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1.  ICP4-induced miR-101 attenuates HSV-1 replication 
Scientific Reports  2016;6:23205.
Hepes simplex Virus type 1 (HSV-1) is an enveloped DNA virus that can cause lytic and latent infection. miRNAs post-transcriptionally regulate gene expression, and our previous work has indicated that HSV-1 infection induces miR-101 expression in HeLa cells. The present study demonstrates that HSV-1-induced miR-101 is mainly derived from its precursor hsa-mir-101-2, and the HSV-1 immediate early gene ICP4 (infected-cell polypeptide 4) directly binds to the hsa-mir-101-2 promoter to activate its expression. RNA-binding protein G-rich sequence factor 1 (GRSF1) was identified as a new target of miR-101; GRSF1 binds to HSV-1 p40 mRNA and enhances its expression, facilitating viral proliferation. Together, ICP4 induces miR-101 expression, which downregulates GRSF1 expression and attenuates the replication of HSV-1. This allows host cells to maintain a permissive environment for viral replication by preventing lytic cell death. These findings indicate that HSV-1 early gene expression modulates host miRNAs to regulate molecular defense mechanisms. This study provides novel insight into host-virus interactions in HSV-1 infection and may contribute to the development of antiviral therapeutics.
PMCID: PMC4794718  PMID: 26984403
2.  Variants for HDL-C, LDL-C and Triglycerides Identified from Admixture Mapping and Fine-Mapping Analysis in African-American Families 
Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African-Americans.
Methods and Results
The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglycerides. The analysis was performed in 1,905 unrelated African-American subjects from the National Heart, Lung and Blood Institute’s Family Blood Pressure Program. Regions showing admixture evidence were followed-up with family-based association analysis in 3,556 African-American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age2, sex, body-mass-index, and genome-wide mean ancestry to minimize the confounding due to population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (LDL-C), 8 (HDL-C), 14 (triglycerides) and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52,939 SNPs were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with HDL-C (2 SNPs), LDL-C (4 SNPs) and triglycerides (5 SNPs). The family data was used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions including genes with known associations for cardiovascular disease.
This study identified regions on chromosomes 7, 8, 14 and 19 and 11 SNPs from the fine-mapping analysis that were associated with HDL-C, LDL-C and triglycerides for further studies of cardiovascular disease in African-Americans.
PMCID: PMC4378661  PMID: 25552592
lipids; genetics; association studies; African-Americans; admixture mapping analysis
3.  Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs 
Scientific Reports  2016;6:19429.
We performed genome-wide meta-analysis of lipid traits on three samples of Mexican and Mexican American ancestry comprising 4,383 individuals, and followed up significant and highly suggestive associations in three additional Hispanic samples comprising 7,876 individuals. Genome-wide significant signals were observed in or near CELSR2, ZNF259/APOA5, KANK2/DOCK6 and NCAN/MAU2 for total cholesterol, LPL, ABCA1, ZNF259/APOA5, LIPC and CETP for HDL cholesterol, CELSR2, APOB and NCAN/MAU2 for LDL cholesterol, and GCKR, TRIB1, ZNF259/APOA5 and NCAN/MAU2 for triglycerides. Linkage disequilibrium and conditional analyses indicate that signals observed at ABCA1 and LIPC for HDL cholesterol and NCAN/MAU2 for triglycerides are independent of previously reported lead SNP associations. Analyses of lead SNPs from the European Global Lipids Genetics Consortium (GLGC) dataset in our Hispanic samples show remarkable concordance of direction of effects as well as strong correlation in effect sizes. A meta-analysis of the European GLGC and our Hispanic datasets identified five novel regions reaching genome-wide significance: two for total cholesterol (FN1 and SAMM50), two for HDL cholesterol (LOC100996634 and COPB1) and one for LDL cholesterol (LINC00324/CTC1/PFAS). The top meta-analysis signals were found to be enriched for SNPs associated with gene expression in a tissue-specific fashion, suggesting an enrichment of tissue-specific function in lipid-associated loci.
PMCID: PMC4726092  PMID: 26780889
4.  Gene by Environment Investigation of Incident Lung Cancer Risk in African-Americans 
EBioMedicine  2016;4:153-161.
Genome-wide association studies have identified polymorphisms linked to both smoking exposure and risk of lung cancer. The degree to which lung cancer risk is driven by increased smoking, genetics, or gene–environment interactions is not well understood.
We analyzed associations between 28 single nucleotide polymorphisms (SNPs) previously associated with smoking quantity and lung cancer in 7156 African-American females in the Women's Health Initiative (WHI), then analyzed main effects of top nominally significant SNPs and interactions between SNPs, cigarettes per day (CPD) and pack-years for lung cancer in an independent, multi-center case–control study of African-American females and males (1078 lung cancer cases and 822 controls).
