Ding Y.,University of Texas Health Science Center at Houston |
He D.,Wayne State University |
Florentin D.,Wayne State University |
Frolov A.,Dan ncan Cancer Center |
And 4 more authors.
Clinical Cancer Research | Year: 2013
Background: Semaphorin 4F (S4F) has roles in embryologic axon guidance and is expressed in adults. S4F is involved in cancer-induced neurogenesis. Methods: Prostate cells were transfected with S4F retrovirus. Cells and controls were used for a bromodeoxyuridine (BrdUrd) incorporation assay (proliferation) and in vitro scratch and Matrigel Transwell chamber invasion assay (migration). Monoclonal antibodies were developed using baculovirusexpressed recombinant GST-S4F and used to immunostain tissue microarrays. Slides were imaged using deconvolution and analyzed using tissue segmentation. Data were correlated with clinicopathologic parameters, other biomarkers and survival analysis conducted. Heterogeneity of S4F expression was analyzed with unsupervised clustering algorithms. Results: Proliferation rates measured by BrdUrd incorporation were higher in all S4F-transfected cells. S4F overexpression was associated with increased motility of the cancer cells. S4F expression was overexpressed in high-grade prostatic intraepithelial neoplasia/prostate cancer than normal epithelium. S4F expression correlated with seminal vesicle invasion. Patients with high values of S4F in prostate cancer cytoplasm are at significantly higher risk of biochemical recurrence, by univariate and multivariate analyses. S4F cytoplasmic expression in prostate cancer cells also correlates with nerve density in prostate cancer and perineural invasion diameter. Correlations were identified with NF-kB and inversely with apoptosis in perineural invasion. Conclusion: These data show that S4F is significantly involved in human prostate cancer progression. S4F is a key regulator of the interactions between nerves in the tumor microenvironment and cancer cells. Because of the importance of cancer nerve interaction in the biology of cancer and its clinical implication, S4F can be considered a major therapeutic target. © 2013 American Association for Cancer Research.
Chen K.,Dan ncan Cancer Center |
Xi Y.,Dan ncan Cancer Center |
Pan X.,Dan ncan Cancer Center |
Pan X.,Baylor College of Medicine |
And 5 more authors.
Genome Research | Year: 2013
Recent developments in next-generation sequencing have enabled whole-genome profiling of nucleosome organizations. Although several algorithms for inferring nucleosome position from a single experimental condition have been available, it remains a challenge to accurately define dynamic nucleosomes associated with environmental changes. Here, we report a comprehensive bioinformatics pipeline, DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. Using both simulated and real nucleosome data, we demonstrated that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic nucleosomes. The single-nucleotide resolution analysis of DANPOS allows us to detect all three categories of nucleosome dynamics, such as position shift, fuzziness change, and occupancy change, using a uniform statistical framework. Pathway analysis indicates that each category is involved in distinct biological functions. We also analyzed the influence of sequencing depth and suggest that even 200-fold coverage is probably not enough to identify all the dynamic nucleosomes. Finally, based on nucleosome data from the human hematopoietic stem cells (HSCs) and mouse embryonic stem cells (ESCs), we demonstrated that DANPOS is also robust in defining functional dynamic nucleosomes, not only in promoters, but also in distal regulatory regions in the mammalian genome. © 2013, Published by Cold Spring Harbor Laboratory Press.
Lin F.Y.,Baylor College of Medicine |
Lin F.Y.,Texas Childrens Cancer Center |
Lin F.Y.,Dan ncan Cancer Center |
Chintagumpala M.,Baylor College of Medicine |
And 2 more authors.
Current Oncology Reports | Year: 2015
Ependymomas are a heterogeneous group of neuroepithelial tumors of children and adults. In pediatric cases, the standard of care has long consisted of neurosurgical resection to the greatest extent acceptable followed by adjuvant involved field irradiation. Complete macroscopic surgical resection has remained the only consistent clinical variable known to improve survival. Adjuvant chemotherapy has yet to predictably affect outcome, possibly due to the molecular heterogeneity of histologically similar tumors. The administration of chemotherapy subsequently remains limited to clinical trials. However, recent comprehensive genomic, transcriptomic, and epigenetic interrogations of ependymomas have uncovered unique molecular characteristics and subtypes that correlated with clinical features such as age, neuroanatomical location, and prognosis. These findings represent a potential paradigm shift and provide a biologic rationale for targeted therapeutic strategies and risk-adapted administration of conventional treatment modalities. In this review, we focus on intracranial WHO grade II and III ependymoma of children and discuss conventional management strategies, followed by recent biologic findings and novel therapeutics currently under investigation. © 2015, Springer Science+Business Media New York.
