Biomedical subjects

Charles Kooperberg

Publications and source records attributed to Charles Kooperberg.

49 records · Page 3Linked to original sources

PubMed2003

Combining biomarkers to detect disease with application to prostate cancer.

In early detection of disease, combinations of biomarkers promise improved discrimination over diagnostic tests based on single markers. An example of this is in prostate cancer screening, where additional markers have been sought to improve the specificity of the conventional Prostate-Specific Antigen (PSA) test. A marker of particular interest is the percent free PSA. Studies evaluating the benefits of percent free PSA reflect the need for a methodological approach that is statistically valid and useful in the clinical setting. This article presents methods that address this need. We focus on and-or combinations of biomarker results that we call logic rules and present novel definitions for the ROC curve and the area under the curve (AUC) that are applicable to this class of combination tests. Our estimates of the ROC and AUC are amenable to statistical inference including comparisons of tests and regression analysis. The methods are applied to data on free and total PSA levels among prostate cancer cases and matched controls enrolled in the Physicians' Health Study.

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PubMed2003

Yeast Isw1p forms two separable complexes in vivo.

There are several classes of ATP-dependent chromatin remodeling complexes, which modulate the structure of chromatin to regulate a variety of cellular processes. The budding yeast, Saccharomyces cerevisiae, encodes two ATPases of the ISWI class, Isw1p and Isw2p. Previously Isw1p was shown to copurify with three other proteins. Here we identify these associated proteins and show that Isw1p forms two separable complexes in vivo (designated Isw1a and Isw1b). Biochemical assays revealed that while both have equivalent nucleosome-stimulated ATPase activities, Isw1a and Isw1b differ in their abilities to bind to DNA and nucleosomal substrates, which possibly accounts for differences in specific activities in nucleosomal spacing and sliding. In vivo, the two Isw1 complexes have overlapping functions in transcriptional regulation of some genes yet distinct functions at others. In addition, these complexes show different contributions to cell growth at elevated temperatures.

Adenosine Triphosphatases↗

PubMed2002

Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing.

Replication of the genome before mitotic cell division is a highly regulated process that ensures the fidelity of DNA duplication. DNA replication initiates at specific locations, termed origins of replication, and progresses in a defined temporal order during the S phase of the cell cycle. The relationship between replication timing and gene expression has been the subject of some speculation. A recent genome-wide analysis in Saccharomyces cerevisiae showed no association between replication timing and gene expression. In higher eukaryotes, the limited number of genomic loci analyzed has not permitted a firm conclusion regarding this association. To explore the relationship between DNA replication and gene expression in higher eukaryotes, we developed a strategy to measure the timing of DNA replication for thousands of genes in a single DNA array hybridization experiment. Using this approach, we generated a genome-wide map of replication timing for Drosophila melanogaster. Moreover, by surveying over 40% of all D. melanogaster genes, we found a strong correlation between DNA replication early in S phase and transcriptional activity. As this correlation does not exist in S. cerevisiae, this interplay between DNA replication and transcription may be a unique characteristic of higher eukaryotes.

Animals↗

PubMed2002

Estimating the statistical significance of gene expression changes observed with oligonucleotide arrays.

We present a simple method to assign approximate P-values to gene expression changes detected with Affymetrix oligonucleotide arrays and software. The method pools data for groups of genes and a small number of like-to-like comparisons in order to estimate the significance of changes observed for single genes in comparisons of experimental interest. Statistical significance levels are based on the observed variability in the fractional majority of probe pairs that indicate increasing or decreasing differential expression in comparisons of technical replicates. From this reference distribution or error model, we compute the expected frequency for fractional majorities in comparisons for N > or = 2. These computed distributions are the source of P-value estimates for changes seen in the experimental comparisons. The method is intended to complement the Affymetrix software and to rationalize gene selection for experimental designs involving limited replication.

Animals↗

PubMed2002

Evaluating test statistics to select interesting genes in microarray experiments.

