Previous studies have suggested that chronic obstructive pulmonary disease (COPD) is an independent risk factor for lung cancer. There are some evidence that people with diabetes are at a risk of developing many forms of cancer, but inconclusive with regard to lung cancer. The aim of this study was to evaluate whether COPD with or without type 2 diabetes mellitus (T2DM) influences the risk of developing lung cancer.
This is a retrospective cohort study consisting of 20,730 subjects newly diagnosed with COPD (“cases”). Their data was collected from the National Health Insurance system of Taiwan from 1998 to 2010. Among these patients, 5,820 patients had T2DM and 14,910 patients did not have T2DM. The retrospective matched control group consisted of 20,729 subjects without either COPD or T2DM. The control group was matched with the cases for sex, age, and index year (the year that the patient was diagnosed with COPD). The subjects were followed until the end of 2011.
The findings of our study showed that the risk of lung cancer was higher in the COPD group than in the non-COPD group, with adjusted hazard ratio (HR) of 5.02 [95% confidence interval (CI) = 4.23–5.94] among total case group, adjusted HR was 5.38 (95% CI = 4.52–6.40) in the cohort without T2DM and adjusted HR was 4.05 (95% CI = 3.26–5.03) in the cohort with T2DM. We observed a significantly protective effect from lung cancer (adjusted HR = 0.75, 95% CI = 0.63–0.90) of diabetic cohort than non-diabetic cohort among patients with COPD.
Patients with COPD had a significantly higher risk of developing lung cancer than healthy people. However, there was a protective effect of T2DM for lung cancer among patients with COPD. Further investigation may be needed to corroborate the mechanism or bring up reliable reasons.
PMCID: PMC4031125  PMID: 24854189
14.  Association between putative functional variants in the PSMB9 gene and risk of melanoma - re-analysis of published melanoma genome-wide association studies 
Pigment cell & melanoma research  2013;26(3):10.1111/pcmr.12069.
To mine possibly hidden causal single nucleotide polymorphisms (SNPs) in the etiology of melanoma, we investigated the association of SNPs in 76 M/G1 transition genes with melanoma risk using our published genome-wide association study (GWAS) dataset with 1804 melanoma cases and 1,026 cancer-free controls. We found multiple SNPs with P < 0.01 and performed validation studies for 18 putative functional SNPs in PSMB9 in other two GWAS datasets. Two SNPs (rs1351383 and rs2127675) were associated with melanoma risk in the GenoMEL dataset (P = 0.013 and 0.004, respectively), but failed validation in the Australia dataset. Genotype-phenotype analysis revealed these two SNPs were significantly correlated with mRNA expression levels of PSMB9. Further experiments revealed that the promoter SNP rs2071480, which is in high LD with rs1351383 and rs2127675, involved in influencing transcription factor binding and gene expression. Taken together, our data suggested that functional variants in PSMB9 may contribute to melanoma susceptibility.
PMCID: PMC3721546  PMID: 23360169
GWAS; Cell cycle; PSMB9; Polymorphism; melanoma
15.  Emerging mechanisms of T-tubule remodelling in heart failure 
Cardiovascular Research  2013;98(2):204-215.
Cardiac excitation–contraction coupling occurs primarily at the sites of transverse (T)-tubule/sarcoplasmic reticulum junctions. The orderly T-tubule network guarantees the instantaneous excitation and synchronous activation of nearly all Ca2+ release sites throughout the large ventricular myocyte. Because of the critical roles played by T-tubules and the array of channels and transporters localized to the T-tubule membrane network, T-tubule architecture has recently become an area of considerable research interest in the cardiovascular field. This review will focus on the current knowledge regarding normal T-tubule structure and function in the heart, T-tubule remodelling in the transition from compensated hypertrophy to heart failure, and the impact of T-tubule remodelling on myocyte Ca2+ handling function. In the last section, we discuss the molecular mechanisms underlying T-tubule remodelling in heart disease.
