Biomedical subjects

D Siegmund

Publications and source records attributed to D Siegmund.

At least 19 recordsLinked to original sources

PubMed2006

TRAIL promotes metastasis of human pancreatic ductal adenocarcinoma.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has attracted considerable attention for its potential use in tumor therapy, as some recombinant variants of this ligand induce apoptosis in tumor cells without harming most normal cells. Here, we show that TRAIL strongly induces the expression of the proinflammatory cytokines interleukin-8 and monocyte chemoattractant protein 1 and enhances the invasion of apoptosis-resistant pancreatic ductal adenocarcinoma cells in vitro by upregulation of the urokinase-type plasminogen activator expression. Most importantly, we also demonstrate for the first time that TRAIL treatment results in strongly increased distant metastasis of pancreatic tumors in vivo. We orthotopically transplanted human pancreatic ductal adenocarcinoma cells to the pancreata of severe combined immunodeficiency mice and observed a dramatic increase in metastatic spread including a sixfold increase in the volume and fourfold increase in the number of liver metastases upon TRAIL treatment. Our results point to the necessity to carefully evaluate in vivo side effects of TRAIL and to select therapy conditions that not only enhance apoptosis induction but in addition prevent proinvasive and proinflammatory non-apoptotic TRAIL signaling.

Animals↗

PubMed2006

QTL mapping under ascertainment.

Mapping quantitative trait loci (QTL) using ascertained sibships is discussed. It is shown that under the standard normality assumption of variance components analysis the efficient scores are unchanged by ascertainment, and two different schemes of ascertainment correction suggested in the literature are asymptotically equivalent. The use of conditional maximum likelihood estimators derived under the normality assumption to estimate nuisance parameters is shown to result in only a small loss of power compared to the case of known parameters, even when the distribution of phenotypes is non-normal and/or the ascertainment criterion is ill defined.

Chromosome Mapping↗

PubMed2004

Mapping quantitative traits with random and with ascertained sibships.

Use of a robust score statistic based on a variance components model to map quantitative trait loci in randomly sampled pedigrees is reviewed. Sibships ascertained through a single proband are discussed. Under a standard assumption of multivariate normality, two suggested methods of ascertainment correction are shown to be asymptotically equivalent when the number of sibships is large.

Chromosome Mapping↗

PubMed2003

Statistical analysis of direct identity-by-descent mapping.

Genetic mismatch scanning has been suggested as a method for using affected pairs of ostensibly unrelated but putatively distantly related affecteds in isolated populations to map disease genes. We model the regions of identity-by-descent of these affected pairs as a continuous time two state process with unknown parameters that depend on the (unknown) relationships, and we estimate the unknown parameters from the observed data. Simulated data involving pairs of first to fourth cousins show that the procedure thus obtained has properties similar, albeit slightly inferior, to the case where the relationships of the affected pairs, hence the parameters governing the processes, are known.

Chromosome Mapping↗

PubMed2002

Upward bias in estimation of genetic effects.

Because of the large number of tests for linkage that are performed in genome scans, the naive estimator of the size of a genetic effect in cases of borderline significance can be inflated and lead to unrealistic expectations for successful replication. As a remedy, this report proposes lower confidence limits that account for the multiple comparisons of the genome scan.

Bias↗

PubMed2001

Tumor necrosis factor (TNF) and phorbol ester induce TNF-related apoptosis-inducing ligand (TRAIL) under critical involvement of NF-kappa B essential modulator (NEMO)/IKKgamma.

We show that tumor necrosis factor (TNF) and phorbol 12-myristate 13-acetate (PMA) induce TNF-related apoptosis-inducing ligand (TRAIL) in T cells. In cells deficient for NF-kappaB essential modulator (NEMO)/IKKgamma, an essential component of the NF-kappaB-inducing I-kappaB kinase (IKK) complex, induction of TRAIL expression was completely abrogated but was recovered in cells restored for IKKgamma expression. In cells deficient for receptor-interacting protein expression TNF, but not PMA-induced TRAIL expression was blocked. Inhibition of protein synthesis with cycloheximide blocked PMA, but not TNF-induced up-regulation of TRAIL. As both TNF and PMA rapidly induce NF-kappaB activation this suggests that NEMO/IKKgamma-dependent activation of the NF-kappaB pathway is necessary but not sufficient for up-regulation of TRAIL in T cells. The capability of the NF-kappaB pathway to induce the potent death ligand TRAIL may explain the reported proapoptotic features of this typically antiapoptotic pathway.

Apoptosis Regulatory Proteins↗

PubMed2001

Fas-associated death domain protein (FADD) and caspase-8 mediate up-regulation of c-Fos by Fas ligand and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) via a FLICE inhibitory protein (FLIP)-regulated pathway.

