Biomedical subjects

Ulla Hansen

Publications and source records attributed to Ulla Hansen.

15 recordsLinked to original sources

PubMed2005

Localization of tissue inhibitor of metalloproteinases 1 (TIMP-1) in human colorectal adenoma and adenocarcinoma.

Tissue inhibitor of matrix metalloproteases 1 (TIMP-1) inhibits the proteolytic activity of matrix metalloproteases and hereby prevents cancer invasion. However, TIMP-1 also possesses other functions such as inhibition of apoptosis, induction of malignant transformation and stimulation of cell-growth. We have previously demonstrated that TIMP-1 is elevated in blood from colorectal cancer patients and that high TIMP-1 levels predict poor prognosis. To clarify the role of TIMP-1 in colorectal tumorigenesis, the expression pattern of TIMP-1 in benign and malignant colorectal tumors was studied. In all of 24 cases of colorectal adenocarcinoma TIMP-1 mRNA was detected by in situ hybridization. In all cases TIMP-1 expression was found in fibroblast-like cells located at the invasive front but was seen only sporadically in normal mucosa. No TIMP-1 mRNA was seen in any of the cases in benign or malignant epithelial cells, in vascular cells or smooth muscle cells. Comparison of sections processed for TIMP-1 in situ hybridization with sections immunohistochemically stained with antibodies against TIMP-1 showed good correlation between TIMP-1 mRNA and immunoreactivity. Combining TIMP-1 in situ hybridization with immunohistochemical staining for alpha-smooth muscle actin or CD68 showed TIMP-1 mRNA in myofibroblasts but not in macrophages. TIMP-1 mRNA was detected in 2 of 7 adenomatous polyps in the adenoma area: in both cases associated with focal stromal inflammation at the epithelial-stromal interface. In conclusion, TIMP-1 expression is a rare event in benign human colon tissue but is highly expressed by myofibroblasts in association with invading colon cancer cells.

Adenocarcinoma↗

PubMed2004

High expression of endothelial cell nitric oxide synthase in peritumoral microvessels predicts increased disease-free survival in colorectal cancer.

We have previously shown that a high frequency of microvessels expressing endothelial cell nitric oxide synthase (ecNOS) in the area surrounding the primary tumor (peritumoral ecNOS-expressing microvessel density: PEMVD) is a favorable prognostic indicator in breast cancer. Studies of a retrospective material of 186 colorectal tumors (Duke's stage B) now show that PEMVD is a significant and independent prognostic indicator for disease-free survival also in these patients. These data reinforce our hypothesis that a high level of expression of ecNOS in microvessels in the tumor-adjacent area protects against tumor metastasis.

Adult↗

PubMed2004

Lineage-specific and ubiquitous biological roles of the mammalian transcription factor LSF.

Transcriptional regulation in mammalian cells is driven by a complex interplay of multiple transcription factors that respond to signals from either external or internal stimuli. A single transcription factor can control expression of distinct sets of target genes, dependent on its state of post-translational modifications, interacting partner proteins, and the chromatin environment of the cellular genome. Furthermore, many transcription factors can act as either transcriptional repressors or activators, depending on promoter and cellular contexts [Alvarez, M., Rhodes, S.J., Bidwell, J.P., 2003. Context-dependent transcription: all politics is local. Gene 313, 43-57]. Even in this light, the versatility of LSF (Late SV40 Factor) is remarkable. A hallmark of LSF is its unusual DNA binding domain, as evidenced both by lack of homology to any other established DNA-binding domains and by its DNA recognition sequence. Although a dimer in solution, LSF requires additional multimerization with itself or partner proteins in order to interact with DNA. Transcriptionally, LSF can function as an activator or a repressor. It is a direct target of an increasing number of signal transduction pathways. Biologically, LSF plays roles in cell cycle progression and cell survival, as well as in cell lineage-specific functions, shown most strikingly to date in hematopoietic lineages. This review discusses how the unique aspects of LSF DNA-binding activity may make it particularly susceptible to regulation by signal transduction pathways and may relate to its distinct biological roles. We present current progress in elucidation of both tissue-specific and more universal cellular roles of LSF. Finally, we discuss suggestive data linking LSF to signaling by the amyloid precursor protein and to Alzheimer's disease, as well as to the regulation of latency of the human immunodeficiency virus (HIV).

Animals↗

PubMed2004

Limited agreement among three global gene expression methods highlights the requirement for non-global validation.