A randomization procedure to evaluate the significance level and the false-discovery rate in complex microarray experiments is proposed. A related graph can be used to compare different test statistics that can be used to analyze the same experiment. This graph is closely related to receiver operator characteristic (ROC) curves. The proposed method is applied to a subset of the data from a cell-line experiment related to Huntington's disease. A small simulation study compares the effectiveness of the proposed procedure with the significance analysis of microarrays (SAM) procedure.

Computer Simulation↗

PubMed2002

Dysregulation of gene expression in the R6/2 model of polyglutamine disease: parallel changes in muscle and brain.

Previous analyses of gene expression in a mouse model of Huntington's disease (R6/2) indicated that an N-terminal fragment of mutant huntingtin causes downregulation of striatal signaling genes and particularly those normally induced by cAMP and retinoic acid. The present study expands the regional and temporal scope of this previous work by assessing whether similar changes occur in other brain regions affected in Huntington's disease and other polyglutamine diseases and by discerning whether gene expression changes precede the appearance of disease signs. Oligonucleotide microarrays were employed to survey the expression of approximately 11,000 mRNAs in the cerebral cortex, cerebellum and striatum of symptomatic R6/2 mice. The number and nature of gene expression changes were similar among these three regions, influenced as expected by regional differences in baseline gene expression. Time-course studies revealed that mRNA changes could only reliably be detected after 4 weeks of age, coincident with development of early pathologic and behavioral changes in these animals. In addition, we discovered that skeletal muscle is also a target of polyglutamine-related perturbations in gene expression, showing changes in mRNAs that are dysregulated in brain and also muscle-specific mRNAs. The complete dataset is available at www.neumetrix.info.

Animals↗

PubMed2002

Polyglutamine and transcription: gene expression changes shared by DRPLA and Huntington's disease mouse models reveal context-independent effects.

Recent evidence indicates that transcriptional abnormalities may play an important role in the pathophysiology of polyglutamine diseases. In the present study, we have explored the extent to which polyglutamine-related changes in gene expression may be independent of protein context by comparing mouse models of dentatorubral-pallidoluysian atrophy (DRPLA) and Huntington's disease (HD). Microarray gene expression profiling was conducted in mice of the same background strain in which the same promoter was employed to direct the expression of full-length atrophin-1 or partial huntingtin transproteins (At-65Q or N171-82Q mice). A large number of overlapping gene expression changes were observed in the cerebella of At-65Q and N171-82Q mice. Six of the gene expression changes common to both huntingtin and atrophin-1 transgenic mice were also observed in the cerebella of mouse models expressing full-length mutant ataxin-7 or the androgen receptor. These results demonstrate that some of the gene expression effects of expanded polyglutamine proteins occur independently of protein context.

Animals↗

PubMed2002

Increased huntingtin protein length reduces the number of polyglutamine-induced gene expression changes in mouse models of Huntington's disease.

Both transcriptional dysregulation and proteolysis of mutant huntingtin (htt) are postulated to be important components of Huntington's disease (HD) pathogenesis. In previous studies, we demonstrated that transgenic mice that express short mutant htt fragments containing 171 or fewer N-terminal residues (R6/2 and N171-82Q mice) recapitulate many of the mRNA changes observed in human HD brain. To examine whether htt protein length influences the ability of its expanded polyglutamine domain to alter gene expression, we conducted mRNA profiling analyses of mice that express an extended N-terminal fragment (HD46, HD100; 964 amino acids) or full-length (YAC72; 3144 amino acids) mutant htt transprotein. Oligonucleotide microarray analyses of HD46 and YAC72 mice identified fewer differentially expressed mRNAs than were seen in transgenic mice expressing short N-terminal mutant htt fragments. Histologic analyses also detected limited changes in these mice (small decreases in adenosine A2a receptor mRNA and dopamine D2 receptor binding in HD100 animals; small increases in dopamine D1 receptor binding in HD46 and HD100 mice). Neither HD46 nor YAC72 mice exhibited altered mRNA levels similar to those observed previously in R6/2 mice, N171-82Q mice or human HD patients. These findings suggest that htt protein length influences the ability of an expanded polyglutamine domain to alter gene expression. Furthermore, our findings suggest that short N-terminal fragments of mutant htt might be responsible for the gene expression alterations observed in human HD brain.