Fas, a death domain-containing member of the tumor necrosis factor receptor family and its ligand FasL have been predominantly studied with respect to their capability to induce cell death. However, a few studies indicate a proliferation-inducing signaling activity of these molecules too. We describe here a novel signaling pathway of FasL and the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) that triggers transcriptional activation of the proto-oncogene c-fos, a typical target gene of mitogenic pathways. FasL- and TRAIL-mediated up-regulation of c-Fos was completely dependent on the presence of Fas-associated death domain protein (FADD) and caspase-8, but caspase activity seemed to be dispensable as a pan inhibitor of caspases had no inhibitory effect. Upon overexpression of the long splice form of cellular FADD-like interleukin-1-converting enzyme (FLICE) inhibitory protein (cFLIP) in Jurkat cells, FasL- and TRAIL-induced up-regulation of c-Fos was almost completely blocked. The short splice form of FLIP, however, showed a rather stimulatory effect on c-Fos induction. Together these data demonstrate the existence of a death receptor-induced, FADD- and caspase-8-dependent pathway leading to c-Fos induction that is inhibited by the long splice form FLIP-L.

Adaptor Proteins, Signal Transducing↗

PubMed2001

p53 upregulates cFLIP, inhibits transcription of NF-kappaB-regulated genes and induces caspase-8-independent cell death in DLD-1 cells.

One of the main functions of the tumor suppressor p53 is the induction of programmed cell death. Here we investigated in detail the molecular mechanisms that underlay p53 transactivation-dependent apoptosis in the human colon cancer cell line DLD-1. Although p53 upregulated the death receptors Fas, TRAIL-R1 and TRAIL-R2 in this cell line, p53-induced cell death occurred without detectable caspase-8 activation whereas, activation of caspase-9 and caspase-3 was readily observed. In addition to the upregulation of death receptors, p53 induced the pro-apoptotic Bcl-2 family members Bik and Bak and downregulated the anti-apoptotic Bcl-xL protein. Moreover, in RNase protection assay analyses as well as in reporter gene analyses we found a p53-dependent upregulation of the death receptor-inhibitory protein cFLIP. Together, these data argue for a p53-mediated activation of the mitochondrial pathway of apoptosis. In contrast to recently published data obtained in different cellular systems, there was no evidence for an essential role of NF-kappaB in p53-induced cell death. Moreover, induction of p53 interfered with TNF-induced NF-kappaB activation independently from apoptosis-induction.

Apoptosis↗

PubMed2001

Is peak height sufficient?

The suggestion that more power can be obtained from a genome scan by consideration of "peak width" in addition to "peak height" has been controversial. Regarding this question from the viewpoint of smoothing, one finds that to the extent that smoothing increases the informativeness of individual markers it is possible to obtain increased power; but for markers that are fully informative the value of smoothing is questionable.

Chromosome Mapping↗

PubMed2001

Approximate p-values for local sequence alignments: numerical studies.

Siegmund and Yakir (2000) have given an approximate p-value when two independent, identically distributed sequences from a finite alphabet are optimally aligned based on a scoring system that rewards similarities according to a general scoring matrix and penalizes gaps (insertions and deletions). The approximation involves an infinite sequence of difficult-to-compute parameters. In this paper, it is shown by numerical studies that these reduce to essentially two numerically distinct parameters, which can be computed as one-dimensional numerical integrals. For an arbitrary scoring matrix and affine gap penalty, this modified approximation is easily evaluated. Comparison with published numerical results show that it is reasonably accurate.

Models, Molecular↗

PubMed2001

Mapping quantitative trait loci in oligogenic models.

We discuss strategies for mapping quantitative trait loci with emphasis on certain issues of study design that have recently received attention: e.g. genotyping only selected pedigrees and the comparative value of large pedigrees versus sib pairs. We use a standard variance components model and a parametrization of the genetic effects in which the 'segregation' parameters are locally orthogonal to the 'linkage' parameters. This permits simple explicit expressions for the expectation of the score statistic, which we use to compare the power of different strategies. We also discuss robustness of the score statistic.

Journal Article↗

PubMed2001

NF-kappaB inducers upregulate cFLIP, a cycloheximide-sensitive inhibitor of death receptor signaling.

The caspase 8 homologue FLICE-inhibitory protein (cFLIP) is a potent negative regulator of death receptor-induced apoptosis. We found that cFLIP can be upregulated in some cell lines under critical involvement of the NF-kappaB pathway, but NF-kappaB activation was clearly not sufficient for cFLIP induction in all cell lines. Treatment of SV80 cells with the proteasome inhibitor N-benzoyloxycarbonyl (Z)-Leu-Leu-leucinal (MG-132) or geldanamycin, a drug interfering with tumor necrosis factor (TNF)-induced NF-kappaB activation, inhibited TNF-induced upregulation of cFLIP. Overexpression of a nondegradable IkappaBalpha mutant (IkappaBalpha-SR) or lack of IkappaB kinase gamma expression completely prevented phorbol myristate acetate-induced upregulation of cFLIP mRNA in Jurkat cells. These data point to an important role for NF-kappaB in the regulation of the cFLIP gene. SV80 cells normally show resistance to TNF-related apoptosis-inducing ligand (TRAIL) and TNF, as apoptosis can be induced only in the presence of low concentrations of cycloheximide (CHX). However, overexpression of IkappaBalpha-SR rendered SV80 cells sensitive to TRAIL-induced apoptosis in the absence of CHX, and cFLIP expression was able to reverse the proapoptotic effect of NF-kappaB inhibition. Western blot analysis further revealed that cFLIP, but not TRAF1, A20, and cIAP2, expression levels rapidly decrease upon CHX treatment. In conclusion, these data suggest a key role for cFLIP in the antiapoptotic response of NF-kappaB activation.