PMCID: PMC3697065  PMID: 23393229
T-tubules; Excitation-contraction coupling; Calcium; Heart failure; Junctophilin-2
18.  YTRP: a repository for yeast transcriptional regulatory pathways 
Regulatory targets of transcription factors (TFs) can be identified by the TF perturbation experiments, which reveal the expression changes owing to the perturbation (deletion or overexpression) of TFs. But the identified targets of a given TF consist of both direct and indirect regulatory targets. It has been shown that most of the TFPE-identified regulatory targets are indirect, indicating that TF-gene regulation is mainly through transcriptional regulatory pathways (TRPs) consisting of intermediate TFs. Without identification of these TRPs, it is not easy to understand how a TF regulates its indirect targets. Because there is no such database depositing the potential TRPs for Saccharomyces cerevisiae now, this motivates us to construct the YTRP (Yeast Transcriptional Regulatory Pathway) database. For each TF-gene regulatory pair under different experimental conditions, all possible TRPs in two underlying networks (constructed using experimentally verified TF-gene binding pairs and TF-gene regulatory pairs from the literature) for the specified experimental conditions were automatically enumerated by TRP mining procedures developed from the graph theory. The enumerated TRPs of a TF-gene regulatory pair provide experimentally testable hypotheses for the molecular mechanisms behind a TF and its regulatory target. YTRP is available online at We believe that the TRPs deposited in this database will greatly improve the usefulness of TFPE data for yeast biologists to study the regulatory mechanisms between a TF and its knocked-out targets.
Database URL:
PMCID: PMC3948430  PMID: 24608172
19.  Dietary Exposure to Aluminium and Health Risk Assessment in the Residents of Shenzhen, China 
PLoS ONE  2014;9(3):e89715.
Although there are great changes of dietary in the past few decades in China, few are known about the aluminium exposure in Chinese diet. The aim of this study is to systematically evaluate the dietary aluminium intake level in residents of Shenzhen, China. A total of 853 persons from 244 household were investigated their diet by three days food records. Finally, 149 kinds of foods in 17 food groups were selected to be the most consumed foods. From them, 1399 food samples were collected from market to test aluminium concentration. High aluminium levels were found in jellyfish (median, 527.5 mg/kg), fried twisted cruller (median, 466.0 mg/kg), shell (median, 107.1 mg/kg). The Shenzhen residents' average dietary aluminium exposure was estimated at 1.263 mg/kg bw/week which is lower than the PTWI (provisional tolerable weekly intake). But 0–2 and 3–13 age groups have the highest aluminium intake exceeding the PTWI (3.356 mg/kg bw/week and 3.248 mg/kg bw/week) than other age groups. And the main dietary aluminium exposure sources are fried twisted cruller, leaf vegetables and bean products. Our study suggested that even three decades rapid economy development, children in Shenzhen still have high dietary aluminium exposure risk. How to control high dietary aluminium exposure still is a great public health challenge in Shenzhen, China.
PMCID: PMC3940618  PMID: 24594670
20.  Telomere Length in Peripheral Blood Leukocytes Is Associated with Risk of Colorectal Cancer in Chinese Population 
PLoS ONE  2014;9(2):e88135.
Human telomeres, tandem repeats of TTAGGG nucleotides at the ends of chromosomes, are essential for maintaining genomic integrity and stability. Results of previous epidemiologic studies about the association of telomere length with risk of colorectal cancer (CRC) have been conflicting.
A case-control study was conducted in a Han population in Wuhan, central China. The relative telomere length (RTL) was measured in peripheral blood leukocytes (PBLs) using quantitative real-time polymerase chain reaction (PCR) in 628 CRC cases and 1,256 age and sex frequency matched cancer-free controls. Odds ratios (OR) and 95% confidence intervals (95% CI) were calculated using unconditional logistic regression models to evaluate the association between RTL and CRC risk.
Using median RTL in the controls as the cutoff, individuals with shorter RTL were associated with a significantly increased risk of CRC (adjusted OR = 1.27, 95%CI: 1.05–1.55). When participants were further categorized into 3 and 4 groups according to the tertile and quartile RTL values of controls, significant relationships were still observed between shorter RTL and increased CRC risk (OR per tertile = 1.13, 95%CI: 1.00–1.28, Ptrend = 0.045; OR per quartile = 1.12, 95%CI: 1.03–1.23, Ptrend = 0.012). In stratified analyses, significant association between shorter RTL and increased CRC risk was found in females, individuals younger than 60 years old, never smokers and never drinkers.
This study suggested that short telomere length in PBLs was significantly associated with an increased risk of CRC in Chinese Han population. Further validation in large prospective studies and investigation of the biologic mechanisms are warranted.
PMCID: PMC3912164  PMID: 24498432
21.  Clusterin and Chemoresistance 
Advances in cancer research  2009;105:77-92.
