Search

Supplementary Data 1-4, Table from Targeting Angiogenesis via a c-Myc/Hypoxia-Inducible Factor-1α–Dependent Pathway in Multiple Myeloma

Bone marrow angiogenesis is associated with multiple myeloma (MM) progression. Here, we report high constitutive hypoxia-inducible factor-1α (Hif-1α) expression in MM cells, which is associated with oncogenic c-Myc. A drug screen for anti-MM agents that decrease Hif-1α and c-Myc levels identified a variety of compounds, including bortezomib, lenalidomide, enzastaurin, and adaphostin. Functionally, based on transient knockdowns and overexpression, our data delineate a c-Myc/Hif-1α–dependent pathway mediating vascular endothelial growth factor production and secretion. The antiangiogenic activity of our tool compound, adaphostin, was subsequently shown in a zebrafish model and translated into a preclinical in vitro and in vivo model of MM in the bone marrow milieu. Our data, therefore, identify Hif-1α as a novel molecular target in MM and add another facet to anti-MM drug activity. [Cancer Res 2009;69(12):5082–90]

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor–normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

BackgroundReproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS.ResultsTo dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×.ConclusionsOur findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.

Standardized benchmarking methods and tools are essential to robust accuracy assessment of NGS variant calling. Benchmarking variant calls requires careful attention to definitions of performance metrics, sophisticated comparison approaches, and stratification by variant type and genome context. To address these needs, the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team convened representatives from sequencing technology developers, government agencies, academic bioinformatics researchers, clinical laboratories, and commercial technology and bioinformatics developers for whom benchmarking variant calls is essential to their work. This team addressed challenges in (1) matching variant calls with different representations, (2) defining standard performance metrics, (3) enabling stratification of performance by variant type and genome context, and (4) developing and describing limitations of high-confidence calls and regions that can be used as “truth”. Our methods are publicly available on GitHub (https://github.com/ga4gh/benchmarking-tools) and in a web-based app on precisionFDA, which allow users to compare their variant calls against truth sets and to obtain a standardized report on their variant calling performance. Our methods have been piloted in the precisionFDA variant calling challenges to identify the best-in-class variant calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and critically evaluating the results.

The US Vaccine Adverse Event Reporting System contains case reports of autoimmune diseases (ADs) occurring following vaccinations. ADs are rare and occur in unvaccinated people, making the potential association between vaccines and ADs challenging to evaluate. Developing mechanistic pathways that link genes, immune mediators, vaccine components and ADs would be helpful for hypothesis generation, enhancing theories of biologic plausibility and grouping rare autoimmune adverse events to increase the ability to detect and evaluate safety signals. Here, we propose a conceptual framework for investigating the genetics of ADs as safety signals following vaccination, potentially contributing to the identification of relevant biomarkers. We also discuss a study design that incorporates genetic information into postmarket clinical evaluation of autoimmune adverse events following vaccination.

Previously, we have demonstrated that interleukin-4 receptor α (IL-4Rα) is overexpressed on a variety of human cancers and can serve as target for IL-4 immunotoxin comprised of IL-4 and a mutated Pseudomonas exotoxin. However, its expression and association with grade and clinical stage of bladder cancer has not been studied. IL-4Rα expression was examined in human bladder cancer cell lines, mouse xenografts, and biopsy specimens at mRNA and protein levels by real-time RT-PCR and IHC/ISH techniques. We also examined the effect of IL-4 on proliferation and invasion of bladder carcinoma cell lines. For tissue microarray (TMA) results, we analyzed the precision data using exact binomial proportion with exact two-sided P-values. We used Cochran-Armitage Statistics with exact two-sided P-values to examine the trend analysis of IL-4Rα over grade or stage of the bladder cancer specimens. The influence of age and gender covariates was also analyzed using multiple logistic regression models. IL-4Rα is overexpressed in five bladder cancer cell lines, while normal bladder and human umbilical vein cell lines (HUVEC) expressed at low levels. Two other chains of IL-4 receptor complex, IL-2RγC and IL-13Rα1, were absent or weakly expressed. IL-4 modestly inhibited the cell proliferation, but enhanced cell invasion of bladder cancer cell lines in a concentration-dependent manner. Bladder cancer xenografts in immunodeficient mice also maintained IL-4Rα overexpression in vivo. Analysis of tumor biopsy specimens in TMAs revealed significantly higher IL-4Rα immunostaining (≥ 2+) in Grade 2 (85%) and Grade 3 (97%) compared to Grade 1 tumors (0%) (P ≤ 0.0001). Similarly, 9% stage I tumors were positive for IL-4Rα (≥ 2+) compared to 84% stage II (P ≤ 0.0001) and 100% stages III-IV tumors (P ≤ 0.0001). IL-13Rα1 was also expressed in tumor tissues but at low levels and it did not show any correlation with the grade and stage of disease. However, the IL-2RγC was not expressed. Ten normal bladder specimens demonstrated ≤ 1+ staining for IL-4Rα and IL-13Rα1 and no staining for IL-2RγC. These results demonstrate that IL-4Rα is overexpressed in human bladder cancer, which correlates with advanced grade and stage of the disease. Thus, IL-4Rα may be a bladder tumor-associated protein and a prognostic biomarker.

We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific-filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.

