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Memphis, TN, United States

Gadd S.,Northwestern University | Huff V.,University of Houston | Huang C.-C.,Northwestern University | Cristy Ruteshouser E.,University of Houston | And 7 more authors.
Neoplasia (United States) | Year: 2012

Wilms tumors (WT) have provided broad insights into the interface between development and tumorigenesis. Further understanding is confounded by their genetic, histologic, and clinical heterogeneity, the basis of which remains largely unknown. We evaluated 224 WT for global gene expression patterns; WT1, CTNNB1, and WTX mutation; and 11p15 copy number and methylation patterns. Five subsets were identified showing distinct differences in their pathologic and clinical features: these findings were validated in 100 additional WT. The gene expression pattern of each subset was compared with published gene expression profiles during normal renal development. A novel subset of epithelial WT in infants lacked WT1, CTNNB1, and WTX mutations and nephrogenic rests and displayed a gene expression pattern of the postinduction nephron, and none recurred. Three subsets were characterized by a low expression of WT1 and intralobar nephrogenic rests. These differed in their frequency of WT1 and CTNNB1 mutations, in their age, in their relapse rate, and in their expression similarities with the intermediate mesoderm versus the metanephric mesenchyme. The largest subset was characterized by biallelic methylation of the imprint control region 1, a gene expression profile of the metanephric mesenchyme, and both interlunar and perilobar. © 2012 Neoplasia Press, Inc. All rights reserved. Source


Feige M.J.,TU Munich | Hendershot L.M.,Saint Jude Childrens Research Hospital | Buchner J.,TU Munich
Trends in Biochemical Sciences | Year: 2010

B cells use unconventional strategies for the production of a seemingly unlimited number of antibodies from a very limited amount of DNA. These methods dramatically increase the likelihood of producing proteins that cannot fold or assemble appropriately. B cells are therefore particularly dependent on 'quality control' mechanisms to oversee antibody production. Recent in vitro experiments demonstrate that Ig domains have evolved diverse folding strategies ranging from robust spontaneous folding to intrinsically disordered domains that require assembly with their partner domains to fold; in vivo experiments reveal that these different folding characteristics form the basis for cellular checkpoints in Ig transport. Taken together, these reports provide a detailed understanding of how B cells monitor and ensure the functional fidelity of Ig proteins. © 2009 Elsevier Ltd. Source


Jane Tseng Y.,National Taiwan University | Martin E.,Novartis | Bologa C.G.,University of New Mexico | Shelat A.A.,Saint Jude Childrens Research Hospital
Journal of Computer-Aided Molecular Design | Year: 2013

The "Cheminformatics aspects of high throughput screening (HTS): from robots to models" symposium was part of the computers in chemistry technical program at the American Chemical Society National Meeting in Denver, Colorado during the fall of 2011. This symposium brought together researchers from high throughput screening centers and molecular modelers from academia and industry to discuss the integration of currently available high throughput screening data and assays with computational analysis. The topics discussed at this symposium covered the data-infrastructure at various academic, hospital, and National Institutes of Health-funded high throughput screening centers, the cheminformatics and molecular modeling methods used in real world examples to guide screening and hit-finding, and how academic and non-profit organizations can benefit from current high throughput screening cheminformatics resources. Specifically, this article also covers the remarks and discussions in the open panel discussion of the symposium and summarizes the following talks on "Accurate Kinase virtual screening: biochemical, cellular and selectivity", "Selective, privileged and promiscuous chemical patterns in high-throughput screening" and "Visualizing and exploring relationships among HTS hits using network graphs". © 2013 Springer Science+Business Media Dordrecht. Source


Yang X.,Merck And Co. | Zhang B.,Merck And Co. | Molony C.,Merck And Co. | Chudin E.,Merck And Co. | And 17 more authors.
Genome Research | Year: 2010

Liver cytochrome P450s (P450s) play critical roles in drug metabolism, toxicology, and metabolic processes. Despite rapid progress in the understanding of these enzymes, a systematic investigation of the full spectrum of functionality of individual P450s, the interrelationship or networks connecting them, and the genetic control of each gene/enzyme is lacking. To this end, we genotyped, expression-profiled, and measured P450 activities of 466 human liver samples and applied a systems biology approach via the integration of genetics, gene expression, and enzyme activity measurements. We found that most P450s were positively correlated among themselves and were highly correlated with known regulators as well as thousands of other genes enriched for pathways relevant to the metabolism of drugs, fatty acids, amino acids, and steroids. Genome-wide association analyses between genetic polymorphisms and P450 expression or enzyme activities revealed sets of SNPs associated with P450 traits, and suggested the existence of both cis-regulation of P450 expression (especially for CYP2D6) and more complex trans-regulation of P450 activity. Several novel SNPs associated with CYP2D6 expression and enzyme activity were validated in an independent human cohort. By constructing a weighted coexpression network and a Bayesian regulatory network, we defined the human liver transcriptional network structure, uncovered subnetworks representative of the P450 regulatory system, and identified novel candidate regulatory genes, namely, EHHADH, SLC10A1, and AKR1D1. The P450 subnetworks were then validated using gene signatures responsive to ligands of known P450 regulators in mouse and rat. This systematic survey provides a comprehensive view of the functionality, genetic control, and interactions of P450s. © 2010 by Cold Spring Harbor Laboratory Press. Source


Green D.M.,Saint Jude Childrens Research Hospital | Nolan V.G.,Saint Jude Childrens Research Hospital | Kawashima T.,Fred Hutchinson Cancer Research Center | Stovall M.,University of Texas M. D. Anderson Cancer Center | And 5 more authors.
Fertility and Sterility | Year: 2011

Objective: To evaluate the effect of hypothalamic/pituitary radiation (HPT RT) dose on the occurrence of first pregnancy. Design: Retrospective cohort study of childhood cancer 5-year survivors (CCS) diagnosed between 1970 and 1986 before 21 years of age at one of 26 North American pediatric cancer treatment centers. Setting: Self-administered questionnaire. Patient(s): A total of 3,619 female CCS who participated in the Childhood Cancer Survivor Study and received no or scatter (≤0.1 Gy) radiation to the ovaries and 2,081 female siblings (Sibs) of the participants. Intervention(s): None. Main Outcome Measure(s): Self-reported pregnancy events. Result(s): As a group, CCS were as likely to report being pregnant as Sibs (hazard ratio 1.07, 95% confidence interval 0.97-1.19). Multivariable models showed a significant decrease in the risk of pregnancy with HPT RT doses ≥22 Gy compared with those CCS receiving no HPT RT. Conclusion(s): These results support the hypothesis that exposures of 22-27 Gy HPT RT may be a contributing factor to infertility among female CCS. © 2011 by American Society for Reproductive Medicine. Source

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