Construction of a computable cell proliferation network focused on non-diseased lung cells.

BACKGROUND: Critical to advancing the systems-level evaluation of complex biological processes is the development of comprehensive networks and computational methods to apply to the analysis of systems biology data (transcriptomics, proteomics/phosphoproteomics, metabolomics, etc.). Ideally, these networks will be specifically designed to capture the normal, non-diseased biology of the tissue or cell types under investigation, and can be used with experimentally generated systems biology data to assess the biological impact of perturbations like xenobiotics and other cellular stresses. Lung cell proliferation is a key biological process to capture in such a network model, given the pivotal role that proliferation plays in lung diseases including cancer, chronic obstructive pulmonary disease (COPD), and fibrosis. Unfortunately, no such network has been available prior to this work. RESULTS: To further a systems-level assessment of the biological impact of perturbations on non-diseased mammalian lung cells, we constructed a lung-focused network for cell proliferation. The network encompasses diverse biological areas that lead to the regulation of normal lung cell proliferation (Cell Cycle, Growth Factors, Cell Interaction, Intra- and Extracellular Signaling, and Epigenetics), and contains a total of 848 nodes (biological entities) and 1597 edges (relationships between biological entities). The network was verified using four published gene expression profiling data sets associated with measured cell proliferation endpoints in lung and lung-related cell types. Predicted changes in the activity of core machinery involved in cell cycle regulation (RB1, CDKN1A, and MYC/MYCN) are statistically supported across multiple data sets, underscoring the general applicability of this approach for a network-wide biological impact assessment using systems biology data. CONCLUSIONS: To the best of our knowledge, this lung-focused Cell Proliferation Network provides the most comprehensive connectivity map in existence of the molecular mechanisms regulating cell proliferation in the lung. The network is based on fully referenced causal relationships obtained from extensive evaluation of the literature. The computable structure of the network enables its application to the qualitative and quantitative evaluation of cell proliferation using systems biology data sets. The network is available for public use.

The role of hypoxia in 2-butoxyethanol-induced hemangiosarcoma.

To understand the molecular mechanisms underlying compound-induced hemangiosarcomas in mice, and therefore, their human relevance, a systems biology approach was undertaken using transcriptomics and Causal Network Modeling from mice treated with 2-butoxyethanol (2-BE). 2-BE is a hemolytic agent that induces hemangiosarcomas in mice. We hypothesized that the hemolysis induced by 2-BE would result in local tissue hypoxia, a well-documented trigger for endothelial cell proliferation leading to hemangiosarcoma. Gene expression data from bone marrow (BM), liver, and spleen of mice exposed to a single dose (4 h) or seven daily doses of 2-BE were used to develop a mechanistic model of hemangiosarcoma. The resulting mechanistic model confirms previous work proposing that 2-BE induces macrophage activation and inflammation in the liver. In addition, the model supports local tissue hypoxia in the liver and spleen, coupled with increased erythropoeitin signaling and erythropoiesis in the spleen and BM, and suppression of mechanisms that contribute to genomic stability, events that could be contributing factors to hemangiosarcoma formation. Finally, an immunohistochemistry method (Hypoxyprobe) demonstrated that tissue hypoxia was present in the spleen and BM. Together, the results of this study identify molecular mechanisms that initiate hemangiosarcoma, a key step in understanding safety concerns that can impact drug decision processes, and identified hypoxia as a possible contributing factor for 2-BE-induced hemangiosarcoma in mice.

RelB NF-kappaB represses estrogen receptor alpha expression via induction of the zinc finger protein Blimp1.

Aberrant constitutive expression of NF-kappaB subunits, reported in more than 90% of breast cancers and multiple other malignancies, plays pivotal roles in tumorigenesis. Higher RelB subunit expression was demonstrated in estrogen receptor alpha (ERalpha)-negative breast cancers versus ERalpha-positive ones, due in part to repression of RelB synthesis by ERalpha signaling. Notably, RelB promoted a more invasive phenotype in ERalpha-negative cancers via induction of the BCL2 gene. We report here that RelB reciprocally inhibits ERalpha synthesis in breast cancer cells, which contributes to a more migratory phenotype. Specifically, RelB is shown for the first time to induce expression of the zinc finger repressor protein Blimp1 (B-lymphocyte-induced maturation protein), the critical mediator of B- and T-cell development, which is transcribed from the PRDM1 gene. Blimp1 protein repressed ERalpha (ESR1) gene transcription. Commensurately higher Blimp1/PRDM1 expression was detected in ERalpha-negative breast cancer cells and primary breast tumors. Induction of PRDM1 gene expression was mediated by interaction of Bcl-2, localized in the mitochondria, with Ras. Thus, the induction of Blimp1 represents a novel mechanism whereby the RelB NF-kappaB subunit mediates repression, specifically of ERalpha, thereby promoting a more migratory phenotype.

