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Cui X.,University of Texas at San Antonio | Meng J.,Xian Jiaotong - Liverpool University | Zhang S.,Northwestern Polytechnical University | Chen Y.,Greehey Childrens Cancer Research Institute | And 3 more authors.
Bioinformatics | Year: 2016

Motivation: N6-methyl-adenosine (m6A) is the most prevalent mRNA methylation but precise prediction of its mRNA location is important for understanding its function. A recent sequencing technology, known as Methylated RNA Immunoprecipitation Sequencing technology (MeRIP-seq), has been developed for transcriptome-wide profiling of m6A. We previously developed a peak calling algorithm called exomePeak. However, exomePeak over-simplifies data characteristics and ignores the reads' variances among replicates or reads dependency across a site region. To further improve the performance, new model is needed to address these important issues of MeRIP-seq data. Results: We propose a novel, graphical model-based peak calling method, MeTPeak, for transcriptome-wide detection of m6A sites from MeRIP-seq data. MeTPeak explicitly models read count of an m6A site and introduces a hierarchical layer of Beta variables to capture the variances and a Hidden Markov model to characterize the reads dependency across a site. In addition, we developed a constrained Newton's method and designed a log-barrier function to compute analytically intractable, positively constrained Beta parameters. We applied our algorithm to simulated and real biological datasets and demonstrated significant improvement in detection performance and robustness over exomePeak. Prediction results on publicly available MeRIP-seq datasets are also validated and shown to be able to recapitulate the known patterns of m6A, further validating the improved performance of MeTPeak. © 2016 The Author 2016. Published by Oxford University Press. Source

Dayanc B.E.,Roswell Park Cancer Institute | Dayanc B.E.,Inonu University | Bansal S.,Roswell Park Cancer Institute | Bansal S.,Greehey Childrens Cancer Research Institute | And 3 more authors.
International Journal of Hyperthermia | Year: 2013

Purpose: Previously we showed that mild thermal stress increased natural killer (NK) cell-mediated tumour cytotoxicity and that this could be blocked by anti-NKG2D or anti-MICA (major histolocompatability complex (MHC) class I related chain A) antibodies. Here, we investigated the role of the transcription factor heat shock factor 1 (HSF1) in thermal regulation of MICA expression in tumour cells in vitro and in vivo. Materials and methods: Hyperthermia experiments were conducted in vitro and in mice using a target temperature of 39.5 °C. Apoptotic cells and NK cells in situ were visualised by use of the TUNEL assay or expression of NKp46 respectively. Using Colo205 cells, HSF1 message was blocked utilising siRNA while luciferase reporter assays were used to measure the activity of the MICA promoter in vitro. Cell surface MICA was measured by flow cytometry. Results: Following whole body hyperthermia (WBH), tumour tissues showed an increase in NK cells and apoptosis. Mild thermal stress resulted in a transient increase in surface MICA and enhanced NK cytotoxicity of the Colo205 colon cancer cell line. Silencing (mRNA) HSF1 expression in Colo205 cells prevented the thermal enhancement of MICA message and surface protein levels, with partial loss of thermally enhanced NK cytotoxicity. Mutations of the HSF1 binding site on the MICA promoter implicated HSF1 in the thermal enhancement of MICA. Some, but not all, patient-derived colon tumour derived xenografts also exhibited an enhanced MICA message expression after WBH. Conclusions: Up-regulation of MICA expression in Colo205 cells and enhanced sensitivity to NK cell killing following mild thermal stress is dependent upon HSF1. © 2013 Informa UK Ltd. Source

Lei X.,Greehey Childrens Cancer Research Institute | Lei X.,University of Texas Health Science Center at San Antonio | Bai Z.,Greehey Childrens Cancer Research Institute | Bai Z.,University of Texas Health Science Center at San Antonio | And 14 more authors.
Nature Cell Biology | Year: 2010