Domestic goats in Syria may provide an interesting source of genetic variability due to its proximity to the centers of domestication. This study aimed to assess the morphological variation, genetic diversity and population substructure of the Syrian goat populations. Commonly, three goat genotypes are distinguished in Syria, namely Jabali or mountain goat, Baladi or local goat and Shami or Damascus (a well-known dairy goat). A pre-tested semi-structured questionnaire was used in recording both qualitative (coat color, eye color, horn length, horn orientation, nose profile) and quantitative (height at wither, chest girth, cannon length, body length, ear length and ear width) morphological data. Data from a total of 5,730 individual goats of the three goat populations reared in ten representative provinces of Syria were collected and analyzed using GenStat version 14 statistical packages. Results of the morphological analysis confirmed that there were clear morphological variations among the three goat populations. The three goat populations are mainly distinguished by their straight (Baladi, 71.1% and Jabali, 82.8%) and curved (Shami, 89.5%) nose profiles. Substantial phenotypic variability was found among and within the breeds suggesting that these goat breeds have not yet undergone an organized breeding program. The genetic variability and population substructures from 398 individual animals of the three breeds were genotyped using 12 DNA microsatellite markers from Food and Agricultural Organization (FAO) panel. All microsatellites typed were found to be polymorphic and a total of 41 distinct alleles were detected on Baladi, Jabali and Shami goat populations. The Syrian goat populations had observed and expected heterozygosity values that ranged from 0.50 to 0.62 and 0.74 to 0.85, respectively, and an average of 13.97 alleles per locus across breeds. For all loci, an average inbreeding values (FIS) of low to moderate level was obtained across the three goat breeds, which ranged from 0.29 (Shami goats) to 0.34 (Baladi goats) indicating the absence of mating between close relatives within these populations. The observed positive FIS coefficients among the studied goat breeds also suggested heterozygote deficiencies. The analyses of the molecular data using STRUCURE program indicated there were two primary populations, which did support the results based on morphological data of the same goat populations that clustered these goat populations into two main groups and confirmed the admixture nature of the Baladi and Jabali goat populations, while the Shami goat breed was well differentiated and grouped into a separate cluster that suggests its evolutionary and genetic uniqueness. The analysis of molecular variance (AMOVA) results detected genetic variations within individuals in a population (96%). The high genetic variability within individuals in a population provides a good base for designing genetic improvement programs under the existing goat management systems. Key words : Characterization, cluster, genetic differentiation, population structure, Syria.

Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.

Chromosomal instability—a hallmark of epithelial cancers—is an ongoing process that results in aneuploidy and karyotypic heterogeneity of a cancer cell population. Previously, we stratified cancer cell lines in the NCI-60 drug discovery panel based on their karyotypic complexity and heterogeneity. Using this stratification in conjunction with drug response data for the cell lines allowed us to identify classes of chemical compounds whose growthinhibitory activity correlates with karyotypic complexity and chromosomal instability. In this article, we asked the question: What are the biological processes, pathways, or genes associated with chromosomal instability of cancer cells? We found that increased instability of the chromosomal content in a cancer cell population, particularly, persistent gains and losses of chromosomes, is associated with elevated expression of genes involved with aggressive cellular behavior, including invasion- and metastasis-associated changes in cell communication, adhesion, motility, and migration. These same karyotypic features are negatively correlated with the expression of genes involved in cell cycle checkpoints, DNA repair, and chromatin maintenance.

Thyroid cancer is a rapidly increasing endocrine cancer. Since interleukin-4 receptor (IL-4R) is overexpressed in human solid cancer, we examined expression of IL-4R in 50 cases of anaplastic thyroid cancer (ATC), 37 well-differentiated papillary cancer (WDPC), 35 well-differentiated follicular cancer of thyroid (WDFC), and 37 normal thyroid specimens by immunohistochemistry (IHC) and in-situ hybridization (ISH) techniques. We demonstrated that IL-4Rα was overexpressed in 36/50 (72%) ATC, 20/35 (57%) WDFC, and 11/37 (30%) WDPC tumors. Other two subunits of IL-4R, interleukin-13 receptor α1 (IL-13Rα1) and interleukin-2 receptor gamma (IL-2RγC), were either weakly expressed or absent. As ATC is a highly aggressive cancer with higher incidence of IL-4Rα expression, we characterized IL-4R in 3 ATC cell lines. RT-qPCR and IFA results showed that IL-4Rα is overexpressed while IL-13Rα1 is weakly expressed. Control human umbilical vein endothelial cell line (HUVEC) showed weak expression of IL-4Rα. Binding and competition studies with 125I-IL-4 in ATC cell lines demonstrated that IL-4 specifically bound to IL-4Rα on cell surface. ATC cell lines were highly sensitive to a chimeric fusion cytotoxin consisting of circularly permuted IL-4 and truncated Pseudomonas exotoxin (IL-4-PE), which killed them in a concentration dependent manner. IL-4-PE also blocked colony formation of ATC cell lines in clonogenic assays. IL-4-PE mediated a significant antitumor activity in mouse models of ATC. Intratumoral administration of IL-4-PE caused significant regression of established tumors in a dose dependent manner and increased the overall survival without any visible toxicity. Thus, IL-4Rα in ATC may represent a novel therapeutic target and IL-4-PE may serve as an investigational therapeutic option for ATC.