Burstein M.D.,Structural and Computation Biology and Molecular Biophysics Graduate Program |
Robinson J.O.,Center for Medical Ethics and Health Policy |
Hilsenbeck S.G.,Dan ncan Cancer Center |
McGuire A.L.,Center for Medical Ethics and Health Policy |
And 2 more authors.
Pediatrics | Year: 2014
OBJECTIVE: In the United States, data from federally funded genomics studies are stored in national databases, which may be accessible to anyone online (public release) or only to qualified researchers (restricted release). The availability of such data exposes participants to privacy risk and limits the ability to withdraw from research. This exposure is especially challenging for pediatric participants, who are enrolled in studies with parental permission. The current study examines genomic research participants' attitudes to explore differences in data sharing (DS) preferences between parents of pediatric patients and adult patients. METHODS: A total of 113 parents of pediatric patients and 196 adult participants from 6 genomics studies were randomly assigned to 3 experimental consent forms. Participants were invited to a follow-up structured interview exploring DS preferences, study understanding, and attitudes. Descriptive analyses and regression models were built on responses. RESULTS: Most parents (73.5%) and adult participants (90.3%) ultimately consented to broad public release. However, parents were significantly more restrictive in their data release decisions, not because of understanding or perceived benefits of participation but rather autonomy and control. Parents want to be more involved in the decision about DS and are significantly more concerned than adult participants about unknown future risks. CONCLUSIONS: Parents have the same altruistic motivations and grasp of genomics studies as adult participants. However, they are more concerned about future risks to their child, which probably motivates them to choose more restrictive DS options, but only when such options are made available. © 2014 by the American Academy of Pediatrics.
Zhang B.,Baylor College of Medicine |
Chen H.,Baylor College of Medicine |
Zhang L.,Baylor College of Medicine |
Dakhova O.,Baylor College of Medicine |
And 8 more authors.
Oncogene | Year: 2014
Dicer is an RNase III enzyme essential for the maturation of the majority of microRNAs. Recent studies have revealed downregulation or hemizygous loss of Dicer in many tumor models and demonstrated that suppressing Dicer activity enhances tumorigenic activities of lung and breast cancer cells, which support Dicer as a haploinsufficient tumor suppressor in these cancer models. Surprisingly, we found that knocking down Dicer expression suppresses the growth and tumorigenic capacity of human prostate cancer cell lines, but enhances migratory capacities of some prostate cancer cell lines. Dicer is upregulated in human prostate cancer specimens, but lower Dicer expression portends a shorter time to recurrence. Complete ablation of Dicer activity in a Pten null mouse model for prostate cancer significantly halts tumor growth and progression, demonstrating that microRNAs have a critical role in maintaining cancer cell fitness. In comparison, hemizygous loss of Dicer in the same model also reduces primary tumor burden, but induces a more locally invasive phenotype and causes seminal vesicle obstruction at high penetrance. Disrupting Dicer activity leads to an increase in apoptosis and senescence in these models, presumably through upregulation of P16/INK4a and P27/Kip1. Collectively, these results highlight a pleotropic role of Dicer in tumorigenesis that is not only dosage-dependent but also tissue context-dependent. © 2014 Macmillan Publishers Limited All rights reserved.
Amirian E.S.,Dan ncan Cancer Center |
Ittmann M.M.,Dan ncan Cancer Center |
Ittmann M.M.,Baylor College of Medicine |
Scheurer M.E.,Dan ncan Cancer Center |
Scheurer M.E.,Baylor College of Medicine
Prostate | Year: 2011
BACKGROUND The arachidonic acid (AA) pathway is suspected to be involved in the development of various cancers, including prostate cancer. However, the role of single nucleotide polymorphisms (SNPs) of AA pathway genes remains unclear. The purpose of this case-control study was to evaluate the association between prostate cancer risk and 14 such SNPs in the PTGS2, PTGES2, ALOX5, ALOX5AP, and LTA4H genes. METHODS Genotyping was conducted on 585 white prostate cancer cases and 585 healthy, age-matched controls. The best genetic model for each SNP was determined using Akaike's information criterion. Odds ratios for the association between each SNP and prostate cancer risk were calculated, both overall and stratified by obesity (BMI ≥ 30). Haplotype analysis was conducted for the PTGES2 SNPs. RESULTS LTA4H rs1978331 was inversely associated with prostate cancer risk overall (unadjusted, overdominant model OR = 0.68, 95% CI: 0.51-0.91 for TC vs. TT/CC). Among non-obese individuals, the GG genotype of PTGES2 rs10987883 was associated with an increased risk for prostate cancer (unadjusted, recessive model OR = 3.23, 95% CI: 1.27-8.23). CONCLUSIONS Our results indicate that SNPs in certain AA metabolism genes may influence prostate cancer susceptibility. Furthermore, it is possible that obesity, which induces a chronic state of low-level inflammation in addition to several metabolic sequelae, may modify the impact of these SNPs. These findings should be confirmed in a larger study with power to detect differential effects by obesity. Copyright © 2011 Wiley-Liss, Inc.