Nine nominally significant SNPs for CPD in WHI were associated with incident lung cancer (corrected p-values from 0.027 to 6.09 × 10− 5). CPD was found to be a nominally significant effect modifier between SNP and lung cancer for six SNPs, including CHRNA5 rs2036527[A](betaSNP*CPD = − 0.017, p = 0.0061, corrected p = 0.054), which was associated with CPD in a previous genome-wide meta-analysis of African-Americans.
These results suggest that chromosome 15q25.1 variants are robustly associated with CPD and lung cancer in African-Americans and that the allelic dose effect of these polymorphisms on lung cancer risk is most pronounced in lighter smokers.
•Genetic by environment (e.g., cigarettes/day, CPD) interactions for lung cancer are understudied in non-European ancestry populations.•We analyzed interactions between nominal smoking quantity SNPs (n = 7156 discovery sample) and CPD and risk of lung cancer (n = 1078 cases, n = 822 controls).•Six SNPs were effect modifiers of CPD for lung cancer, suggesting that the allelic dose effect is most pronounced in light smokers.
Lung cancer is the leading cause of cancer death, disproportionately affecting African-Americans. Prior studies have reported specific genetic markers linked to both smoking quantity and risk of lung cancer in multiple ethnic/racial groups. Investigators analyzed associations between 28 polymorphisms and average cigarettes smoked per day (CPD) in 7156 African-American females and examined interactions between the top polymorphisms and CPD in a cohort of African-American males and females (1078 lung cancer cases and 822 health control patients). The results suggested that six polymorphisms within one genomic region increased lung cancer risk in African-Americans, which was most pronounced in light smokers.
PMCID: PMC4776066  PMID: 26981579
African-Americans; Environment; Genetics; Lung Cancer; rs2036527; Single Nucleotide Polymorphisms; Smoking
5.  Trans-ethnic meta-analysis of white blood cell phenotypes 
Human Molecular Genetics  2014;23(25):6944-6960.
White blood cell (WBC) count is a common clinical measure used as a predictor of certain aspects of human health, including immunity and infection status. WBC count is also a complex trait that varies among individuals and ancestry groups. Differences in linkage disequilibrium structure and heterogeneity in allelic effects are expected to play a role in the associations observed between populations. Prior genome-wide association study (GWAS) meta-analyses have identified genomic loci associated with WBC and its subtypes, but much of the heritability of these phenotypes remains unexplained. Using GWAS summary statistics for over 50 000 individuals from three diverse populations (Japanese, African-American and European ancestry), a Bayesian model methodology was employed to account for heterogeneity between ancestry groups. This approach was used to perform a trans-ethnic meta-analysis of total WBC, neutrophil and monocyte counts. Ten previously known associations were replicated and six new loci were identified, including several regions harboring genes related to inflammation and immune cell function. Ninety-five percent credible interval regions were calculated to narrow the association signals and fine-map the putatively causal variants within loci. Finally, a conditional analysis was performed on the most significant SNPs identified by the trans-ethnic meta-analysis (MA), and nine secondary signals within loci previously associated with WBC or its subtypes were identified. This work illustrates the potential of trans-ethnic analysis and ascribes a critical role to multi-ethnic cohorts and consortia in exploring complex phenotypes with respect to variants that lie outside the European-biased GWAS pool.
PMCID: PMC4245044  PMID: 25096241
6.  Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative 
Human Molecular Genetics  2014;23(24):6634-6643.
We report a genome-wide association study (GWAS) and admixture analysis of glaucoma in 12 008 African-American and Hispanic women (age 50–79 years) from the Women's Health Initiative (WHI). Although GWAS of glaucoma have been conducted on several populations, this is the first to look at glaucoma in individuals of African-American and Hispanic race/ethnicity. Prevalent and incident glaucoma was determined by self-report from study questionnaires administered at baseline (1993–1998) and annually through 2005. For African Americans, there was a total of 658 prevalent cases, 1062 incident cases and 6067 individuals who never progressed to glaucoma. For our replication cohort, we used the WHI Hispanics, including 153 prevalent cases, 336 incident cases and 2685 non-cases. We found an association of African ancestry with glaucoma incidence in African Americans (hazards ratio 1.62, 95% CI 1.023–2.56, P = 0.038) and in Hispanics (hazards ratio 3.21, 95% CI 1.32–7.80, P = 0.011). Although we found that no previously identified glaucoma SNPs replicated in either the WHI African Americans or Hispanics, a risk score combining all previously reported hits was significant in African-American prevalent cases (P = 0.0046), and was in the expected direction in the incident cases, as well as in the Hispanic incident cases. Additionally, after imputing to 1000 Genomes, two less common independent SNPs were suggestive in African Americans, but had too low of an allele frequency in Hispanics to test for replication. These results suggest the possibility of a distinct genetic architecture underlying glaucoma in individuals of African ancestry.