Chromosome rearrangement, a hallmark of cancer, has profound effects on carcinogenesis and tumor phenotype. We used a panel of 60 human cancer cell lines (the NCI-60) as a model system to identify relationships among DNA copy number, mRNA expression level, and drug sensitivity. For each of 64 cancer-relevant genes, we calculated all 4,096 possible Pearson's correlation coefficients relating DNA copy number (assessed by comparative genomic hybridization using bacterial artificial chromosome microarrays) and mRNA expression level (determined using both cDNA and Affymetrix oligonucleotide microarrays). The analysis identified an association of ERBB2 overexpression with 3p copy number, a finding supported by data from human tumors and a mouse model of ERBB2-induced carcinogenesis. When we examined the correlation between DNA copy number for all 353 unique loci on the bacterial artificial chromosome microarray and drug sensitivity for 118 drugs with putatively known mechanisms of action, we found a striking negative correlation (−0.983; 95% bootstrap confidence interval, −0.999 to −0.899) between activity of the enzyme drug l-asparaginase and DNA copy number of genes near asparagine synthetase in the ovarian cancer cells. Previous analysis of drug sensitivity and mRNA expression had suggested an inverse relationship between mRNA levels of asparagine synthetase and l-asparaginase sensitivity in the NCI-60. The concordance of pharmacogenomic findings at the DNA and mRNA levels strongly suggests further study of l-asparaginase for possible treatment of a low-synthetase subset of clinical ovarian cancers. The DNA copy number database presented here will enable other investigators to explore DNA transcript-drug relationships in their own domains of research focus. [Mol Cancer Ther 2006;5(4):853–67]

For analysis of multidrug resistance, a major barrier to effective cancer chemotherapy, we profiled mRNA expression of the 48 known human ABC transporters in 60 diverse cancer cell lines (the NCI-60) used by the National Cancer Institute to screen for anticancer activity. The use of real-time RT-PCR avoided artifacts commonly encountered with microarray technologies. By correlating the results with the growth inhibitory profiles of 1,429 candidate anticancer drugs tested against the cells, we identified which transporters are more likely than others to confer resistance to which agents. Unexpectedly, we also found and validated compounds whose activity is potentiated, rather than antagonized, by the MDR1 multidrug transporter. Such compounds may serve as leads for development.

This paper deals with a nonparametric estimation problem of an integral-type functional from indirect observations where the observation Y e(t) is a sum of a known function of an unobservable process X e(t) and a Gaussian white noise, and X e(t) is a sum of an unknown function a(t) and a Gaussian process. The minimax lower bound on the quality of nonparametric estimation is derived and an asymptotically efficient estimator is proposed. The paper concludes with some examples including one about reduction to parameter estimation.

Background Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. Results We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. Conclusions We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0694-1) contains supplementary material, which is available to authorized users.

Dietary patterns that involve a decrease in fat and an increase in fruit and vegetable (FV) intake have been suggested to decrease cancer risks. In this study, intervention methods to selectively modify dietary fat and/or FV intakes were developed. Compliance to the diets and the effects on body weight are shown, because both of these dietary changes can impact on and be confounded by changes in energy intake. A total of 122 women with a family history of breast cancer were randomized onto one of four diets for 12 mo. Counseling methods were devised to increase amount and variety of FV consumed with or without a decrease in fat intake using modified exchange list diets. Women on the low-fat and combination low-fat/high-FV diet arms decreased their fat intakes to approximately 16% of energy. Women on the high-FV and the combination low-fat/high-FV diet arms increased FV intakes to approximately 11 servings/day. Despite counseling efforts to maintain baseline energy intakes, mean body weight increased significantly by 6 pounds in women in the high-FV diet arm and decreased significantly by 5 pounds in women in the low-fat diet arm. Percent body fat also was increased in the high-FV diet arm and decreased in the low-fat diet arm. Body weight and percent body fat in the combination diet arm did not change significantly. Control of energy intake, therefore, appears to have been achieved only when the addition of FV to the diet was balanced by a decrease in fat intake and both dietary components were enumerated daily. Maintenance of energy intake, therefore, did not appear to be attained intrinsically when individuals were counseled to make changes in the composition of their diets.

Background Dietary intervention research with free-living subjects relies on the ability of study participants to meet their dietary goals within the study timeframe. Little is known about underlying factors affecting compliance. Method Here, we examined whether motivation to enrol in a trial of low-fat and/or energy-reduced diets influenced the ability of healthy women to reach their dietary goals quickly. Results Of the women who had energy-reduction goals (n=43), the 18 with an altruistic reason for participation had a much higher energy reduction success rate at 4 weeks (83%) than the 25 who gave self-rewarding reasons (48%). Conclusions Education, body weight, family history of cancer and previous diet experience did not appreciably affect dietary outcomes. This observation suggests that the societal importance of the research should be stressed in strategies that seek to affect rapid reduction of energy intake in clinical trials.

The food frequency questionnaire (FFQ) is commonly utilized for assessment of dietary fat intake, but its validity among individuals following a low-fat diet is unclear. We evaluated the agreement of nutrient estimates derived from FFQ, 24-h recall, and 3-day food records obtained from 104 participants in a randomized trial of a low-fat dietary intervention for women at elevated breast cancer risk. Comparisons were made for total calories, percent calories from fat, and total fat after 1 yr. Correlation was assessed using standard methods based on a null hypothesis of no agreement between instruments as well as by a methodology based on a null hypothesis that the instruments should be in agreement. With the use of standard methods, FFQ estimates for women on the low-fat diet were significantly correlated to records only for percent calories from fat (r = 0.39), whereas recall and record estimates were significantly correlated for all three dietary variables. Using the new method, we found no significant correlation between FFQ and either recalls or records for women following a low-fat diet but significant correlation between recall and record estimates for total calories (r = 0.67). Traditional correlation testing may overestimate the extent of agreement in dietary instruments among women on a low-fat diet. We found empirical support for the nontraditional method.