MOTIVATION: DNA microarrays have revolutionized biological research, but their reliability and accuracy have not been extensively evaluated. Thorough testing of microarrays through comparison to dissimilar gene expression methods is necessary in order to determine their accuracy. RESULTS: We have systematically compared three global gene expression methods on all available histologically normal samples from five human organ types. The data included 25 Affymetrix high-density oligonucleotide array experiments, 23 expressed sequence tag based expression (EBE) experiments and 5 SAGE experiments. The reported gene-by-gene expression patterns showed a wide range of correlations between pairs of methods. This level of agreement was sufficient for accurate clustering of datasets from the same tissue and dissimilar methods, but highlights the need for thorough validation of individual gene expression measurements by alternate, non-global methods. Furthermore, analyses of mRNA abundance distributions indicate limitations in the EBE and SAGE methods at both high- and low-expression levels.

Algorithms↗

PubMed2004

Genomic targets of nuclear estrogen receptors.

Estrogen influences the physiology of many target tissues in both women and men. The long-term effects of estrogen are mediated predominantly by nuclear estrogen receptors (ERs) functioning as DNA-binding transcription factors. Tissue-specific responses to estrogen therefore result from regulation of different sets of genes. However, it remains perplexing as to what regulatory sequence contexts specify distinct genomic responses. First, this review classifies estrogen response sequences in mammalian target genes. Of note, around one third of known human target genes associate only indirectly with ER, through intermediary transcription factor(s). Then, computational approaches are presented both for refining direct ER-binding sites and for formulating hypotheses regarding the overall genomic expression pattern. Surprisingly, limited evolutionary conservation of specific estrogen-responsive sites is observed between human and mouse. Finally, consideration of the cellular functions of regulated human genes suggests links between particular biological roles and specific types of estrogen response elements, although with the important caveat that only a restricted set of target genes is available. These analyses support the view that specific, hormone-driven gene expression programs can result from the interplay of environmental and cellular cues with the distinct types of estrogen-response sequences.

Animals↗

PubMed2004

Detection of functional DNA motifs via statistical over-representation.

The interaction of proteins with DNA recognition motifs regulates a number of fundamental biological processes, including transcription. To understand these processes, we need to know which motifs are present in a sequence and which factors bind to them. We describe a method to screen a set of DNA sequences against a precompiled library of motifs, and assess which, if any, of the motifs are statistically over- or under-represented in the sequences. Over-represented motifs are good candidates for playing a functional role in the sequences, while under-representation hints that if the motif were present, it would have a harmful dysregulatory effect. We apply our method (implemented as a computer program called Clover) to dopamine-responsive promoters, sequences flanking binding sites for the transcription factor LSF, sequences that direct transcription in muscle and liver, and Drosophila segmentation enhancers. In each case Clover successfully detects motifs known to function in the sequences, and intriguing and testable hypotheses are made concerning additional motifs. Clover compares favorably with an ab initio motif discovery algorithm based on sequence alignment, when the motif library includes only a homolog of the factor that actually regulates the sequences. It also demonstrates superior performance over two contingency table based over-representation methods. In conclusion, Clover has the potential to greatly accelerate characterization of signals that regulate transcription.

Animals↗

PubMed2004

Site2genome: locating short DNA sequences in whole genomes.

SUMMARY: Many biological papers describe short, functional DNA sites without specifying their exact positions in the genome. We have developed a Web server that automates the tedious task of locating such sites in eukaryotic genomes, thus giving access to the context of rich annotations that are increasingly available for genome sequences. AVAILABILITY: http://zlab.bu.edu/site2genome/

Algorithms↗

PubMed2004

Finding functional sequence elements by multiple local alignment.

Algorithms that detect and align locally similar regions of biological sequences have the potential to discover a wide variety of functional motifs. Two theoretical contributions to this classic but unsolved problem are presented here: a method to determine the width of the aligned motif automatically; and a technique for calculating the statistical significance of alignments, i.e. an assessment of whether the alignments are stronger than those that would be expected to occur by chance among random, unrelated sequences. Upon exploring variants of the standard Gibbs sampling technique to optimize the alignment, we discovered that simulated annealing approaches perform more efficiently. Finally, we conduct failure tests by applying the algorithm to increasingly difficult test cases, and analyze the manner of and reasons for eventual failure. Detection of transcription factor-binding motifs is limited by the motifs' intrinsic subtlety rather than by inadequacy of the alignment optimization procedure.

Algorithms↗

PubMed2004

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.