PMCID: PMC4240199  PMID: 25027321
7.  Transcription Factor Runx3 Is Induced by Influenza A Virus and Double-Strand RNA and Mediates Airway Epithelial Cell Apoptosis 
Scientific Reports  2015;5:17916.
Influenza A virus (IAV) targets airway epithelial cells and exploits the host cell machinery to replicate, causing respiratory illness in annual epidemics and pandemics of variable severity. The high rate of antigenic drift (viral mutation) and the putative antigenic shift (reassortant strains) have raised the need to find the host cell inducible factors modulating IAV replication and its pathogenesis to develop more effective antiviral treatment. In this study, we found for the first time that transcription factor Runx3, a developmental regulator and tumor suppressor, was induced by IAV H1N1 and H3N2, viral RNA, a synthetic analog of viral double-stranded RNA (dsRNA) polyinosinic-polycytidylic acid, and type-II interferon-γ (IFNγ) in human airway epithelial cells. Whereas Runx3 was essentially not induced by type-I IFNα and type-III IFNλ, we show that Runx3 induction by IAV infection and viral RNA is mediated through the innate immune receptor MDA5 and the IκB kinase-β−NF-κB pathway. Moreover, we provide substantial evidence indicating that Runx3 plays a crucial role in airway epithelial cell apoptosis induced by IAV infection and dsRNA through the activation of extrinsic and intrinsic apoptosis pathways. Thus, we have identified Runx3 as an inducible and important transcription factor modulating IAV-induced host epithelial cell apoptosis.
PMCID: PMC4672321  PMID: 26643317
8.  Upregulated in Hepatitis B virus-associated hepatocellular carcinoma cells, miR-331-3p promotes proliferation of hepatocellular carcinoma cells by targeting ING5 
Oncotarget  2015;6(35):38093-38106.
Hepatitis B virus (HBV) is a major risk factor for development and progression of hepatocellular carcinoma (HCC). It has been reported that viral infection can interfere with cellular microRNA (miRNA) expression and participate in the pathogenesis of oncogenicity. Our miRNAs array data indicated that miR-331-3p expression in HCC cell lines increased, but the relationship between miR-331-3p expression and HBV activity is unclear. Here, we observed elevated expression of miR-331-3p in different HCC cell lines expressing HBV. HBV, especially HBx, promotes miR-331-3p expression by enhancing its promoter activity. Using a miRNA target prediction database miRBase, we identified ING5 to be a novel target gene of miR-331-3p. miR-331-3p could inhibit ING5 expression by directly targeting its 3′-untranslated region (3′-UTR). As predicted, HBV was confirmed to repress ING5 at both mRNA and protein levels by promoting miR-331-3p expression. Our result indicated that miR-331-3p expression promotes proliferation of SMMC7721 cells by inhibiting ING5. ING5 overexpression promoted cell apoptosis in HCC cell lines. We also found ING5 expression was decreased in tumor tissue of HCC patient with HBV infection compared to its expression in para-carcinoma tissues. Conclusion: These results showed that miR-331-3p is upregulated by HBV and promotes proliferation of HCC cells though repression of ING5 expression. These data provide new insights for understanding the mechanisms of HBV-related HCC pathogenesis.
PMCID: PMC4741986  PMID: 26497554
HCC; HBV; miRNA; miR-331-3p; ING5
9.  miR-346 and miR-138 competitively regulate hTERT in GRSF1- and AGO2-dependent manners, respectively 
Scientific Reports  2015;5:15793.
miRNAs typically downregulate the expression of target genes by binding to their 3′UTR, and dysregulation of miRNAs may contribute to tumorigenesis. Here, we found that miR-346 and miR-138 competitively bind to a common region in the 3′UTR of hTERT mRNA and have opposite effects on the expression and function of hTERT in human cervical cancer cells. Furthermore, G-rich RNA sequence binding factor 1 (GRSF1) mediates the miR-346-dependent upregulation of hTERT by binding to the miR-346 middle sequence motif (CCGCAU) which forms a “bulge loop” when miR-346 is bound to the hTERT 3′UTR, facilitating the recruitment of hTERT mRNA to ribosomes to promote translation in an AGO2-independent manner. Conversely, miR-138 suppresses hTERT expression in an AGO2-dependent manner. Interestingly, replacement of the miR-138 middle sequence with that of miR-346 results in an upregulation of hTERT expression in a GRSF1-dependent manner. Moreover, miR-346 depends on GRSF1 to upregulate another target gene, activin A receptor, type IIB (ACVR2B), in which miR-346 “CCGCAU” motif is essential. These findings reveal novel mechanisms of miRNA-mediated upregulation of target gene expression and describe the coordinated action of multiple miRNAs to control the fate of a single target mRNA through binding to its 3′UTR.
PMCID: PMC4623477  PMID: 26507454
10.  CREB1-driven expression of miR-320a promotes mitophagy by down-regulating VDAC1 expression during serum starvation in cervical cancer cells 
Oncotarget  2015;6(33):34924-34940.