Animals↗

PubMed2002

Early transcriptional profiles in huntingtin-inducible striatal cells by microarray analyses.

Gene expression studies conducted with mouse models of Huntington's disease (HD) have revealed profound modifications in gene transcription. However, the complexity of in vivo tissue hampers definition of very early transcriptional modifications and does not allow discrimination between cell-autonomous changes and those resulting from intercellular activity processes. To identify early, cell-autonomous transcriptional changes, we compared gene expression profiles of clonal striata-derived cells expressing different N-terminal 548-amino-acid huntingtin fragments (with 26, 67, 105 or 118 glutamines) under the control of a doxycycline-regulated promoter. In these cells, mutant huntingtin did not form aggregates or cause cell death; therefore, the gene expression profiles report transcriptional changes reflecting early pathogenic events. We found that genes involved in cell signaling, transcription, lipid metabolism and vesicle trafficking were affected, in some cases, within 12 hours of mutant protein induction. Interestingly, this study revealed differential expression of a number of genes involved in cholesterol and fatty acid metabolism, suggesting that these metabolic pathways may play a role in HD pathogenesis.

Animals↗

PubMed2002

Risks and benefits of estrogen plus progestin in healthy postmenopausal women: principal results From the Women's Health Initiative randomized controlled trial.

CONTEXT: Despite decades of accumulated observational evidence, the balance of risks and benefits for hormone use in healthy postmenopausal women remains uncertain. OBJECTIVE: To assess the major health benefits and risks of the most commonly used combined hormone preparation in the United States. DESIGN: Estrogen plus progestin component of the Women's Health Initiative, a randomized controlled primary prevention trial (planned duration, 8.5 years) in which 16608 postmenopausal women aged 50-79 years with an intact uterus at baseline were recruited by 40 US clinical centers in 1993-1998. INTERVENTIONS: Participants received conjugated equine estrogens, 0.625 mg/d, plus medroxyprogesterone acetate, 2.5 mg/d, in 1 tablet (n = 8506) or placebo (n = 8102). MAIN OUTCOMES MEASURES: The primary outcome was coronary heart disease (CHD) (nonfatal myocardial infarction and CHD death), with invasive breast cancer as the primary adverse outcome. A global index summarizing the balance of risks and benefits included the 2 primary outcomes plus stroke, pulmonary embolism (PE), endometrial cancer, colorectal cancer, hip fracture, and death due to other causes. RESULTS: On May 31, 2002, after a mean of 5.2 years of follow-up, the data and safety monitoring board recommended stopping the trial of estrogen plus progestin vs placebo because the test statistic for invasive breast cancer exceeded the stopping boundary for this adverse effect and the global index statistic supported risks exceeding benefits. This report includes data on the major clinical outcomes through April 30, 2002. Estimated hazard ratios (HRs) (nominal 95% confidence intervals [CIs]) were as follows: CHD, 1.29 (1.02-1.63) with 286 cases; breast cancer, 1.26 (1.00-1.59) with 290 cases; stroke, 1.41 (1.07-1.85) with 212 cases; PE, 2.13 (1.39-3.25) with 101 cases; colorectal cancer, 0.63 (0.43-0.92) with 112 cases; endometrial cancer, 0.83 (0.47-1.47) with 47 cases; hip fracture, 0.66 (0.45-0.98) with 106 cases; and death due to other causes, 0.92 (0.74-1.14) with 331 cases. Corresponding HRs (nominal 95% CIs) for composite outcomes were 1.22 (1.09-1.36) for total cardiovascular disease (arterial and venous disease), 1.03 (0.90-1.17) for total cancer, 0.76 (0.69-0.85) for combined fractures, 0.98 (0.82-1.18) for total mortality, and 1.15 (1.03-1.28) for the global index. Absolute excess risks per 10 000 person-years attributable to estrogen plus progestin were 7 more CHD events, 8 more strokes, 8 more PEs, and 8 more invasive breast cancers, while absolute risk reductions per 10 000 person-years were 6 fewer colorectal cancers and 5 fewer hip fractures. The absolute excess risk of events included in the global index was 19 per 10 000 person-years. CONCLUSIONS: Overall health risks exceeded benefits from use of combined estrogen plus progestin for an average 5.2-year follow-up among healthy postmenopausal US women. All-cause mortality was not affected during the trial. The risk-benefit profile found in this trial is not consistent with the requirements for a viable intervention for primary prevention of chronic diseases, and the results indicate that this regimen should not be initiated or continued for primary prevention of CHD.