We have developed a computational method for transcriptional regulatory network inference, CARRIE (Computational Ascertainment of Regu latory Relationships Inferred from Expression), which combines microarray and promoter sequence analysis. CARRIE uses sources of data to identify the transcription factors (TFs) that regulate gene expression changes in response to a stimulus and generates testable hypotheses about the regulatory network connecting these TFs to the genes they regulate. The promoter analysis component of CARRIE, ROVER (Relative OVER-abundance of cis-elements), is highly accurate at detecting the TFs that regulate the response to a stimulus. ROVER also predicts which genes are regulated by each of these TFs. CARRIE uses these transcriptional interactions to infer a regulatory network. To demonstrate our method, we applied CARRIE to six sets of publicly available DNA microarray experiments on Saccharomyces cerevisiae. The predicted networks were validated with comparisons to literature sources, experimental TF binding data, and gene ontology biological process information.

Binding Sites↗

PubMed2004

Leading-edge myofibroblasts in human colon cancer express plasminogen activator inhibitor-1.

Plasminogen activator inhibitor-1 (PAI-1) is up-regulated strongly in various cancer tissues, including colon cancer tissue. Highly specific rabbit polyclonal antibodies against PAI-1 were used for immunohistochemical localization of PAI-1 in 12 invasive colorectal adenocarcinomas. PAI-1 immunoreactivity was observed in endothelial cells of some vessels located in the submucosa and in several fibroblast-like cells located at the invasive front. No PAI-1 immunoreactivity was seen in cancer cells in any of the 12 cases. Double immunofluorescence using the PAI-1 antibodies together with antibodies against alpha-smooth muscle actin for myofibroblast/smooth muscle cells and CD34 for endothelial cells showed that more than 80% of the PAI-1-positive fibroblast-like cells in all 12 cases were myofibroblasts. In 4 of 12 cases, a few of the PAI-1-positive fibroblast-like cells in the invasive front were CD34+. We conclude that the majority of PAI-1-positive fibroblast-like cells located at the leading edge of the invasive colon cancers are myofibroblasts.

Actins↗

PubMed2003

Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead.

The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary conservation of these biological roles, we have characterized two new family members in Caenorhabditis elegans and Xenopus laevis. The C.elegans member, Ce-GRH-1, groups with the Grainyhead subfamily, while the X.laevis member, Xl-LSF, groups with the LSF subfamily. Ce-GRH-1 binds DNA in a sequence-specific manner identical to that of Drosophila melanogaster Grainyhead. In addition, Ce-GRH-1 binds to sequences upstream of the C.elegans gene encoding aromatic L-amino-acid decarboxylase and genes involved in post-embryonic development, mab-5 and dbl-1. All three C.elegans genes are homologs of D.melanogaster Grainyhead-regulated genes. RNA-mediated interference of Ce-grh-1 results in embryonic lethality in worms, accompanied by soft, defective cuticles. These phenotypes are strikingly similar to those observed previously in D.melanogaster grainyhead mutants, suggesting conservation of the developmental role of these family members over the course of evolution. Our phylogenetic analysis of the expanded LSF/GRH family (including other previously unrecognized proteins/ESTs) suggests that the structural and functional dichotomy of this family dates back more than 700 million years, i.e. to the time when the first multicellular organisms are thought to have arisen.

5' Flanking Region↗

PubMed2003

Mammalian transcription factor LSF is a target of ERK signaling.

LSF is a mammalian transcription factor that is rapidly and quantitatively phosphorylated upon growth induction of resting, peripheral human T cells, as assayed by a reduction in its electrophoretic mobility. The DNA-binding activity of LSF in primary T cells is greatly increased after this phosphorylation event (Volker et al. [1997]: Genes Dev 11:1435-1446). We demonstrate here that LSF is also rapidly and quantitatively phosphorylated upon growth induction in NIH 3T3 cells, although its DNA-binding activity is not significantly altered. Three lines of experimentation established that ERK is responsible for phosphorylating LSF upon growth induction in both cell types. First, phosphorylation of LSF by ERK is sufficient to cause the reduced electrophoretic mobility of LSF. Second, the amount of ERK activity correlates with the extent of LSF phosphorylation in both primary human T cells and NIH 3T3 cells. Finally, specific inhibitors of the Ras/Raf/MEK/ERK pathway inhibit LSF modification in vivo. This phosphorylation by ERK is not sufficient for activation of LSF DNA-binding activity, as evidenced both in vitro and in mouse fibroblasts. Nonetheless, activation of ERK is a prerequisite for the substantial increase in LSF DNA-binding activity upon activation of resting T cells, indicating that ERK phosphorylation is necessary but not sufficient for activation of LSF in this cell type.