Oxidative DNA damage (ODD) can result from numerous endogenous metabolic processes as well as from exposure to environmental and dietary oxidants. One important type of ODD that may have a role in carcinogenesis is the formation of hydroxylated DNA bases. Our major purpose was to determine the potential for subject accrual for a multisite case-control study of ODD and breast cancer risk within a large urban university medical center. We examined the levels of a hydroxylated thymine residue, 5-hydroxymethyl-2'-deoxyuridine in DNA obtained from the peripheral blood of 26 women with breast cancer and an age-matched group of 29 control women without breast cancer. The isolated DNA was analyzed for levels of 5-hydroxymethyl-2'-deoxyuridine by gas chromatography with mass spectral detection. Our recruitment methods resulted in a relatively high yield of eligible cases (72%) and a lower yield of controls (46%). We evaluated the dose-response relationship of ODD level to breast cancer risk, using quartiles of ODD. The covariate-adjusted odds ratio of breast cancer exceeded 2.0 for women in the highest quartile of ODD (compared with the lowest quartile), although this result was not statistically significant. ODD levels were significantly more variable among African-American controls (SD = 224.1) than among white controls (SD = 57.5), p < 0.001. Overall, these results suggest a possible slight increase in breast cancer risk among women in the highest ODD quartile, after adjusting for race, menopausal status, and family history of breast cancer.

Objective We examined the relationship between intakes of specific foods—namely, meats, vegetables, and fruits—with levels of oxidative DNA damage in women consuming their own usual diet or a diet low in fat. Design Blood was obtained from women who had been assigned randomly to a low-fat or nonintervention diet for 3 to 24 months. Levels of 5-hydroxymethyluracil, a type of oxidative DNA damage, were determined. Diet data were obtained from 3-day food records. Subjects/setting The 21 women were participating in an outpatient clinic. All the women were healthy but had a first-degree relative with breast cancer. Intervention The intervention was a self-selected diet with a goal of 15% of energy from fat. Main outcome measures Existing data on oxidative DNA damage levels were evaluated for possible relationships to foods eaten. Intakes of raw and cooked vegetables were examined separately. Meat intake was examined by type of meat (pork, beef, fish, chicken) and by cooking temperature. Statistical analyses Initial univariate analyses relied on Spearman rank correlations of each food item with DNA damage. Further analyses of the data were performed with univariate and multivariate weighted least squares regression models. Results The model that best explained DNA damage levels was a bivariate regression model that included the intake of cooked vegetables and the sum of beef and pork intake. This model accounted for 85% of the variation in DNA damage levels among women. Preliminary results are suggestive of a positive association of DNA damage with beef and pork intake and a negative association with cooked vegetable intake. Application These observations, if confirmed in larger studies, suggest specific dietary changes to reduce oxidative DNA damage levels and possibly cancer risk. J Am Diet Assoc. 1998;98:524–528 .

WOS: 000346677200002 PubMed ID: 25486901 Background: Near universal administration of vaccines mandates intense pharmacovigilance for vaccine safety and a stringently low tolerance for adverse events. Reports of autoimmune diseases (AID) following vaccination have been challenging to evaluate given the high rates of vaccination, background incidence of autoimmunity, and low incidence and variable times for onset of AID after vaccinations. In order to identify biologically plausible pathways to adverse autoimmune events of vaccine-related AID, we used a systems biology approach to create a matrix of innate and adaptive immune mechanisms active in specific diseases, responses to vaccine antigens, adjuvants, preservatives and stabilizers, for the most common vaccine-associated AID found in the Vaccine Adverse Event Reporting System. Results: This report focuses on Guillain-Barre Syndrome (GBS), Rheumatoid Arthritis (RA), Systemic Lupus Erythematosus (SLE), and Idiopathic (or immune) Thrombocytopenic Purpura (ITP). Multiple curated databases and automated text mining of PubMed literature identified 667 genes associated with RA, 448 with SLE, 49 with ITP and 73 with GBS. While all data sources provided valuable and unique gene associations, text mining using natural language processing (NLP) algorithms provided the most information but required curation to remove incorrect associations. Six genes were associated with all four AIDs. Thirty-three pathways were shared by the four AIDs. Classification of genes into twelve immune system related categories identified more "Th17T-cell subtype" genes in RA than the other AIDs, and more "Chemokine plus Receptors" genes associated with RA than SLE. Gene networks were visualized and clustered into interconnected modules with specific gene clusters for each AID, including one in RA with ten C-X-C motif chemokines. The intersection of genes associated with GBS, GBS peptide auto-antigens, influenza A infection, and influenza vaccination created a subnetwork of genes that inferred a possible role for the MAPK signaling pathway in influenza vaccine related GBS. Conclusions: Results showing unique and common gene sets, pathways, immune system categories and functional clusters of genes in four autoimmune diseases suggest it is possible to develop molecular classifications of autoimmune and inflammatory events. Combining this information with cellular and other disease responses should greatly aid in the assessment of potential immune- mediated adverse events following vaccination. FDA though the CERSI (Centers in Excellence in Regulatory Sciences) program [1U01FD004319-01]; FOOD AND DRUG ADMINISTRATIONUnited States Department of Health & Human Services [U01FD004319, U01FD004319, U01FD004319, U01FD004319, U01FD004319, U01FD004319, U01FD004319, U01FD004319, U01FD004319] Funding Source: NIH RePORTER We thank Simina Boca for advice on the statistical analysis. This work was partly funded by the FDA though the CERSI (Centers in Excellence in Regulatory Sciences) program 1U01FD004319-01.