The altered expression of miRNAs in response to stresses contributes to cancer pathogenesis. However, little is known regarding the mechanism by which cellular stresses drive alterations in miRNA expression. Here, we found that serum starvation enhanced mitophagy by downregulating the mitophagy-associated protein voltage-dependent anion channel 1 (VDAC1) and by inducing the expression of miR-320a and the transcription factor cAMP responsive element binding protein 1(CREB1). Furthermore, we cloned the promoter of miR-320a and identified the core promoter of miR-320a in the upstream −16 to −130 region of pre-miR-320a. Moreover, CREB1 was found to bind to the promoter of miR-320a to activate its expression and to induce mitophagy during serum starvation. Collectively, our results reveal a new mechanism underlying serum starvation-induced mitophagy in which serum starvation induces CREB1 expression, in turn activating miR-320a expression, which then down-regulates VDAC1 expression to facilitate mitophagy. These findings may provide new insights into cancer cell survival in response to environmental stresses.
PMCID: PMC4741499  PMID: 26472185
CREB1; miR-320a; mitophagy; serum starvation; VDAC1
11.  Association between COX-2 gene polymorphisms and risk of hepatocellular carcinoma development: a meta-analysis 
BMJ Open  2015;5(10):e008263.
To investigate the association between cyclo-oxygenase-2 (COX-2) polymorphism and the risk of hepatocellular carcinoma (HCC) development.
Systematic review and meta-analysis of COX-2 polymorphism and risk of HCC development among people with or without HCC.
Data sources
EMBASE, PubMed, Public Library of Science, SCOPUS, Web of Knowledge and Chinese National Knowledge Infrastructure were searched for all clinical and experimental case–control studies of COX-2 polymorphism and HCC risk. Studies published up to March 2015 were included.
Review method
Ten studies were included for data extraction, which were mainly from Asian countries.
2538 people with HCC and 3714 without HCC were found to satisfy the inclusion criteria and included in the review. The associations of specific genotypes in the eight polymorphic variants of COX-2 and the risk of HCC development were analysed. GG genotype at the A-1195G polymorphism may be associated with a reduced risk of HCC development: the OR across all studies was 0.87 (95% CI 0.75 to 1.02) for the G allele versus the A allele, 0.72 (0.53 to 0.97) for GG versus AA, 0.72 (0.57 to 0.92) for GG versus GA+AA and 1.05 (0.77 to 1.44) for AA versus GA+GG. Similar results were found when the meta-analysis was repeated separately for the Chinese subgroup. However, more reliable data are needed to demonstrate associations between variants in G-765C, T+8473C, A-1290G, G-899C and introns 1, 5 and 6 polymorphisms and the risk of HCC development.
Only the COX-2 A-1195G gene polymorphism may be associated with a decreased risk of HCC development. These conclusions should be verified in further studies.
PMCID: PMC4606424  PMID: 26438136
cyclooxygenase-2; hepatocellular carcinoma; polymorphism; susceptibility
12.  Phloretin induces apoptosis of non-small cell lung carcinoma A549 cells via JNK1/2 and p38 MAPK pathways 
Oncology Reports  2015;34(6):2871-2879.
Phloretin (Ph) existing in apples, pears and various vegetables is known to have antitumor activities in several cancer cell lines. However, little is known about its effect on human lung cancer cells. The aim of the present study was to see whether Ph could induce apoptosis of non-small cell lung cancer (NSCLC) cells, and explore the possible underlying mechanism of action. We found that Ph markedly induced cell apoptosis of NSCLC cell line A549, and inhibited the migration of A549 cells in a dose-dependent manner. The expression level of BAX, cleaved caspase-3 and -9, and degraded form of PARP was increased and Bcl-2 was decreased after Ph treatment. In addition, the phosphorylation of P38 MAPK, ERK1/2 and JNK1/2 was increased in a dose-dependent manner in parallel with Ph treatment. Inhibition of P38 MAPK and JNK1/2 by specific inhibitors significantly abolished the Ph-induced activation of the caspase-3 and -9. In vivo tumor-suppression assay further indicated that Ph (20 mg/kg) displayed a more significant inhibitory effect on A549 xenografts in tumor growth. All these findings indicate that Ph is able to inhibit NSCLC A549 cell growth by inducing apoptosis through P38 MAPK and JNK1/2 pathways, and therefore may prove to be an adjuvant to the treatment of NSCLC.
PMCID: PMC4722888  PMID: 26503828
phloretin; apoptosis; P38 MAPK; lung cancer; migration
13.  Development and validation of new glomerular filtration rate predicting models for Chinese patients with type 2 diabetes 
Previous researches has depicted that the performance of the recommended glomerular filtration rate (GFR)-estimating equations in the type 2 diabetic population is inferior to that in the non-diabetic population. We attempted to develop new GFR-predicting models for use in Chinese patients with type 2 diabetes in this study.