Antibodies, Monoclonal↗

PubMed1999

Statistical methods for mapping quantitative trait loci from a dense set of markers.

Lander and Botstein introduced statistical methods for searching an entire genome for quantitative trait loci (QTL) in experimental organisms, with emphasis on a backcross design and QTL having only additive effects. We extend their results to intercross and other designs, and we compare the power of the resulting test as a function of the magnitude of the additive and dominance effects, the sample size and intermarker distances. We also compare three methods for constructing confidence regions for a QTL: likelihood regions, Bayesian credible sets, and support regions. We show that with an appropriate evaluation of the coverage probability a support region is approximately a confidence region, and we provide a theroretical explanation of the empirical observation that the size of the support region is proportional to the sample size, not the square root of the sample size, as one might expect from standard statistical theory.

Chromosome Mapping↗

PubMed1998

Multipoint linkage analysis using affected relative pairs and partially informative markers.

Linkage analysis is a method of identifying regions of the human genome harboring genes affecting the risk for a particular disease. It works by finding chromosomal segments inherited by affected relatives from a common ancestor (i.e., identical by descent or IBD) in excess of that expected by chance. Two complicating factors are that only a relatively small number of genomic locations (marker loci) are examined and the number of distinct realizations (alleles) at each marker is not large. Hence, unambiguous determination of IBD is impossible for any genomic location without additional information. Assuming data from a set of mapped, partially informative markers, we evaluate the effectiveness of a method that analyzes the array of markers on each chromosome jointly (multipoint methods) as a function of the informativeness and density of the markers. For the special case of pairs of half siblings whose parents are also typed, a combination of analysis and simulation is used to obtain insight into the problem of setting thresholds to control the false-positive error rate. Approximations are given for the power, and guidelines are developed to help describe the trade-offs between marker density and informativeness.

Biometry↗

PubMed1997

Combining information within and between pedigrees for mapping complex traits.

This paper is concerned with efficient strategies for gene mapping using pedigrees containing small numbers of affecteds and identity-by-descent data from closely spaced markers throughout the genome. Particular attention is paid to additive traits involving phenocopies and/or locus heterogeneity. For a sample of pedigrees containing a particular configuration of affecteds, e.g., pairs of siblings together with a first cousin, we use a likelihood analysis to find 1-df statistics that are very efficient over a broad range of penetrances and allele frequencies. We identify configurations of affecteds that are particularly powerful for detecting linkage, and we show how pedigrees containing different numbers and configurations of affecteds can be efficiently combined in an overall test statistic.

Chromosome Mapping↗

PubMed1995

Statistical methods for linkage analysis of complex traits from high-resolution maps of identity by descent.

A multilocus model for complex traits is described that generalizes the additive and multiplicative models and hence allows simultaneously for both heterogeneity and gene interaction (epistasis). Statistical methods of linkage analysis are discussed under the assumption that identity by descent data from a dense set of polymorphic markers are available. Three methods, single locus search, simultaneous search and conditional search, are described and compared.

Chromosome Mapping↗

PubMed1994

Oscillatory penicillin formation in carbon-limited batch fermentations of Penicillium chrysogenum.

Circadian oscillations of penicillin productivity with a period of 22 +/- 2 h have been observed in carbon-limited batch fermentations of Penicillium chrysogenum. The specific penicillin production rate oscillated with an amplitude of 20 to 100% of its mean value, depending on the growth rate of the active (respiring and producting) biomass. In spite of this, the penicillin concentration increased almost linearly if the optimum growth rate of the active biomass for maximum penicillin productivity was maintained using microprocessor control. This apparently inconsistent behaviour of the fungus is discussed on the basis of chaos theory.

Biotechnology↗

PubMed1993

Gaussian models for genetic linkage analysis using complete high-resolution maps of identity by descent.

Gaussian-process models are developed to detect genetic linkage using complete high-resolution maps of identity by descent between affected relative pairs. Approximations are given for the significance level and power of the likelihood-ratio test of no linkage and for likelihood-ratio confidence regions for trait loci. The sample sizes required to detect linkage by using different classes of affected relative pairs are compared, and the problem of combining data from different classes of relatives is discussed.

Genetic Linkage↗