Resistance to anticancer agents is one of the primary impediments to effective cancer therapy. Chemoresistance occurs not only to clinically established therapeutic agents but also to novel targeted therapeutics. Both intrinsic and acquired mechanisms have been implicated in drug resistance but it remains controversial which mechanisms are responsible that lead to failure of therapy in cancer patients. Recent focus has turned to clusterin (CLU) as a key contributor to chemoresistance to anticancer agents. Its role has been documented in prostate cancer for paclitaxel/docetaxel resistance as well as in renal, breast, and lung tumor cells. Moreover, it is abnormally upregulated in numerous advanced stage and metastatic cancers spanning prostate, renal, bladder, breast, head and neck, colon, cervical, pancreatic, lung carcinomas, melanoma, and lymphoma. It is noteworthy that only the cytoplasmic/secretory clusterin form (sCLU), and not the nuclear form, is expressed in aggressive late stage tumors, which is in line with its antiapoptotic function. Most significantly, sCLU expression is documented to lead to broad-based resistance to other unrelated chemotherapeutic agents such as doxorubicin, cisplatin, etoposide, and camphothecin. Resistance to targeted death-inducing molecules, tumor necrosis factor, Fas and TRAIL, or histone deacetylase inhibitors can also be mediated by sCLU. Expression of sCLU may be an adaptive response to genotoxic and oxidative stresses but this adaptive response could pose a threat in malignant cells being treated with cytotoxic agents by enhancing their survival potential. The actual mechanisms for sCLU induction are unclear but STAT1 is required for its constitutive upregulation in docetaxel-resistant tumor cells. Known as a protein chaperone, sCLU appears to stabilize Ku70/Bax complexes, sequestering Bax from its ability to induce mitochondrial release of cytochrome c that triggers cell apoptosis. Thus, sCLU has a key role in preventing apoptosis induced by cytotoxic agents and has the potential to be targeted for cancer therapy.
PMCID: PMC3889866  PMID: 19879424
22.  Protein Interactions and Regulation of EscA in Enterohemorrhagic E. coli 
PLoS ONE  2014;9(1):e85354.
Infections caused by enterohemorrhagic Escherichia coli (EHEC) can lead to diarrhea with abdominal cramps and sometimes are complicated by severe hemolytic uremic syndrome. EHEC secretes effector proteins into host cells through a type III secretion system that is composed of proteins encoded by a chromosomal island, locus for the enterocyte effacement (LEE). EspA is the major component of the filamentous structure connecting the bacteria and the host's cells. Synthesis and secretion of EspA must be carefully controlled since the protein is prone to polymerize. CesAB, CesA2, and EscL have been identified as being able to interact with EspA. Furthermore, the intracellular level of EspA declines when cesAB, cesA2, and escL are individually deleted. Here, we report a LEE gene named l0033, which also affects the intracellular level of EspA. We renamed l0033 as escA since its counterpart in enteropathogenic E. coli has been recently described. Similar to CesAB, EscL, and CesA2, EscA interacts with EspA and enhances the protein stability of EspA. However, EscA is also able to interact with inner membrane-associated EscL, CesA2, and EscN, but not with cytoplasmic CesAB. In terms of gene organizations, escA locates in LEE3. Expression of EscA is faithfully regulated via Mpc, the first gene product of LEE3. Since Mpc is tightly regulated to low level, we suggest that EscA is highly synchronized and critical to the process of escorting EspA to its final destination.
PMCID: PMC3890302  PMID: 24454847
23.  PP2A: The Achilles Heal in MDS with 5q Deletion 
Frontiers in Oncology  2014;4:264.
Myelodysplastic syndromes (MDS) represent a hematologically diverse group of myeloid neoplasms, however, one subtype characterized by an isolated deletion of chromosome 5q [del(5q)] is pathologically and clinically distinct. Patients with del(5q) MDS share biological features that account for the profound hypoplastic anemia and unique sensitivity to treatment with lenalidomide. Ineffective erythropoiesis in del(5q) MDS arises from allelic deletion of the ribosomal processing S-14 (RPS14) gene, which leads to MDM2 sequestration with consequent p53 activation and erythroid cell death. Since its approval in 2005, lenalidomide has changed the natural course of the disease. Patients who achieve transfusion independence and/or a cytogenetic response with lenalidomide have a decreased risk of progression to acute myeloid leukemia and an improved overall survival compared to non-responders. Elucidation of the mechanisms of action of lenalidomide in del(5q) MDS has advanced therapeutic strategies for this disease. The selective cytotoxicity of lenalidomide in del(5q) clones derives from inhibition of a haplodeficient phosphatase whose catalytic domain is encoded within the common deleted region on chromosome 5q, i.e., protein phosphatase 2A (PP2Acα). PP2A is a highly conserved, dual specificity phosphatase that plays an essential role in regulation of the G2/M checkpoint. Inhibition of PP2Acα results in cell-cycle arrest and apoptosis in del(5q) cells. Targeted knockdown of PP2Acα using siRNA is sufficient to sensitize non-del(5q) clones to lenalidomide. Through its inhibitory effect on PP2A, lenalidomide stabilizes MDM2 to restore p53 degradation in erythroid precursors, with subsequent arrest in G2/M. Unfortunately, the majority of patients with del(5q) MDS develop resistance to lenalidomide over time associated with PP2Acα over-expression. Targeted inhibition of PP2A with a more potent inhibitor has emerged as an attractive therapeutic approach for patients with del(5q) MDS.