We enrolled 519 type 2 diabetic patients including a development data-set (n = 276), an internal validation data-set (n = 138) and an external validation data-set (n = 105) to establish new GFR-predicting models. 99mTc-DTPA-GFR revised by the dual sample method was referred to as the gold GFR standard.
Based on sex, age, serum creatinine and new predictor variables [body mass index (BMI), hemoglobinA1C, and urinary albumin creatinine ratio], eight new regression models and eight artificial neural network (ANN) models were developed. In the external validation group, only ANN3 was superior in both precision and accuracy over the original CKD-EPI equation (precision, 20.5 vs. 24.2 mL/min/1.73 m2, P < 0.001; 30 % accuracy, 88.6 vs. 80.6 %, P = 0.02).
ANN3 based on sex, age, serum creatinine and BMI is the optimal model for GFR estimation in Chinese patients with type 2 diabetes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12967-015-0674-y) contains supplementary material, which is available to authorized users.
PMCID: PMC4591744  PMID: 26412455
Glomerular filtration rate; Type 2 diabetes; Artificial neural network; Serum creatinine; Body mass index
14.  Effect of Increasing Doses of γ-Radiation on Bone Marrow Stromal Cells Grown on Smooth and Rough Titanium Surfaces 
Stem Cells International  2015;2015:359416.
Radiation therapy for oral and maxillofacial tumors could damage bone marrow stromal cells (BMSCs) in jaw, which caused dental implant failure. However, how radiation affects BMSCs on SLA (sandblasted with large-grits, acid-etched) surfaces is still unknown. The aim of this study was to investigate effect of different dose of γ-radiation on BMSCs on SLA and PT (polished titanium) surfaces. Rat BMSCs were radiated with 2, 4, and 8 Gy γ-radiation and then seeded on both surfaces. Cell adhesion, spreading, and proliferation were tested. The osteogenesis and the adipogenesis ability were examined by Alizarin-Red and Oil-Red staining, respectively. Real-time PCR was performed to detect osteogenic (osteocalcin, OCN; runt-related transcription factor 2, Runx2) and adipogenic (peroxisome proliferator-activated receptor gamma, PPARγ) gene expression at days 7 and 14 postirradiation. Results showed that γ-radiation reduced cell proliferation, adhesion, spreading, and osteogenic differentiation. 2 Gy radiation promoted adipogenic differentiation, but it was significantly decreased when dosage reached 4 Gy. In conclusion, results suggest that γ-radiation influenced BMSCs behaviors in a dosage-dependent manner except adipogenic differentiation, low dose promoted it, and high dose inhibited it. This effect was influenced by surface characteristics, which may explain the different failure rate of various implants in patients after radiation.
PMCID: PMC4518184  PMID: 26257788
15.  Leveraging population admixture to explain missing heritability of complex traits 
Nature genetics  2014;46(12):1356-1362.
Despite recent progress on estimating the heritability explained by genotyped SNPs (hg2), a large gap between hg2 and estimates of total narrow-sense heritability (h2) remains. Explanations for this gap include rare variants, or upward bias in family-based estimates of h2 due to shared environment or epistasis. We estimate h2 from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (hγ2). We show that hγ2 = 2FSTCθ(1−θ)h2, where FSTC measures frequency differences between populations at causal loci and θ is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We examined 21,497 African Americans from three cohorts, analyzing 13 phenotypes. For height and BMI, we obtained h2 estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of hg2 in these and other data, but smaller than family-based estimates of h2.
PMCID: PMC4244251  PMID: 25383972
16.  High Prevalence of Isolated Nocturnal Hypertension in Chinese Patients With Chronic Kidney Disease 
Isolated nocturnal hypertension (INH) has been studied among the general population and hypertensive patients. However, little insight is available on the prevalence of INH and its role in target-organ damage among patients with chronic kidney disease (CKD).
Methods and Results
We recruited 1282 CKD patients admitted to our hospital division. Patients were divided into 4 groups: INH; isolated daytime hypertension; day–night sustained; and ambulatory normotension. Multiple linear regression analyses were used to evaluate the correlation between INH and renal/cardiovascular parameters. A total of 262 (20.44%) CKD patients had isolated nocturnal hypertension and 651 (50.78%) had day–night sustained hypertension, whereas only 350 (27.30%) patients showed normotension and 19 (1.48%) had isolated daytime hypertension. Multivariate logistic regression analysis showed that INH was associated mainly with age, estimated glomerular filtration rate, clinic diastolic blood pressure, and that INH was determined only by age, estimated glomerular filtration rate, and clinic diastolic blood pressure. The prevalence of impaired renal function, left ventricular hypertrophy, and carotid intima-media thickness in patients with INH were higher than in normotensive patients (P<0.05), whereas impaired renal function and left ventricular hypertrophy in these patients were lower than patients in the day–night sustained hypertension group (P<0.05). INH was correlated with estimated glomerular filtration rate, left ventricular mass index, and carotid intima-media thickness according to multiple linear regression analyses.