Comparative molecular physiological genomics. Heterologous probing of cDNA arrays.

The use of DNA microarrays has gained wider acceptance as a standard tool for molecular biology studies over the past decade. In particular, biomedical studies embraced this technology as soon as arrays were produced for the common laboratory species. Slower to develop, however, has been the use of microarray screening with non-standard animal models, even though these species present fascinating physiological phenomena for study. The very high cost and huge amount of work involved in developing and producing a DNA array or microarray for a new species is prohibitive for most researchers working in comparative biology. The alternative is to explore the use of heterologous array hybridization, screening for stress-induced gene expression in one species using an array developed for another species. This chapter provides a comprehensive review of the current literature on heterologous DNA array hybridization and explores the factors that must be taken into account when performing heterologous microarray analysis on nonstandard species. Changes in methodology (e.g. hybridization conditions, stringency of washing) to optimize the percent cross reaction, the potential for false positives and false negatives to occur, and techniques for downstream analysis and confirmation of array data are all discussed. Examples of cross-hybridization using human microarrays are discussed using phylogenetically diverse species ranging from ground squirrels to frogs to snails. As with any new technology, the willingness to grasp cross-species analysis has been slow but the future looks bright for heterologous DNA hybridization and microarray analysis now that the initial hurdles have been overcome.

NF-kappaB and epithelial to mesenchymal transition of cancer.

During progression of an in situ to an invasive cancer, epithelial cells lose expression of proteins that promote cell-cell contact, and acquire mesenchymal markers, which promote cell migration and invasion. These events bear extensive similarities to the process of epithelial to mesenchymal transition (EMT), which has been recognized for several decades as critical feature of embryogenesis. The NF-kappaB family of transcription factors plays pivotal roles in both promoting and maintaining an invasive phenotype. After briefly describing the NF-kappaB family and its role in cancer, in this review we will first describe studies elucidating the functions of NF-kappaB in transcription of master regulator genes that repress an epithelial phenotype. In the second half, we discuss the roles of NF-kappaB in control of mesenchymal genes critical for promoting and maintaining an invasive phenotype. Overall, NF-kappaB is identified as a key target in prevention and in the treatment of invasive carcinomas.

Trastuzumab-resistant HER2-driven breast cancer cells are sensitive to epigallocatechin-3 gallate.

Overexpression of the epidermal growth factor receptor family member HER2 is found in approximately 30% of breast cancers and is a target for immunotherapy. Trastuzumab, a humanized monoclonal antibody against HER2, is cytostatic when added alone and highly successful in clinical settings when used in combination with other chemotherapeutic agents. Unfortunately, HER2 tumors in patients develop resistance to trastuzumab or metastasize to the brain, which is inaccessible to antibody therapy. Previously, we showed that the green tea polyphenol epigallocatechin-3 gallate (EGCG) inhibits growth and transformed phenotype of Her-2/neu-driven mouse mammary tumor cells. The different modes of action of EGCG and trastuzumab led us to hypothesize that EGCG will inhibit HER2-driven breast cancer cells resistant to trastuzumab. We studied trastuzumab-resistant BT474 human breast cancer cells, isolated by chronic trastuzumab exposure, and JIMT-1 breast cancer cells, derived from a pleural effusion in a patient who displayed clinical resistance to trastuzumab therapy. EGCG treatment caused a dose-dependent decrease in growth and cellular ATP production, and apoptosis at high concentrations. Akt activity was suppressed by EGCG leading to the induction of FOXO3a and target cyclin-dependent kinase inhibitor p27Kip1 levels. Thus, EGCG in combination with trastuzumab may provide a novel strategy for treatment of HER2-overexpressing breast cancers, given that EGCG can cross the blood-brain barrier.

p38 MAPK regulation of transcription factor targets in muscle and heart of the hibernating bat, Myotis lucifugus.

Mammalian hibernation combines a profound net metabolic rate suppression with the selective up-regulation of key genes whose protein products address specific metabolic needs of the hibernator. The signal transduction pathways and transcription factors involved in regulating hibernation-responsive gene expression are of great interest. The present study suggests an important role for the p38 mitogen-activated protein kinase (p38 MAPK) and selected downstream transcription factors under its control (CREB, ATF-2, Elk-1) in the metabolic response by skeletal muscle during hibernation of little brown bats, Myotis lucifugus. Western blotting was used to quantify both total protein and levels of the phosphorylated, active forms of p38 MAPK, CREB, ATF-2 and Elk-1 in both skeletal muscle and heart of euthermic and hibernating bats. The p38 MAPK pathway was not apparently activated in heart during torpor but skeletal muscle showed strong increases (2.2-11-fold) in the amounts of phosphorylated p38 T180/Y182, CREB S133, ATF-2T69/71 and Elk-1(S383) in the torpid versus aroused state. By contrast both total and phosphorylated levels of Elk-1 in heart were reduced during hibernation to just 30% of the euthermic values. These data implicate p38 MAPK and its transcription factor targets, CREB, ATF-2 and Elk-1 in skeletal muscle maintenance during hibernation.