PMCID: PMC4172014  PMID: 25295231
PP2A; p53; MDM2; RPS14; lenalidomide; deletion 5q; myelodysplastic syndrome
24.  A Novel Chemoimmunomodulating Property of Docetaxel: Suppression of Myeloid-Derived Suppressor Cells in Tumor Bearers 
Myeloid-derived suppressor cells (MDSC) accumulate in tumor-bearing hosts and are associated with immune suppression. To date, there have only been few studies that evaluate the direct effect of chemotherapeutic agents on MDSCs. Agents that inhibit MDSCs may be useful in the treatment of patients with various cancers.
Experimental Design
We investigated the in vivo effects of docetaxel on immune function in 4T1-Neu mammary tumor-bearing mice to examine if a favorable immunomodulatory effect accompanies tumor suppression. Primary focus was on the differentiation status of MDSCs and their ability to modulate T-cell responses.
Docetaxel administration significantly inhibited tumor growth in 4T1-Neu tumor-bearing mice and considerably decreased MDSC proportion in the spleen. The treatment also selectively increased CTL responses. Docetaxel-pretreated MDSCs cocultured with OT-II splenocytes in the presence of OVA323–339 showed OT-II–specific CD4 activation and expansion in vitro. In characterizing the phenotype of MDSCs for M1 (CCR7) and M2 [mannose receptor (CD206)] markers, MDSCs from untreated tumor bearers were primarily MR+ with few CCR7+ cells. Docetaxel treatment polarized MDSCs toward an M1-like phenotype, resulting in 40% of MDSCs expressing CCR7 in vivo and in vitro, and macrophage differentiation markers such as MHC class II, CD11c, and CD86 were upregulated. Interestingly, docetaxel induced cell death selectively in MR+ MDSCs while sparing the M1-like phenotype. Finally, inhibition of signal transducer and activator of transcription 3 may in part be responsible for the observed results.
These findings suggest potential clinical benefit for the addition of docetaxel to current immunotherapeutic protocols.
PMCID: PMC3874864  PMID: 20702612
25.  Induction of Clusterin by AKT—Role in Cytoprotection against Docetaxel in Prostate Tumor Cells 
Molecular cancer therapeutics  2010;9(6):10.1158/1535-7163.MCT-09-0880.
Clusterin (CLU), in its cytoplasmic form, is abundant in many advanced cancers and has been established to be cytoprotective against chemotherapeutic agents including docetaxel. However, little is known of the mechanism of its induction. Here, we provide evidence that AKT plays a critical role in upregulating cytoplasmic/secretory sCLU, which is responsible for docetaxel resistance. Western blot analysis indicated that docetaxel-resistant sublines derived from DU145 and PC3 prostate tumor cell lines displayed a markedly increased phospho-AKT level closely accompanied by heightened sCLU expression when compared with parental cells. To examine if AKT has a role in sCLU expression, AKT blockade was done by treatment with a specific inhibitor, API-2, or dominant-negative AKT transduction before analysis of sCLU gene expression. Loss of AKT function resulted in loss of sCLU and was accompanied by chemosensitization to docetaxel and increased cell death via a caspase-3–dependent pathway. To confirm that AKT affected resistance to docetaxel through sCLU and not through other mediators, tumor cells were first transfected with full-length CLU for overexpression and then treated with the AKT inhibitor API-2. We found that once sCLU was overexpressed, API-2 could not chemosensitize the tumor cells to docetaxel. Thus, the chemoresistance to docetaxel is mediated by sCLU and it can be induced by AKT. Lastly, AKT was found to mediate sCLU induction via signal transducer and activator of transcription 1 activation, which we have earlier shown to drive sCLU gene expression. These results identify a previously unrecognized pathway linking AKT to cytoprotection by sCLU in tumor cells.
PMCID: PMC3874868  PMID: 20501799

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