The prevalence of INH in CKD patients was high, and INH was correlated with target-organ damage in CKD patients.
PMCID: PMC4599541  PMID: 26089178
ambulatory blood pressure monitoring; chronic kidney disease; isolated nocturnal hypertension
17.  Inhibitory effects of emodin, baicalin, schizandrin and berberine on hefA gene: Treatment of Helicobacter pylori-induced multidrug resistance 
AIM: To investigate the inhibitory effects of emodin, baicalin, etc. on the hefA gene of multidrug resistance (MDR) in Helicobacter pylori (H. pylori).
METHODS: The double dilution method was used to screen MDR H. pylori strains and determine the minimum inhibitory concentrations (MICs) of emodin, baicalin, schizandrin, berberine, clarithromycin, metronidazole, tetracycline, amoxicillin and levofloxacin against H. pylori strains. After the screened MDR stains were treated with emodin, baicalin, schizandrin or berberine at a 1/2 MIC concentration for 48 h, changes in MICs of amoxicillin, tetracycline, levofloxacin, metronidazole and clarithromycin were determined. MDR strains with reduced MICs of amoxicillin were selected to detect the hefA mRNA expression by real-time quantitative PCR.
RESULTS: A total of four MDR H. pylori strains were screened. Treatment with emodin, baicalin, schizandrin and berberine significantly decreased the MICs of amoxicillin and tetracycline against some strains, decreased by 1 to 2 times, but did not significantly change the MICs of clarithromycin, levofloxacin, and metronidazole against MDR strains. In the majority of strains with reduced MICs of amoxicillin, hefA mRNA expression was decreased; one-way ANOVA (SPSS 12.0) used for comparative analysis, P < 0.05.
CONCLUSION: Emodin, baicalin, schizandrin and berberine significantly decreased the MICs of amoxicillin and tetracycline against some H. pylori strains, possibly by mechanisms associated with decreasing hefA mRNA expression.
PMCID: PMC4394083  PMID: 25892872
Traditional Chinese medicine; Multidrug resistance; Helicobacter pylori; Efflux pump; hefA
18.  Association analyses confirm five susceptibility loci for systemic lupus erythematosus in the Han Chinese population 
Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease. Currently, numerous genetic loci of SLE have been confirmed. Here we try to further explore additional genes contributing to SLE susceptibility in this study.
Forty nine single nucleotide polymorphisms (SNPs) with moderate-risk for SLE in previous study were genotyped in a large-scale replication study with a total of 3,522 cases and 8,252 controls using the Sequenom Massarray system. Association analyses were performed using logistic regression with gender or sample cohorts as a covariate through PLINK 1.07 software.
This replication effort confirmed five reported SLE susceptibility loci reaching genome-wide levels of significance (Pmeta <5.00 × 10−08): TNFSF4 (rs1418190, odds ratio (OR) = 0.81, Pmeta = 1.08 × 10−08; rs4916219, OR = 0.80, Pmeta = 7.77 × 10−09), IRF8 (rs2934498, OR = 1.25, Pmeta = 4.97 × 10−09), miR-146a (rs2431697, OR = 0.69, Pmeta = 1.15 × 10−22), CD44 (rs2732547, OR = 0.82, Pmeta = 1.55 × 10−11), and TMEM39A (rs12494314, OR = 0.84, Pmeta = 1.01 × 10−09). Further logistic regression analysis indicated that the genetic effects within TNFSF4 detected in this study are independent from our previously reported signals.
This study increases the number of established susceptibility loci for SLE in Han Chinese population and highlights the contribution of multiple variants of modest effect. Although further studies will be required to identify the causal alleles within these loci, the findings make a significant step forward in our understanding of the genetic contribution to SLE in Chinese population.
Electronic supplementary material
The online version of this article (doi:10.1186/s13075-015-0602-9) contains supplementary material, which is available to authorized users.
PMCID: PMC4404072  PMID: 25890262
19.  miR-1236 down-regulates alpha-fetoprotein, thus causing PTEN accumulation, which inhibits the PI3K/Akt pathway and malignant phenotype in hepatoma cells 
Oncotarget  2015;6(8):6014-6028.
Alpha fetoprotein (AFP) is a clinical biomarker of hepatocellular carcinoma (HCC). Here, we found that miR-1236 is down-regulated, whereas AFP is highly expressed in HCC tissues and cells. We demonstrated that miR-1236 directly targets the 3′UTR of AFP and down-regulates its expression. Also, miR-1236 inhibited and AFP stimulated proliferation, migration, invasion and vasculogenic mimicry (VM) of HCC. In agreement, AFP over-expression counteracted the inhibitory effect of miR-1236. We demonstrated that AFP promoted the ubiquitination of PTEN, thus decreasing PTEN levels, while miR-1236 inhibited the PI3K/Akt pathway.