Differential expression of selected mitochondrial genes in hibernating little brown bats, Myotis lucifugus.

High rates of non-shivering thermogenesis by brown adipose tissue accompanied by additional shivering thermogenesis in skeletal muscle provide the powerful reheating of body organs that allows hibernating mammals to return from their state of cold torpor back to euthermic function. Previous studies have suggested that changes to brown adipose mitochondria occur during hibernation and are partially responsible for its capacity for non-shivering thermogenesis. The current study shows that selected mitochondrial enzyme activities are elevated and selected genes and proteins are induced during torpor in brown adipose tissue of the little brown bat, Myotis lucifugus. Cytochrome oxidase activity in brown adipose tissue was more than 3-fold higher during torpor than in euthermic animals. Transcript levels of mitochondria-encoded genes, coxII and nad4, were also 3-4-fold higher during torpor, as evidenced by northern blotting. By contrast, transcripts of these genes were unchanged in skeletal muscle during torpor. Protein levels of carnitine palmitoyl transferase-1beta, an enzyme embedded in the outer membrane of the mitochondria that is the rate-limiting step enzyme in beta-oxidation, were also elevated by 2-fold during torpor in brown adipose but were unchanged in skeletal muscle. Cloning and sequencing of a 624 bp segment of cpt-1beta revealed a number of amino acid substitutions in the bat protein as compared to CPT-1beta from other mammals; these may be beneficial for enzyme function at low body temperatures during torpor. This study provides further evidence for a key role of mitochondria in hibernation.

Inducible IkappaB kinase/IkappaB kinase epsilon expression is induced by CK2 and promotes aberrant nuclear factor-kappaB activation in breast cancer cells.

Aberrant activation of nuclear factor-kappaB (NF-kappaB) transcription factors has been implicated in the pathogenesis of breast cancer. We previously showed elevated activity of IkappaB kinase alpha (IKKalpha), IKKbeta, and protein kinase CK2 in primary human breast cancer specimens and cultured cells. A novel inducible IKK protein termed IKK-i/IKKepsilon has been characterized as a potential NF-kappaB activator. Here, we provide evidence that implicates IKK-i/IKKepsilon in the pathogenesis of breast cancer. We show IKK-i/IKKepsilon expression in primary human breast cancer specimens and carcinogen-induced mouse mammary tumors. Multiple breast cancer cell lines showed higher levels of IKK-i/IKKepsilon and kinase activity compared with untransformed MCF-10F breast epithelial cells. Interestingly, IKK-i/IKKepsilon expression correlated with CK2alpha expression in mammary glands and breast tumors derived from MMTV-CK2alpha transgenic mice. Ectopic CK2 expression in untransformed cells led to increased IKK-i/IKKepsilon mRNA and protein levels. Inhibition of CK2alpha via the pharmacologic inhibitor apigenin or upon transfection of a CK2 kinase-inactive subunit reduced IKK-i/IKKepsilon levels. Expression of a kinase-inactive IKK-i/IKKepsilon mutant in breast cancer cells reduced NF-kappaB activity as judged by transfection assays of reporters driven either by NF-kappaB elements or the promoters of two NF-kappaB target genes, cyclin D1 and relB. Importantly, the kinase-inactive IKK-i/IKKepsilon mutant reduced the endogenous levels of these genes as well as the ability of breast cancer cells to grow in soft agar or form invasive colonies in Matrigel. Thus, CK2 induces functional IKK-i/IKKepsilon, which is an important mediator of the activation of NF-kappaB that plays a critical role in the pathogenesis of breast cancer.

Cloning and expression of PPAR-gamma and PGC-1alpha from the hibernating ground squirrel, Spermophilus tridecemlineatus.