The growth inhibitory properties of alpha-tocopheryl hemisuccinate (vitamin E succinate) and related compounds were examined in MCF-7 human breast tumor cells and MCF-10A normal-like human breast cells since they have been suggested to be an effective antitumor compound. The data showed that both alpha-tocopherol hemisuccinate and a structurally-similar compound, cholesteryl hemisuccinate, inhibited the growth of MCF-7 and MCF-10A cells, while alpha-tocopherol, cholesterol, cholesteryl sulfate and Tris succinate had little effect on cell growth. The ether analogs of the succinate esters, alpha-tocopheryloxybutyric acid and cholesteryloxybutyric acid, also inhibited growth of MCF-7 and MCF-10A cells, indicating that hydrolysis of the succinate esters by esterases is not required for the antiproliferative effects. The antiproliferative effects of these succinate esters and ethers may be related to their physiochemical properties that allow incorporation into cell membranes.

Bone marrow angiogenesis is associated with multiple myeloma (MM) progression. Here, we report high constitutive hypoxia-inducible factor-1α (Hif-1α) expression in MM cells, which is associated with oncogenic c-Myc. A drug screen for anti-MM agents that decrease Hif-1α and c-Myc levels identified a variety of compounds, including bortezomib, lenalidomide, enzastaurin, and adaphostin. Functionally, based on transient knockdowns and overexpression, our data delineate a c-Myc/Hif-1α–dependent pathway mediating vascular endothelial growth factor production and secretion. The antiangiogenic activity of our tool compound, adaphostin, was subsequently shown in a zebrafish model and translated into a preclinical in vitro and in vivo model of MM in the bone marrow milieu. Our data, therefore, identify Hif-1α as a novel molecular target in MM and add another facet to anti-MM drug activity. [Cancer Res 2009;69(12):5082–90]

Genomic classifiers using DNA microarrays are becoming powerful tools in the medical community with the potential to revolutionize the diagnosis and treatment of disease. However, despite the tremendous interest in using these classifiers in diagnosis and the management of disease, few genomic classifiers have made it into clinical practice. Some of the major challenges for the development and validation of genomic classifiers will be discussed in this article together with some of their difficulties.

E-cadherin (E-cad) is a transmembrane adhesion glycoprotein, the expression of which is often reduced in invasive or metastatic tumors. To assess E-cad's distribution among different types of cancer cells, we used bisulfite-sequencing for detailed, base-by-base measurement of CpG methylation in E-cad's promoter region in the NCI-60 cell lines. The mean methylation levels of the cell lines were distributed bimodally, with values pushed toward either the high or low end of the methylation scale. The 38 epithelial cell lines showed substantially lower (28%) mean methylation levels compared with the nonepithelial cell lines (58%). The CpG site at -143 with respect to the transcriptional start was commonly methylated at intermediate levels, even in cell lines with low overall DNA methylation. We also profiled the NCI-60 cell lines using Affymetrix U133 microarrays and found E-cad expression to be correlated with E-cad methylation at highly statistically significant levels. Above a threshold of ∼20% to 30% mean methylation, the expression of E-cad was effectively silenced. Overall, this study provides a type of detailed analysis of methylation that can also be applied to other cancer-related genes. As has been shown in recent years, DNA methylation status can serve as a biomarker for use in choosing therapy. [Mol Cancer Ther 2007;6(2):391–403]

This study examined whether subjects who participated in a 12-mo intervention would maintain their diets 1 yr after the study ended and whether the diets of household members were affected. Premenopausal women, who had at least one first-degree relative with breast cancer (n = 122), were randomized to one of four diets: control, low fat (15% of energy), high fruit and vegetable (FV, nine servings per day), and combination low fat, high FV. Study subjects and one household member were asked to complete the Block '95 food-frequency questionnaire (FFQ) at baseline, 1 yr, and 2 yr. Study subjects also completed 24-h recalls and 4-day food records at baseline and Year 1. Fat and FV intakes by all three assessment methods compared reasonably well except that fat intakes by FFQ were somewhat higher. FV intakes by FFQ in the high-FV and combination arms increased significantly from 4 servings per day to about 10 servings per day at Year 1 and 7 servings per day at Year 2. FV intakes increased much more modestly in the low-fat and control arms. Fat intakes in the low-fat and combination arms were lower at Year 1 than Year 2, but mean Year 2 fat intakes of 26-28% were still significantly lower than those at baseline. In household members, the only significant change was a small decrease in energy from fat at Year 1 in the household members of subjects who were in the combination arm. These results indicate that study subjects were making large dietary changes independently of their household members and that fat and FV intakes in study subjects 1 yr after intervention stopped were still substantially different from intakes at baseline.

Cancer is a genetic disease caused by genomic instability. In many cancers, this instability is manifested by chromosomal reconfigurations and karyotypic complexity. These features are particular hallmarks of the epithelial cancers that are some of the malignancies most resistant to long term control by current chemotherapeutic agents. We have asked whether we could use karyotypic complexity and instability as determinants for the screening of potential anticancer compounds. Using a panel of well characterized cancer cell lines, we have been able to identify specific groups of chemical compounds that are more cytotoxic toward the relatively more karyotypically complex and unstable panel members. Thus, we delineate an approach for the identification of “lead compounds” for anticancer drug discovery complementary to those that are focused at the outset on a given gene or pathway.