PMCID: PMC4467418  PMID: 25714026
microRNA; microRNA-1236; AFP; PTEN; hepatocellular cancer
20.  SD-208, a Novel Protein Kinase D Inhibitor, Blocks Prostate Cancer Cell Proliferation and Tumor Growth In Vivo by Inducing G2/M Cell Cycle Arrest 
PLoS ONE  2015;10(3):e0119346.
Protein kinase D (PKD) has been implicated in many aspects of tumorigenesis and progression, and is an emerging molecular target for the development of anticancer therapy. Despite recent advancement in the development of potent and selective PKD small molecule inhibitors, the availability of in vivo active PKD inhibitors remains sparse. In this study, we describe the discovery of a novel PKD small molecule inhibitor, SD-208, from a targeted kinase inhibitor library screen, and the synthesis of a series of analogs to probe the structure-activity relationship (SAR) vs. PKD1. SD-208 displayed a narrow SAR profile, was an ATP-competitive pan-PKD inhibitor with low nanomolar potency and was cell active. Targeted inhibition of PKD by SD-208 resulted in potent inhibition of cell proliferation, an effect that could be reversed by overexpressed PKD1 or PKD3. SD-208 also blocked prostate cancer cell survival and invasion, and arrested cells in the G2/M phase of the cell cycle. Mechanistically, SD-208-induced G2/M arrest was accompanied by an increase in levels of p21 in DU145 and PC3 cells as well as elevated phosphorylation of Cdc2 and Cdc25C in DU145 cells. Most importantly, SD-208 given orally for 24 days significantly abrogated the growth of PC3 subcutaneous tumor xenografts in nude mice, which was accompanied by reduced proliferation and increased apoptosis and decreased expression of PKD biomarkers including survivin and Bcl-xL. Our study has identified SD-208 as a novel efficacious PKD small molecule inhibitor, demonstrating the therapeutic potential of targeted inhibition of PKD for prostate cancer treatment.
PMCID: PMC4352033  PMID: 25747583
21.  Primary signet-ring cell carcinoma of the lung treated with crizotinib: A case report 
Oncology Letters  2015;9(5):2205-2207.
Primary signet-ring cell adenocarcinoma (SRCA) of the lung is an extremely rare subtype of lung adenocarcinoma with a poor prognosis. The presence of an SRC component is considered to be a prominent clinicopathological characteristic of EML4-ALK-positive non-small cell lung cancer (NSCLC). Crizotinib, an anaplastic lymphoma kinase inhibitor, has been approved for the treatment of EML4-ALK NSCLC by previous studies, but its effect on SRCA, an extremely rare subtype of lung adenocarcinoma, has yet to be elucidated. Therefore, the present study aimed to evaluate the clinical response of SRCA to crizotinib, and examine the potential use of crizotinib as a treatment for the carcinoma. A 43-year-old male was admitted to the Qingdao Municipal Hospital (Qingdao, China) with dyspnea. Chest computed tomography (CT) revealed a mass in the middle lobe of the right lung. Transbronchial lung biopsies revealed the presence of SRCA (70%) mixed with poorly-differentiated adenocarcinoma (30%). Immunohistochemically, the SRCA cells were positive for cytokeratin (CK)7 and thyroid transcription factor-1, and negative for CK20. An inversion of the EML4-ALK gene was detected by fluorescence in situ hybridization and crizotinib was injected by nasogastric tube. The patient was highly responsive to crizotinib. The symptoms of dyspnea were relieved and the volumes of pericardial and pleural effusion were gradually reduced. A CT scan revealed lung tumor regression. The overall response was a partial response. Therefore, crizotinib exists an attractive therapeutic option for patients with SRCA. However, in the present study, acquired drug resistance to crizotinib developed after only one month of treatment. It would consequently be valuable to investigate the mechanisms underlying acquired crizotinib resistance in future studies.
PMCID: PMC4467348  PMID: 26137041
crizotinib; primary signet-ring cell adenocarcinoma; EML4-ALK
22.  Management of primary gastric small cell carcinoma in China 
Background: Primary gastric small cell carcinomas (GSCCs) are increasingly identified by endoscopy, and account for 15-20% of all gastric neuroendocrine tumors (NETs). GSCCs have the worst prognosis with the highest rate of metastases. Purpose: To provide useful information for clinicians and researchers to better manage patients with GSCC, we studied the clinical features of GSCC and explored the corresponding therapies and prognosis. Methods: A literature search was conducted through PUBMED, EMBASE, CNKI and WanFang Databases using search terms “stomach” or “gastric” and “small cell carcinoma” or “poorly differentiated neuroendocrine carcinoma”, for the period 1999 to 2012. And the cases reported were all from China. Relevant articles were identified through manual review. The reference lists of these articles were reviewed to include further appropriate articles. Results: Two hundred and five eligible cases were analyzed. The median age of patients was 62 years, with a male-to-female ratio of 5.4:1. Of the tumors, 53.17% were located in the upper stomach, 25.37% in the mid, 18.54% in the distal stomach, the remaining 2.93% were found in the total stomach. The mean size was 68mm in maximum diameter, with a range of 15-150 mm. Of the one hundred and thirty-five patients, fifty appeared to be pure GSCCs, eighty-five were mixed. The median overall survival time of 195 patients was 18.50 months. The 1-, 2-, and 5-year average survival rates of 142 patients were 66.75%, 37.13%, and 20.15%, respectively. Conclusions: GSCC is a rare tumor and it is notoriously aggressive with a strong propensity for both regional and distant spread. Therapies including surgical resection, chemotherapy, and local radiotherapy, by itself or in combination with other treatment, have been used to treat GSCCs in China. To identify the most effective treatment modalities for GSCCs, we still need prospective, multicenter, randomized clinical researches.