Kaposi's sarcoma-associated herpesvirus (KSHV) is causally linked to several acquired immune deficiency syndrome-related malignancies, including Kaposi's sarcoma, primary effusion lymphoma (PEL) and a subset of multicentric Castleman's disease. Control of viral lytic replication is essential for KSHV latency, evasion of the host immune system and induction of tumours. Here, we show that deletion of a 14 microRNA (miRNA) cluster from the KSHV genome significantly enhances viral lytic replication as a result of reduced NF-κB activity. The miRNA cluster regulates the NF-kappa;B pathway by reducing expression of IBα protein, an inhibitor of NF-kappa;B complexes. Computational and miRNA seed mutagenesis analyses were used to identify KSHV miR-K1, which directly regulates the IBα protein level by targeting the 3′UTR of its transcript. Expression of miR-K1 is sufficient to rescue NF-kappa;B activity and inhibit viral lytic replication, whereas inhibition of miR-K1 in KSHV-infected PEL cells has the opposite effect. Thus, KSHV encodes an miRNA to control viral replication by activating the NF-kappa;B pathway. These results demonstrate an important role for KSHV miRNAs in regulating viral latency and lytic replication by manipulating the host survival pathway. © 2010 Macmillan Publishers Limited. All rights reserved. Source

Kurmasheva R.T.,Greehey Childrens Cancer Research Institute | Houghton P.J.,Greehey Childrens Cancer Research Institute
Cancer Chemotherapy and Pharmacology | Year: 2016

In the USA, the overall cure rate for all childhood cancers is seventy percent, and in many patients that ultimately fail curative therapy, initial responses to current multimodality treatments (surgery, radiation therapy and chemotherapy) is good, with overall 5-year event-free survival approaching 80 %. However, current approaches to curative therapy result in significant morbidity and long-term sequelae, including cardiac dysfunction and cognitive impairment. Furthermore, dose-intensive chemotherapy with conventional agents has not significantly improved outcomes for patients that present with advanced or metastatic disease. Classical cytotoxic agents remain the backbone for curative therapy of both hematologic and solid tumors of childhood. While ‘molecularly’ targeted agents have shown some clinical activity, responses are often modest and of short duration; hence, there is a need to identify new classes of cytotoxic agent that are effective in patients at relapse and that have reduced or different toxicity profiles to normal tissues. Here we review the pediatric preclinical testing program experience of testing novel agents, and the value and limitations of preclinical xenograft models and genetically engineered mouse models for developing novel agents for treatment of childhood cancer. © 2016 Springer-Verlag Berlin Heidelberg Source

Shen-Gunther J.,U.S. Army | Rebeles J.,Greehey Childrens Cancer Research Institute | Rebeles J.,University of North Carolina at Chapel Hill
Gynecologic Oncology | Year: 2013

Goals To define the analytical and clinical performance of a human papillomavirus (HPV) custom-designed microarray targeting the HPV L1 gene for viral genotyping. Methods Microarray probes were designed by cataloging the genome sequence of all 120 known HPV types to generate tiling probes using eArray® software against the unique L1 capsid gene segments targeted by MY09/11 and FAP59/64 primers. The microarray (1 slide × 8 arrays × 60 K features) synthesized in situ by inkjet printing was tested using synthetic type-specific HPV DNA and existing HPV DNA from cervical cytology. The synthetic HPV L1 segments (genotypes 6, 11, 16, 18, 31, 33, 35, 45, 53, 58, 66, 73, 83) were manufactured from sequences stored in the NCBI taxonomy database. Using the hybridization patterns of the synthetic HPV DNA as the Support Vector Machine classifier, HPV DNA from patient samples were genotyped and compared to antecedent DNA sequencing/BLAST® results for concordance. Results 16 cytology-derived HPV DNA samples and 13 synthetic type-specific HPV DNA samples were tested singly, in duplicate, or in combination on 40 arrays. The synthetic HPV DNA hybridization patterns were found to be uniquely distinctive to serve well as a classifier of unknown HPV-containing specimens. For the 16 HPV DNA + samples classified, 15 were concordant with DNA sequencing results. In 6/16 (38%) samples, the microarray hybridization pattern revealed ≥ 2 concurrent HPV infections. Conclusion The novel "HPV Array" was sensitive and specific for detecting single and multiple infections. This proof-of-principle project demonstrated the accuracy and advantages of microarray technology for HPV genotyping. Source

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