The peroxisome proliferator-activated receptor (PPAR) family of transcription factors play a key role in lipid metabolism and have been implicated in a number of disease states, most notably of which is obesity. Controlled regulation of lipid metabolism is a key ingredient for successful hibernation. Partial cDNA sequences for one of the PPAR proteins, PPARgamma and the PPARgamma co-activator (PGC-1alpha) have been cloned from the hibernating ground squirrel, Spermophilus tridecemlineatus and show differential regulation during hibernation at the mRNA level using relative RT-PCR and at the protein level via immunoblotting in brown adipose tissue (BAT), heart, skeletal muscle and white adipose tissue (WAT). The cDNA sequence for PGC-1alpha revealed a number of amino acid substitutions and two were worthy of note, one resulting in the loss of a potential protein kinase C (PKC) site, while another resulted in the creation of a PKC site, suggesting that PKC may be important in regulating PGC-1alpha. RT-PCR revealed a near 2-fold up-regulation of PPARgamma in BAT and to a lesser extent (<1.5-fold) in heart and WAT, while PGC-1alpha displayed significantly higher levels of expression in skeletal muscle during hibernation (3.1-fold, p < 0.005). The protein levels of PPARy were significantly increased in BAT and WAT (1.5 and 1.8-fold, respectively) while PGC-1alpha displayed significant changes in expression in heart (3.5-fold) and skeletal muscle (1.8-fold). Our current findings indicate a role for increased expression of PPARy and PGC-1alpha in hibernating animals.

Up-regulation of a thioredoxin peroxidase-like protein, proliferation-associated gene, in hibernating bats.

Two-dimensional gel electrophoresis was used to assess differential protein expression between euthermic and hibernating states in heart of Myotis lucifugus. A hibernation-induced protein was identified by mass spectrometry as a thioredoxin peroxidase-like protein known as PAG. Western blotting confirmed up-regulation (>2-fold) and RT-PCR also revealed up-regulation (>5-fold) of pag mRNA. Cloning revealed a highly conserved sequence suggesting a conserved function for PAG. Oxidative stress markers, p-IkappaB-alpha (Ser 32) and p-HSP27 (Ser 78/82), were also up-regulated in heart and skeletal muscle during hibernation. Although there are selected increases in gene/protein expression during hibernation, general translation inhibition occurs as part of metabolic rate depression. This was confirmed by elevated levels of the inactive forms of the eIF2alpha (Ser 51) in both heart and skeletal muscle (2- to 5-fold higher than in euthermia) and the eEF2 (Thr 51) in skeletal muscle (a 15-fold increase). This study suggests that hibernators may use up-regulation of specific proteins to counteract oxidative stress.

Up-regulation of fatty acid-binding proteins during hibernation in the little brown bat, Myotis lucifugus.

Hibernating animals rely primarily on lipids throughout winter as their primary fuel source, thus it is hypothesized that an increase in genes and proteins relating to lipid transport will increase accordingly. The cloning and expression of heart type fatty acid-binding protein (h-fabp) from a mammalian hibernator, the little brown bat Myotis lucifugus, is presented. Northern blot analysis revealed that transcript levels of h-fabp were significantly higher during hibernation in brown adipose tissue and skeletal muscle compared with levels in euthermic bats. Similarly, heterologous probing with rat adipose type a-fabp found 3.9-fold higher levels of a-fabp transcripts in brown adipose from hibernating animals. Levels of A- and H-FABP protein were quantified in tissues of euthermic versus hibernating animals by Western blotting. A-FABP was 4-fold higher in brown adipose of hibernating, compared with euthermic bats, whereas H-FABP was significantly higher in hibernator brown adipose, heart and skeletal muscle. The present work implicates FABPs as important elements related to the hibernating state in mammals; alterations in gene and protein expression along with amino acid substitutions are shown. These likely contribute to optimizing the function of FABPs at the low body temperatures (near 0 degrees C) experienced in the hibernating state.

Differential expression of Akt, PPARgamma, and PGC-1 during hibernation in bats.

The effects of hibernation on the expression of Akt (protein kinase B), the peroxisome proliferator-activated receptor gamma isoform (PPARgamma), and the PPARgamma coactivator PGC-1 were assessed in seven tissues of the little brown bat, Myotis lucifugus. Western blotting revealed that the levels of active phosphorylated Akt were strongly reduced in brain, kidney, liver, and white adipose during torpor as compared with aroused animals and that total Akt protein was also reduced in white adipose during torpor. By contrast, both total and phospho-Akt were elevated in brown adipose tissue, the thermogenic organ. PPARgamma and PGC-1 levels showed parallel changes in all organs. Both were strongly suppressed in brain, but levels increased significantly in all other organs during hibernation (except for PGC-1 in heart). Reduced Akt activity is consistent with a probable reduced insulin response during torpor that facilitates the mobilization of lipid reserves for fuel supply and is further supported by increased gene expression of enzymes and proteins involved in lipid catabolism under the stimulation of enhanced PPARgamma and PGC-1 levels.