Luta G.,Georgetown University |
Ford M.B.,MBFord Consulting |
Bondy M.,Dan ncan Cancer Center |
Bondy M.,Baylor College of Medicine |
And 2 more authors.
Cancer Epidemiology | Year: 2013
Background: Recent research suggests that the Bayesian paradigm may be useful for modeling biases in epidemiological studies, such as those due to misclassification and missing data. We used Bayesian methods to perform sensitivity analyses for assessing the robustness of study findings to the potential effect of these two important sources of bias. Methods: We used data from a study of the joint associations of radiotherapy and smoking with primary lung cancer among breast cancer survivors. We used Bayesian methods to provide an operational way to combine both validation data and expert opinion to account for misclassification of the two risk factors and missing data. For comparative purposes we considered a " full model" that allowed for both misclassification and missing data, along with alternative models that considered only misclassification or missing data, and the naïve model that ignored both sources of bias. Results: We identified noticeable differences between the four models with respect to the posterior distributions of the odds ratios that described the joint associations of radiotherapy and smoking with primary lung cancer. Despite those differences we found that the general conclusions regarding the pattern of associations were the same regardless of the model used. Overall our results indicate a nonsignificantly decreased lung cancer risk due to radiotherapy among nonsmokers, and a mildly increased risk among smokers. Conclusions: We described easy to implement Bayesian methods to perform sensitivity analyses for assessing the robustness of study findings to misclassification and missing data. © 2012 Elsevier Ltd.
Caruana I.,Baylor College of Medicine |
Savoldo B.,Baylor College of Medicine |
Hoyos V.,Baylor College of Medicine |
Weber G.,Baylor College of Medicine |
And 6 more authors.
Nature Medicine | Year: 2015
Adoptive transfer of chimeric antigen receptor (CAR)-redirected T lymphocytes (CAR-T cells) has had less striking therapeutic effects in solid tumors than in lymphoid malignancies. Although active tumor-mediated immunosuppression may have a role in limiting the efficacy of CAR-T cells, functional changes in T lymphocytes after their ex vivo manipulation may also account for the reduced ability of cultured CAR-T cells to penetrate stroma-rich solid tumors compared with lymphoid tissues. We therefore studied the capacity of human in vitro-cultured CAR-T cells to degrade components of the extracellular matrix (ECM). In contrast to freshly isolated T lymphocytes, we found that in vitro-cultured T lymphocytes lack expression of the enzyme heparanase (HPSE), which degrades heparan sulfate proteoglycans, the main components of ECM. We found that HPSE mRNA is downregulated in in vitro-expanded T cells, which may be a consequence of p53 (officially known as TP53, encoding tumor protein 53) binding to the HPSE gene promoter. We therefore engineered CAR-T cells to express HPSE and showed their improved capacity to degrade the ECM, which promoted tumor T cell infiltration and antitumor activity. The use of this strategy may enhance the activity of CAR-T cells in individuals with stroma-rich solid tumors. © 2015 Nature America, Inc. All rights reserved.
Yiu T.T.,Texas Childrens Cancer Center |
Yiu T.T.,Dan ncan Cancer Center |
Li W.,Dan ncan Cancer Center |
Li W.,Baylor College of Medicine
Epigenomics | Year: 2015
Despite improvement in clinical treatment of childhood cancer, it remains the leading cause of disease-related mortality in children with survivors often suffering from treatment-related toxicity and premature death. Because childhood cancer is vastly different from cancer in adults, a thorough understanding of the underlying molecular mechanisms specific to childhood cancer is essential. Although childhood cancer contains much fewer mutations, a subset of cancer subtypes has a higher frequency of mutations in gene encoding epigenetic regulators. Thus, in this review, we will focus on epigenetic deregulations in childhood cancers, the use of genome-wide analysis for cancer subtype classification, prediction of clinical outcomes and the influence of folate on epigenetic mechanisms. © 2015 2015 Future Medicine Ltd.
Sun D.,Dan ncan Cancer Center |
Xi Y.,Dan ncan Cancer Center |
Rodriguez B.,Dan ncan Cancer Center |
Park H.J.,Dan ncan Cancer Center |
And 4 more authors.
Genome Biology | Year: 2014
Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Binomial hierarchical model and is capable of processing two billion reads in 24 CPU hours. Here, using simulated and real BS-seq data, we demonstrate that MOABS outperforms other leading algorithms, such as Fisher's exact test and BSmooth. Furthermore, MOABS analysis can be easily extended to differential 5hmC analysis using RRBS and oxBS-seq. MOABS is available at http://code.google.com/p/moabs/. © 2014 Sun et al.; licensee BioMed Central Ltd.