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Articles by C Zeng
Total Records ( 4 ) for C Zeng
  C Zang , D. E Schones , C Zeng , K Cui , K Zhao and W. Peng
 

Motivation: Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse species. Chromatin modification profiles are frequently noisy and diffuse, spanning regions ranging from several nucleosomes to large domains of multiple genes. Much of the early work on the identification of ChIP-enriched regions for ChIP-Seq data has focused on identifying localized regions, such as transcription factor binding sites. Bioinformatic tools to identify diffuse domains of ChIP-enriched regions have been lacking.

Results: Based on the biological observation that histone modifications tend to cluster to form domains, we present a method that identifies spatial clusters of signals unlikely to appear by chance. This method pools together enrichment information from neighboring nucleosomes to increase sensitivity and specificity. By using genomic-scale analysis, as well as the examination of loci with validated epigenetic states, we demonstrate that this method outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles. We demonstrate the application of this unbiased method in important issues in ChIP-Seq data analysis, such as data normalization for quantitative comparison of levels of epigenetic modifications across cell types and growth conditions.

  M Varella Garcia , A. P Schulte , H. J Wolf , W. J Feser , C Zeng , S Braudrick , X Yin , F. R Hirsch , T. C Kennedy , R. L Keith , A. E Baron , S. A Belinsky , Y. E Miller , T Byers and W. A. Franklin
 

Lung cancer usually is disseminated (advanced) and has a poor prognosis at diagnosis. Current and former smokers are at a high risk for lung cancer and are candidates for prevention and early detection strategies. Sputum is a potential source of biomarkers that might determine either lung cancer risk or the presence of early lung cancer, but no current sputum test is sufficiently sensitive and specific for effective screening. We used fluorescence in situ hybridization (FISH) to measure chromosomal aneusomy (CA) in sputum samples collected prospectively from 100 incident lung cancer cases and 96 controls (matched on age, gender, and date of collection) nested within an ongoing high-risk cohort. The CA-FISH assay was aimed at four DNA targets: epidermal growth factor receptor, MYC, 5p15, and CEP 6. The sensitivity of a positive CA-FISH assay (abnormal for two or more of the four markers) for lung cancer was substantially higher for samples collected within 18 months (76% sensitivity) than for samples collected more than 18 months (31%) before lung cancer diagnosis. Sensitivity was higher for squamous cell cancers (94%) than for other histologic types (69%). CA-FISH specificity based on samples collected within 18 months before diagnosis was 88%. The adjusted odds ratio (OR) of lung cancer for specimens collected within 18 months before a cancer diagnosis was higher for the CA-FISH assay [OR, 29.9; 95% confidence interval (95% CI), 9.5-94.1] than for previously studied ORs of cytologic atypia (OR, 1.8; 95% CI, 1.3-2.6) and gene promoter methylation (OR, 6.5; 95% CI, 1.2-35.5). Whether CA-FISH is an indicator of extreme risk for incident lung cancer or detects exfoliated cancer cells is unknown. The apparent promise of CA-FISH in sputum for assessing lung cancer risk and/or for lung cancer early detection now needs to be validated in a clinical screening trial. Cancer Prev Res; 3(4); 447–53. ©2010 AACR.

  J. F Steiner , P. M Ho , B. L Beaty , L. M Dickinson , R Hanratty , C Zeng , H. M Tavel , E. P Havranek , A. J Davidson , D. J Magid and R. O. Estacio
 

Background— Although many studies have identified patient characteristics or chronic diseases associated with medication adherence, the clinical utility of such predictors has rarely been assessed. We attempted to develop clinical prediction rules for adherence with antihypertensive medications in 2 healthcare delivery systems.

Methods and Results— We performed retrospective cohort studies of hypertension registries in an inner-city healthcare delivery system (n=17 176) and a health maintenance organization (n=94 297) in Denver, Colo. Adherence was defined by acquisition of 80% or more of antihypertensive medications. A multivariable model in the inner-city system found that adherent patients (36.3% of the total) were more likely than nonadherent patients to be older, white, married, and acculturated in US society, to have diabetes or cerebrovascular disease, not to abuse alcohol or controlled substances, and to be prescribed fewer than 3 antihypertensive medications. Although statistically significant, all multivariate odds ratios were 1.7 or less, and the model did not accurately discriminate adherent from nonadherent patients (C statistic=0.606). In the health maintenance organization, where 72.1% of patients were adherent, significant but weak associations existed between adherence and older age, white race, the lack of alcohol abuse, and fewer antihypertensive medications. The multivariate model again failed to accurately discriminate adherent from nonadherent individuals (C statistic=0.576).

Conclusions— Although certain sociodemographic characteristics or clinical diagnoses are statistically associated with adherence to refills of antihypertensive medications, a combination of these characteristics is not sufficiently accurate to allow clinicians to predict whether their patients will be adherent with treatment.

  J Li , H Huang , L Sun , M Yang , C Pan , W Chen , D Wu , Z Lin , C Zeng , Y Yao , P Zhang and E. Song
 

Purpose: We aim to examine miR-21 expression in tongue squamous cell carcinomas (TSCC) and correlate it with patient clinical status, and to investigate its contribution to TSCC cell growth, apoptosis, and tumorigenesis.

Experimental Design: MicroRNA profiling was done in 10 cases of TSCC with microarray. MiR-21 overexpression was quantitated with quantitative reverse transcription-PCR in 103 patients, and correlated to the pathoclinical status of the patients. Immunohistochemistry was used to examine the expression of TPM1 and PTEN, and terminal deoxynucleotidyl transferase–mediated dUTP labeling to evaluate apoptosis. Moreover, miR-21 antisense oligonucleotide (ASO) was transfected in SCC-15 and CAL27 cell lines, and tumor cell growth was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, adherent colony formation, and soft agar assay, whereas apoptosis was determined by Annexin V assay, cytochrome c release, and caspase 3 assay. Tumorigenesis was evaluated by xenografting SCC-15 cells in nude mice.

Results: MiR-21 is overexpressed in TSCC relative to adjacent normal tissues. The level of miR-21 is reversely correlated with TPM1 and PTEN expression and apoptosis of cancer cells. Multivariate analysis showed that miR-21 expression is an independent prognostic factor indicating poor survival. Inhibiting miR-21 with ASO in TSCC cell lines reduces survival and anchorage-independent growth, and induces apoptosis in TSCC cell lines. Simultaneous silencing of TPM1 with siRNA only partially recapitulates the effect of miR-21 ASO. Furthermore, repeated injection of miR-21 ASO suppresses tumor formation in nude mice by reducing cell proliferation and inducing apoptosis.

Conclusions: miR-21 is an independent prognostic indicator for TSCC, and may play a role in TSCC development by inhibiting cancer cell apoptosis partly via TPM1 silencing.

 
 
 
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