Oxidative DNA damage in blood appears to be useful as a marker of systemic oxidative stress levels. Dietary factors such as fat and energy intakes have been indicated to affect oxidative stress levels, and this may be an important mechanism by which diet can modulate cancer risk. The primary objective of this study was to investigate the effects of dietary intervention in premenopausal women on the levels of one type of oxidative DNA damage: 5-hydroxymethyl-2'-deoxyuridine. The trial randomly assigned women to control, low-fat, low-energy or combination low-fat/low-energy diets for 12 weeks. Blood samples were obtained every 2 weeks, and DNA was analysed for the levels of 5-hydroxymethyl-2'-deoxyuridine. Levels of DNA damage declined with time in each diet arm, including the control arm. The decreases were greater in the two arms with low-energy intake, but not significantly so. The numbers of women who exhibited decreased 5-hydroxymethyl-2'-deoxyuridine levels at 12 weeks versus baseline levels, however, was significantly greater in women assigned to any intervention diet (79%) than in the control arm (50%). Low-fat and low-energy diets therefore had a small effect on changes in oxidative DNA damage levels. The women participating in this study were not selected on the basis of increased cancer risk; therefore, they may have had low baseline levels of damage that were not amenable to further reduction by dietary change.

For analysis of multidrug resistance, a major barrier to effective cancer chemotherapy, we profiled mRNA expression of the 48 known human ABC transporters in 60 diverse cancer cell lines (the NCI-60) used by the National Cancer Institute to screen for anticancer activity. The use of real-time RT-PCR avoided artifacts commonly encountered with microarray technologies. By correlating the results with the growth inhibitory profiles of 1,429 candidate anticancer drugs tested against the cells, we identified which transporters are more likely than others to confer resistance to which agents. Unexpectedly, we also found and validated compounds whose activity is potentiated, rather than antagonized, by the MDR1 multidrug transporter. Such compounds may serve as leads for development.

We have designed and developed a Gene Ontology based navigation tool, GoMiner, which organizes lists of interesting genes from a microarray or a protein array experiment for biological interpretation. It provides quantitative and statistical output files and useful visualization (e.g., a tree -like structure) to map the list of genes to its biological functional categories. It also provides links to other resources such as pubmed, locuslink, and biological molecular interaction map and signaling pathway packages.

We used spectral karyotyping to provide a detailed analysis of karyotypic aberrations in the diverse group of cancer cell lines established by the National Cancer Institute for the purpose of anticancer drug discovery. Along with the karyotypic description of these cell lines we defined and studied karyotypic complexity and heterogeneity (metaphase-to-metaphase variations) based on three separate components of genomic anatomy: (a) ploidy; (b) numerical changes; and (c) structural rearrangements. A wide variation in these parameters was evident in these cell lines, and different association patterns between them were revealed. Analysis of the breakpoints and other specific features of chromosomal changes across the entire set of cell lines or within particular lineages pointed to a striking lability of centromeric regions that distinguishes the epithelial tumor cell lines. We have also found that balanced translocations are as frequent in absolute number within the cell lines derived from solid as from hematopoietic tumors. Important similarities were noticed between karyotypic changes in cancer cell lines and that seen in primary tumors. This dataset offers insights into the causes and consequences of the destabilizing events and chromosomal instability that may occur during tumor development and progression. It also provides a foundation for investigating associations between structural genome anatomy and cancer molecular markers and targets, gene expression, gene dosage, and resistance or sensitivity to tens of thousands of molecular compounds.

The cytochrome P-450 (CYP) and glutathione S-transferase (GST) enzyme systems may influence the biological effects of carcinogens, including estrogens. As such, these enzymes may predict the developmental risk of breast cancer, as well as be potential targets for chemoprevention. The purpose of this study was to compare the expression of GST-Pi and CYPs 1A1, 2B6, 2E1, and 3A4 in paired samples of normal and malignant breast tissue from patients with breast cancer and women undergoing reduction mammoplasty.Expression of CYPs 1A1, 2B6, 2E1, 3A4, and GST-Pi was quantified in breast tissue from 33 patients with breast cancer and in 17 women without history of cancer who underwent reduction mammoplasty. The expression of CYP 1A1, 2B6, 2E1, 3A4, and GST-Pi was quantified by immunoblotting.CYP 1A1, 2E1, and 3A4 expression was significantly lower (P0.05) in malignant tissue as compared with morphologically normal adjacent tissue. Conversely, GST-Pi expression was marginally lower in the normal tissue (P = 0.08). No significant difference in enzyme expression was seen between the tissue from reduction mammoplasty and normal tissue from breast cancer patients. There was a trend for higher expression of CYP 2B6 and GST-Pi in the estrogen receptor expressing tumors than those tumors without expression (P0.28).The expression of these enzymes was similar in morphologically normal breast tissue from patients with or without breast cancer. The expression of CYPs was down-regulated in the tumor tissue. The clinical significance of CYP alterations in breast cancer will need further characterization.

Objective: We examined plasma levels of carotenoids, tocopherols, and total antioxidant activity in women before and after dietary intervention to reduce fat and/or energy intakes. Dietary fat and energy may affect intake and bioavailability of carotenoids and tocopherols, and these micronutrient levels in turn can contribute to the antioxidant capacity of plasma. Methods: Women were randomized onto one of four diets for 12 wk: non-intervention, low fat (15% of energy from fat with maintenance of energy intake), low energy (25% energy reduction with maintenance of percentage of energy from fat), and combined low fat and low energy. Fasting plasma was available for analysis from a subset ( n = 41) of women enrolled in the study. Results: Levels of carotenoids and tocopherols did not change significantly over 12 wk on any diet arm, despite a modest but statistically significant increase in fruit and vegetable intake in the women following the low-fat diet (from 3.3 to 5.2 servings/d excluding potatoes). Levels of Trolox-equivalent antioxidant capacity (TEAC), total cholesterol, and two major plasma antioxidants (urate and bilirubin) also did not change significantly. Of the individual micronutrients measured, lycopene and lutein/zeaxanthin correlated most strongly with TEAC values, and the correlation with lycopene was statistically significant before intervention. Conclusions: The decreases in dietary fat and energy intakes in this study were quite large, but this did not appear to have detrimental effects on plasma micronutrient levels, nor did it appreciably affect plasma antioxidants. Because lycopene levels were significantly associated with plasma TEAC before intervention, interventions that increase levels of lycopene might be more likely to increase the antioxidant capacity of plasma.