PMCID: PMC4402734  PMID: 25932087
Small cell carcinoma; poorly differentiated neuroendocrine carcinoma; stomach; gastric
23.  A variational Bayes discrete mixture test for rare variant association 
Genetic epidemiology  2014;38(1):21-30.
Recently, many statistical methods have been proposed to test for associations between rare genetic variants and complex traits. Most of these methods test for association by aggregating genetic variations within a predefined region, such as a gene. Although there is evidence that “aggregate” tests are more powerful than the single marker test, these tests generally ignore neutral variants and therefore are unable to identify specific variants driving the association with phenotype. We propose a novel aggregate rare-variant test that explicitly models a fraction of variants as neutral, tests associations at the gene-level, and infers the rare-variants driving the association. Simulations show that in the practical scenario where there are many variants within a given region of the genome with only a fraction causal our approach has greater power compared to other popular tests such as the Sequence Kernel Association Test (SKAT), the Weighted Sum Statistic (WSS), and the collapsing method of Morris and Zeggini (MZ). Our algorithm leverages a fast variational Bayes approximate inference methodology to scale to exome-wide analyses, a significant computational advantage over exact inference model selection methodologies. To demonstrate the efficacy of our methodology we test for associations between von Willebrand Factor (VWF) levels and VWF missense rare-variants imputed from the National Heart, Lung, and Blood Institute’s Exome Sequencing project into 2,487 African Americans within the VWF gene. Our method suggests that a relatively small fraction (~10%) of the imputed rare missense variants within VWF are strongly associated with lower VWF levels in African Americans.
PMCID: PMC4030763  PMID: 24482836
Exome sequencing study; approximate inference; von Willebrand Factor genetics
24.  MiR-23a Facilitates the Replication of HSV-1 through the Suppression of Interferon Regulatory Factor 1 
PLoS ONE  2014;9(12):e114021.
MicroRNAs (miRNAs) are small, non-coding RNAs that negatively regulate gene expression. It has been reported that miRNAs are involved in host-virus interaction, but evidence that cellular miRNAs promote virus replication has been limited. Here, we found that miR-23a promoted the replication of human herpes simplex virus type 1 (HSV-1) in HeLa cells, as demonstrated by a plaque-formation assay and quantitative real-time PCR. Furthermore, interferon regulatory factor 1 (IRF1), an innate antiviral molecule, is targeted by miR-23a to facilitate viral replication. MiR-23a binds to the 3′UTR of IRF1 and down-regulates its expression. Suppression of IRF1 expression reduced RSAD2 gene expression, augmenting HSV-1 replication. Ectopic expression of IRF1 abrogated the promotion of HSV-1 replication induced by miR-23a. Notably, IRF1 contributes to innate antiviral immunity by binding to IRF-response elements to regulate the expression of interferon-stimulated genes (ISGs) and apoptosis, revealing a complex interaction between miR-23a and HSV-1. MiR-23a thus contributes to HSV-1 replication through the regulation of the IRF1-mediated antiviral signal pathway, which suggests that miR-23a may represent a promising target for antiviral treatments.
PMCID: PMC4252059  PMID: 25461762
25.  Briarane Diterpenoids from the Gorgonian Dichotella gemmacea 
Marine Drugs  2014;12(12):6178-6189.
Seven new briarane diterpenoids, gemmacolides AS-AY (1–7), were isolated together with ten known analogues (8–17) from the South China Sea gorgonian Dichotella gemmacea. The structures of the new compounds were elucidated by the detailed analysis of spectroscopic data and comparison with reported data. The absolute configuration of compounds was determined based on electronic circular dichroism (ECD) experiments and genetic correlations as well. Compounds 15 and 16 were reported for the first time for the gorgonian. In the preliminary in vitro bioassays, compound 5 showed potential growth inhibitory activity against MG63 cells.
PMCID: PMC4278224  PMID: 25528959
structure elucidation; briarane diterpenoids; tumor cell growth inhibitory activity; gorgonian; Dichotella gemmacea

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