Animals↗

PubMed2002

Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.

The human genome encodes the transcriptional control of its genes in clusters of cis-elements that constitute enhancers, silencers and promoter signals. The sequence motifs of individual cis- elements are usually too short and degenerate for confident detection. In most cases, the requirements for organization of cis-elements within these clusters are poorly understood. Therefore, we have developed a general method to detect local concentrations of cis-element motifs, using predetermined matrix representations of the cis-elements, and calculate the statistical significance of these motif clusters. The statistical significance calculation is highly accurate not only for idealized, pseudorandom DNA, but also for real human DNA. We use our method 'cluster of motifs E-value tool' (COMET) to make novel predictions concerning the regulation of genes by transcription factors associated with muscle. COMET performs comparably with two alternative state-of-the-art techniques, which are more complex and lack E-value calculations. Our statistical method enables us to clarify the major bottleneck in the hard problem of detecting cis-regulatory regions, which is that many known enhancers do not contain very significant clusters of the motif types that we search for. Thus, discovery of additional signals that belong to these regulatory regions will be the key to future progress.

Algorithms↗

PubMed2002

Fe65, a ligand of the Alzheimer's beta-amyloid precursor protein, blocks cell cycle progression by down-regulating thymidylate synthase expression.

The functions of the Alzheimer's beta-amyloid precursor protein (APP) and of its complex with the adaptor protein Fe65 are still unknown. We have demonstrated that Fe65 is also a nuclear protein and APP functions as an extranuclear anchor, thus preventing Fe65 nuclear translocation. According to this finding, it was also demonstrated that Fe65 could play a role in the regulation of transcription. In the present paper we show that the overexpression of Fe65 prevents G(1) --> S cell cycle progression of serum-stimulated fibroblasts and that the contemporary overexpression of APP abolishes this effect of Fe65. The overexpression of Fe65 completely abolishes the activation of a key S phase gene, the thymidylate synthase (TS) gene, driven by the transcription factor LSF/CP2/LBP1 (LSF). This phenomenon is observed only in experimental conditions leading to the accumulation of Fe65 in the nucleus. Similarly, the two other members of the Fe65 protein family, Fe65L1 and Fe65L2, have been found to translocate into the nucleus and to prevent the activation of the TS gene promoter induced by LSF. Two results support the hypothesis that the inhibitory effect of Fe65 on cell cycle progression in fibroblasts is the result of the inhibition of TS gene expression: (i) Fe65 overexpression, but not Fe65 and APP co-expression, prevents the accumulation of endogenous TS upon the exposure of cells to serum, and (ii) thymidine addition to the culture medium completely overcomes the growth arrest caused by Fe65. In neuronal PC12 cells, the overexpression of Fe65 or of Fe65L1 and Fe65L2 blocks cell cycle, as observed in fibroblasts, but thymidine supplementation to culture medium does not revert this block, thus suggesting that Fe65 proteins induce in neuronal cells a gene expression program different from that activated in fibroblasts.

Amino Acid Sequence↗

PubMed2002

The ubiquitously expressed DNA-binding protein late SV40 factor binds Ig switch regions and represses class switching to IgA.

Ig heavy chain class switch recombination (CSR) determines the expression of Ig isotypes. The molecular mechanism of CSR and the factors regulating this process have remained elusive. Recombination occurs primarily within switch (S) regions, located upstream of each heavy chain gene (except Cdelta). These repetitive sequences contain consensus DNA-binding sites for the DNA-binding protein late SV40 factor (LSF) (CP2/leader-binding protein-1c). In this study, we demonstrate by EMSA that purified rLSF, as well as LSF within B cell extracts, directly binds both Smu and Salpha sequences. To determine whether LSF is involved in regulating CSR, two different LSF dominant negative variants were stably expressed in the mouse B cell line I.29 mu, which can be induced to switch from IgM to IgA. Overexpression of these dominant negative LSF proteins results in decreased levels of endogenous LSF DNA-binding activity and an increase in cells undergoing CSR. Thus, LSF represses class switching to IgA. In agreement, LSF DNA-binding activity was found to decrease in whole cell extracts from splenic B cells induced to undergo class switching. To elucidate the mechanism of CSR regulation by LSF, the interactions of LSF with proteins involved in chromatin modification were tested in vitro. LSF interacts with both histone deacetylases and the corepressor Sin3A. We propose that LSF represses CSR by histone deacetylation of chromatin within S regions, thereby limiting accessibility to the switch recombination machinery.

Amino Acid Substitution↗