To study the molecular mechanisms by which drug resistance develops, we compared DU145 humanprostate cancer cells with a subline selected for resistance to camptothecin. Differences in gene expression level were assessed by hybridizing the two cell types against each other using quadruplicate "Oncochip" cDNA microarrays that included 1648 cancer-related genes. Expression levels differing by a factor of1.5 were detected for 181 of the genes. These differences were judged statistically reliable on the basis of a stratum-adjusted Kruskal-Wallis test, after taking into account a dye-dependent variable. The 181 expression-altered genes included a larger than expected number of the "apoptosis-related" genes (P = 0.04). To assess whether this observation reflected a generalized resistance of RCO.1 to apoptosis, we exposed the cells to a range of stresses (cisplatin, staurosporine, UV, ionizing radiation, and serum starvation) and found greatly reduced apoptotic responses for RC0.1 (relative to DU145) using flow cytometric Annexin V and terminal deoxynucleotidyl transferase-mediated nick end labeling assays. We next examined the apoptosis-related genes in the context of a molecular interaction map and found expression differences in the direction "expected" on the basis of the apoptosis-resistance of RC0.1 for BAD, caspase-6, and genes that signal via the Akt pathway. Exposure of the cells to wortmannin, an inhibitor of the Akt effector phosphatidylinositol 3-kinase, provided functional support for involvement of the Akt pathway. However, closer examination of the molecular interaction map revealed a paradox: many of the expression differences observed for apoptosis-related genes were in the direction "contrary" to that expected given the resistance of RC0.1. The map indicated that most of these unexpected expression differences were associated with genes involved in the nuclear factor kappa B and transforming growth factor beta pathways. Overall, the patterns that emerged suggested a two-step model for the selection process that led to resistance in RC0.1 cells. The first hypothesized step would involve a decrease in apoptotic susceptibility through changes in the apoptosis-control machinery associated with the Bcl-2 and caspase gene families, and also in antiapoptotic pathways operating through Akt/PKB. The second step would involve changes in multifunctional upstream genes (including some genes in the nuclear factor kappa B and transforming growth factor beta pathways) that can facilitate apoptosis but that would also tend to contribute to cell proliferation in the presence of drug. Thus, we propose that a downstream blockade of apoptosis was "permissive" for the selection of upstream pathway changes that would otherwise have induced apoptosis. This model is analogous to one suggested previously for the relationship between oncogene function and apoptosis in carcinogenesis.

Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. A different approach is described, based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms., Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. We describe here a different approach based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms. The result described here for the NCI-60 cancer cell lines is a consensus set of genes that give similar profiles on spotted cDNA arrays and Affymetrix oligonucleotide chips. Global concordance is parameterized by a 'correlation of correlations' coefficient.

To compare the effects of low-fat, low-energy and combination low-fat/low-energy intervention on changes in six anthropometric measures in Caucasian and African-American free-living women.The effects of dietary counseling strategies for fat and/or energy reduction were examined on anthropometric measures in 86 pre-menopausal women, average BMI of 28 kg/m2, who participated in a 12-week intervention trial called the Women's Diet Study. The dietary goals were 15% of energy from fat and/or 25% reduction in energy intake, relative to reported baseline intake, using a 2 x 2 factorial design. Analysis of covariance models were constructed to evaluate changes in anthropometric measures over the 12 weeks of study.The biggest difference by race was in women who were relatively heavier at baseline, in which case African-American women lost significantly less weight but decreased their waist:hip ratio to a significantly greater extent than Caucasian women. With regard to the effects of diet arm, weight loss varied depending on baseline weight, and in women with higher baseline weights, the combination low-fat/low-energy diet resulted in the most weight loss (6.7 kg, p0.05). Decreases in the other anthropometric measures at week 12 were more uniform across diet arms and did not depend on baseline values. After controlling for previous weight history and race, the decreases in BMI, percent body fat and waist circumference after 12 weeks were statistically equivalent with the low-fat, low-energy or combination low-fat/low-energy diets. The relatively greater decreases in percent body fat and waist circumference with the combination diet versus the low-fat or low-energy diets were not statistically significant.The low-fat, low-energy and combination diets all resulted in similar and statistically significant decreases in BMI, percent body fat and waist circumference over 12 weeks of intervention. The extent of weight loss, however, varied depending on baseline weight, and the combination diet was the only intervention to result in significant weight loss for women who were heavier at baseline. This indicates that, although there may be an advantage for reducing dietary fat in initially heavier women, any of these counseling strategies could be effective for improving anthropometric predictors of health risks associated with overweight status. This is useful since flexibility in dietary choices may facilitate adherence to dietary counseling in some individuals.