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PubMed2002

Distributions of beta sheets in proteins with application to structure prediction.

We recently developed the Rosetta algorithm for ab initio protein structure prediction, which generates protein structures from fragment libraries using simulated annealing. The scoring function in this algorithm favors the assembly of strands into sheets. However, it does not discriminate between different sheet motifs. After generating many structures using Rosetta, we found that the folding algorithm predominantly generates very local structures. We surveyed the distribution of beta-sheet motifs with two edge strands (open sheets) in a large set of non-homologous proteins. We investigated how much of that distribution can be accounted for by rules previously published in the literature, and developed a filter and a scoring method that enables us to improve protein structure prediction for beta-sheet proteins. Proteins 2002;48:85-97.

Algorithms↗

PubMed2002

Improved background correction for spotted DNA microarrays.

Most microarray scanning software for glass spotted arrays provides estimates for the intensity for the "foreground" and "background" of two channels for every spot. The common approach in further analyzing such data is to first subtract the background from the foreground for each channel and to use the ratio of these two results as the estimate of the expression level. The resulting ratios are, after possible averaging over replicates, the usual inputs for further data analysis, such as clustering. If, with this background correction procedure, the foreground intensity was smaller than the background intensity for a channel, that spot (on that array) yields no usable data. In this paper it is argued that this preprocessing leads to estimates of the expression that have a much larger variance than needed when the expression levels are low.

Algorithms↗

PubMedDate not supplied

Validity of self-report for fractures among a multiethnic cohort of postmenopausal women: results from the Women's Health Initiative observational study and clinical trials.

OBJECTIVE: The purpose of this study is to examine the validity of, and factors associated with, the accuracy of self-report (participant-report and proxy-report) for fractures. DESIGN: Study participants were from the Women's Health Initiative Clinical Trial and Observational Study cohorts. All women were postmenopausal; populations included American Indian, Asian/Pacific Islander, black, Hispanic, and non-Hispanic white. The average length of follow-up was 4.3 years. Self-reported fractures were adjudicated by reviewing medical records. The first adjudicated self-report of fractures for each participant was included in the analysis (n = 6,652). RESULTS: We found substantial variations in validity of self-report by the fracture site. Agreements between self-reports for single-site fractures and medical records were high for hip (78%) and forearm/wrist (81%) but relatively lower for clinical spine fractures (51%). The average confirmation rate for all single-site fractures was 71%. Misidentification of fracture sites by participants or proxy-reporters seemed to be a cause of unconfirmed self-reports. Higher confirmation rates were observed in participant-reports than in proxy-reports. Results of the multivariate analysis indicated that multiple factors, such as ethnicity, a history of osteoporosis or fractures, body mass index, years since menopause, smoking status, and number of falls in the past year were significantly (P < 0.05) related to the validity of self-report. CONCLUSION: The validity of self-reports for fracture varies by fracture sites and many other factors. The assessed validity in this study is likely conservative because some of the unconfirmed self-reports may be due to poor medical record systems. The validity of self-reports for hip and forearm/wrist fractures is high in this study, supporting their use in epidemiological studies among postmenopausal women.

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