Previously, we have demonstrated that Interleukin-4 (IL-4) receptor alpha (IL-4Rα) is overexpressed in bladder cancer biopsy specimens and its expression level correlates with the grade and stage of disease. Based on these observations, it is proposed that IL-4Rα is a prognostic biomarker for bladder cancer. To target IL-4Rα, we have developed a recombinant chimeric fusion immunotoxin, which consists of circularly permuted IL-4 and truncated Pseudomonas exotoxin (IL-4-PE) [1]. Here we demonstrate that IL-4-PE is highly cytotoxic to eight bladder cancer cell lines in vitro. The cytotoxicity by IL-4-PE was mediated in a concentration dependent manner and this cytotoxicity was receptor specific as excess IL-4 inhibited cytotoxicity mediated by IL-4-PE. IL-4-PE immunotoxin also killed bladder cancer colonies in a concentration dependent manner in a clonogenic assay. We developed three subcutaneous tumor models in athymic nude mice using three different bladder cancer cell lines (UM-UC-3, SW780 and 5637), which are sensitive to IL-4-PE at a variable degree. These mice were treated with 50 μg/kg, 100 μg/kg of IL-4-PE immunotoxin or vehicle-control intratumorally and monitored for tumor growth and survival. IL-4-PE effectively caused regression of tumors by 70% in all three tumor models compared to vehicle control mice. Responding animals showed complete regression of tumors in 58% of mice at the highest dose in UM-UC-3 tumor model and 54% in SW780 tumor model. Overall, all responding animals showed >8 week longer survival compared to control mice. IL-4-PE immunotoxin at both doses did not show any visible toxicity when administrated intratumorally. Similar safety profile has been observed in the clinic when IL-4-PE was administered intratumorally in glioma trial [2]. Taken together our results demonstrate that IL-4Rα in bladder cancer is a prognostic biomarker and in addition it provides an excellent target for immunotherapy. Additional studies are ongoing to target IL-4Rα with other immunotherapeutic approaches such as cancer vaccines and adoptive cell transfer immunotherapy.

Antioxidant micronutrients found in fruits and vegetables have been shown in numerous studies to be protective against cancer. There is limited information on the relationship between blood antioxidant micronutrient levels and cancer among ethnic minorities. We conducted a pilot case-control study to evaluate the potential for accrual to a study of the association of plasma levels of beta-carotene, retinol, lycopene, alpha-tocopherol, and gamma-tocopherol with breast cancer risk among African American and Caucasian women seen at a large university medical center in Detroit. Cases included women with newly diagnosed invasive breast cancer who had not yet had any cancer-related therapy and who were age-matched to controls within 5 years. Plasma levels of micronutrients were analyzed by high-pressure liquid chromatography. Compared to the expected accrual based on cancer registry data, only 26% (11/42) of African American women with breast cancer enrolled, while 100% (16/16) of Caucasian cases enrolled. Control women were quickly accrued with only a 6% refusal rate. Among African American women, there was a weak inverse association between plasma lycopene levels and breast cancer risk, with a mean level of 0.17mgr;mol/L (SD = 0.18) among cases, and 0.24mgr;mol/L (SD = 0.18) among controls (p = 0.09). There was a weak direct association between plasma retinol levels and breast cancer risk among African American women, with a mean retinol level of 2.37mgr;mol/L (SD = 0.73) among cases and 1.98mgr;mol/L (SD = 0.49) among controls (p = 0.132). The interaction effect of race and lycopene was statistically significant (p = 0.048). Among the lowest lycopene tertile, the risk of breast cancer among Caucasian women was 0.76 and the risk of breast cancer among African American women was 2.29, although these odds ratios were not statistically significant. Our recruitment efforts were largely successful among Caucasian cases and controls, and African American controls, but were unsuccessful among African American cases. The results suggest a possible relationship between plasma lycopene level and breast cancer among African American women, but these results should be confirmed by a larger, more definitive study.

Bone marrow (BM) angiogenesis has been associated with multiple myeloma (MM) progression. Here we demonstrate that oncogenic c-Myc, also prominently associated with adverse prognosis in MM, regulates Hif-1α promoter activity, Hif-1alpha protein levels, and consequently the expression of pro-angiogenic target genes such as VEGF in MM cells. As observed with c-Myc knockdown, anti-MM agents with known anti-angiogenic activity including bortezomib, lenalidomide, and enzastaurin also downregulate Hif-1alpha and VEGF. Moreover, tyrophostin adaphostin induces similar effects, associated with anti-angiogenic activity, in a zebrafish model. The correlation between c-Myc, Hif-1alpha and tumor angiogenesis was further confirmed in a xenograft mouse model of human MM. Mechanistically, our in vitro data show that oncogenic c-Myc stabilizes caspase-8, and thereby protects Hif-1alpha against caspase-8- dependent degradation and attenuation of VEGF secretion. These sequelae also contribute to enhanced VEGF secretion triggered by MM cell-bone marrow stromal cell binding. Indeed, conditioned media from adaphostin- treated co-cultures inhibit endothelial cell growth and tubule formation. In addition, HIF1alpha gene demonstrated significant increased expression (p=0.02, Mann Whitney test) in tumor cells versus plasma cells derived from healthy donors. Importantly, when tested on a dataset of 559 patients, a significant link between HIF1alpha overexpression and poor prognosis was found (p=0,0069). These data further point to the possible relevance of HIF1alpha in the progression of a subset of MM patients. In summary, our data provide strong evidence of a key role of Hif-1alpha in MM angiogenesis and the therapeutic potential of specific Hif-1alpha and c-Myc inhibitors. Moreover they demonstrate additional biologic sequelae of novel MM therapies.

GoMiner, a program package that organizes lists of 'interesting' genes for biological interpretation in the context of the Gene Ontology, has been developed., We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources.