Thomas J. Weber

Network Analysis of Epidermal Growth Factor Signaling Using Integrated Genomic, Proteomic and Phosphorylation Data

To understand how integration of multiple data types can help decipher cellular responses at the systems level, we analyzed the mitogenic response of human mammary epithelial cells to epidermal growth factor (EGF) using whole genome microarrays, mass spectrometry-based proteomics and large-scale western blots with over 1000 antibodies. A time course analysis revealed significant differences in the expression of 3172 genes and 596 proteins, including protein phosphorylation changes measured by western blot. Integration of these disparate data types showed that each contributed qualitatively different components to the observed cell response to EGF and that varying degrees of concordance in gene expression and protein abundance measurements could be linked to specific biological processes. Networks inferred from individual data types were relatively limited, whereas networks derived from the integrated data recapitulated the known major cellular responses to EGF and exhibited more highly connected signaling nodes than networks derived from any individual dataset. While cell cycle regulatory pathways were altered as anticipated, we found the most robust response to mitogenic concentrations of EGF was induction of matrix metalloprotease cascades, highlighting the importance of the EGFR system as a regulator of the extracellular environment. These results demonstrate the value of integrating multiple levels of biological information to more accurately reconstruct networks of cellular response.

A paracrine signal mediates the cell transformation response to low dose gamma radiation in JB6 cells

The carcinogenic response to radiation is complex and may involve adaptive cellular responses as well as a bystander effect mediated by paracrine or intercellular signaling activities. Using a newly developed co‐culture model we have examined whether low dose gamma radiation induces the transformation of JB6 mouse epidermal cells as well as non‐irradiated bystander cells. Cell transformation response is defined as the acquisition of anchorage‐independent growth properties and is quantified by counting colonies on soft agar. Exposure of JB6 cells to low dose (2–20 cGy) gamma radiation resulted in an approximate 1.9 ± 0.1 and 2.8 ± 0.5‐fold increase in cell transformation response when cells were seeded at 1 × 104 or 1 × 105 cells/dish, relative to respective sham exposed controls. We developed a co‐culture model where sham exposed or irradiated JB6 cells were mixed with non‐irradiated JB6 cells that had been stably transfected with the enhanced yellow fluorescent protein (EYFP) to enable the distinction of fluorescent bystander‐specific colonies. A significant increase in the number of bystander‐specific colonies was observed in co‐culture with 10 cGy irradiated JB6 cells (224 ± 9), relative to the number of bystander‐specific colonies arising in co‐culture with sham exposed JB6 cells (55 ± 16). Our results indicate that low dose radiation induces the transformation of JB6 cells and that a soluble paracrine factor that is secreted by irradiated cells induces the transformation of non‐irradiated bystander cells.

Annexin A2 Modulates Radiation-Sensitive Transcriptional Programming and Cell Fate

We previously established annexin A2 as a radioresponsive protein associated with anchorage independent growth in murine epidermal cells. In this study, we demonstrate annexin A2 nuclear translocation in human skin organotypic culture and murine epidermal cells after exposure to X radiation (10–200 cGy), supporting a conserved nuclear function for annexin A2. Whole genome expression profiling in the presence and absence of annexin A2 [shRNA] identified fundamentally altered transcriptional programming that changes the radioresponsive transcriptome. Bioinformatics predicted that silencing AnxA2 may enhance cell death responses to stress in association with reduced activation of pro-survival signals such as nuclear factor kappa B. This prediction was validated by demonstrating a significant increase in sensitivity toward tumor necrosis factor alpha-induced cell death in annexin A2 silenced cells, relative to vector controls, associated with reduced nuclear translocation of RelA (p65) following tumor necrosis factor alpha treatment. These observations implicate an annexin A2 niche in cell fate regulation such that AnxA2 protects cells from radiation-induced apoptosis to maintain cellular homeostasis at low-dose radiation.

Basic Fibroblast Growth Factor Regulates Persistent ERK Oscillations in Premalignant but Not Malignant JB6 Cells

The regulation of extracellular signal-regulated kinase (ERK) oscillations in the context of wound healing and carcinogenesis have been investigated in premalignant and malignant JB6 mouse epidermal cells stimulated with basic fibroblast growth factor (bFGF) and 12-O-tetradecanoyl phorbol-13-acetate (TPA). In premalignant JB6 cells, bFGF stimulation (1) increases cellular phospho-ERK and phospho-c-Jun levels, (2) increases serum-dependent cell proliferation, (3) induces an apparent epithelial-to-mesenchymal transition, and (4) induces the persistent nuclear-cytosolic oscillation of an ERK1-green fluorescent protein (ERK1-GFP) chimera. In contrast, TPA induces persistent activation of ERK in the absence of oscillations and does not induce efficient migration. Treatment of malignant or transformed JB6 cells with bFGF is associated with a transient nuclear translocation of ERK1-GFP but not oscillations or efficient cell migration. Our data suggest that bFGF regulates ERK oscillations in premalignant but not malignant JB6 cells.

Reactive Oxygen Species Alter Autocrine and Paracrine Signaling

Cytochrome P450 (P450) 3A4 (CYP3A4) is the most abundant P450 protein in human liver and intestine and is highly inducible by a variety of drugs and other compounds. The P450 catalytic cycle is known to uncouple and release reactive oxygen species (ROS), but the effects of ROS from P450 and other enzymes in the endoplasmic reticulum have been poorly studied from the perspective of effects on cell biology. In this study, we expressed low levels of CYP3A4 in HepG2 cells, a human hepatocarcinoma cell line, and examined effects on intracellular levels of ROS and on the secretion of a variety of growth factors that are important in extracellular communication. Using the redox-sensitive dye RedoxSensor red, we demonstrate that CYP3A4 expression increases levels of ROS in viable cells. A custom ELISA microarray platform was employed to demonstrate that expression of CYP3A4 increased secretion of amphiregulin, intracellular adhesion molecule 1, matrix metalloprotease 2, platelet-derived growth factor (PDGF), and vascular endothelial growth factor, but suppressed secretion of CD14. The antioxidant N-acetylcysteine suppressed all P450-dependent changes in protein secretion except for CD14. Quantitative RT-PCR demonstrated that changes in protein secretion were consistently associated with corresponding changes in gene expression. Inhibition of the NF-κB pathway blocked P450 effects on PDGF secretion. CYP3A4 expression also altered protein secretion in human mammary epithelial cells and C10 mouse lung cells. Overall, these results suggest that increased ROS production in the endoplasmic reticulum alters the secretion of proteins that have key roles in paracrine and autocrine signaling.

Regulation of the Low-Dose Radiation Paracrine-Specific Anchorage-Independent Growth Response by Annexin A2

Abstract Weber, T. J., Opresko, L. K., Waisman, D. M., Newton, G. J., Quesenberry, R. D., Bollinger, N., Moore, R. J. and Smith, R. D. Regulation of the Low-Dose Radiation Paracrine-Specific Anchorage-Independent Growth Response by Annexin A2. Radiat. Res. 172, 96-105 (2009). Here we identify the release of annexin A2 into the culture medium in response to low-dose X-radiation exposure and establish functional linkages to an established paracrine factor-mediated anchorage-independent growth response. Using a standard bicameral coculture model, we demonstrate that annexin A2 is secreted into the medium by irradiated cells (seeded in upper chamber) and is capable of binding to nonirradiated neighboring cells (seeded in lower chamber). The paracrine factor-mediated anchorage-independent growth response to low-dose X irradiation is reduced when irradiated annexin A2-silenced (shRNA) JB6 cells are co-cultured with nonirradiated cells relative to co-culture with irradiated annexin A2-competent vector control cells. Consistent with this observation, purified bovine annexin A2 tetramer induces anchorage-independent growth. These observations suggest that annexin A2 regulates, in part, the radiation paracrine factor-specific anchorage-independent growth response in JB6 cells.

Ectopic ERK expression induces phenotypic conversion of C10 cells and alters DNA methyltransferase expression

BackgroundMany lung carcinogens activate mitogen activated protein kinase (MAPK) pathways and DNA methyltransferases (DNMTs) are under investigation as therapeutic targets for lung cancer. Our goal is to determine whether C10 type II alveolar epithelial cells are a sensitive model to investigate ERK-dependent transformation and DNMT expression patterns in experimental lung cancer.FindingsEctopic expression of an extracellular signal regulated kinase (ERK)-green fluorescent protein (ERK1-GFP) induces acquisition of growth in soft agar that is selectively associated with latent effects on the expression of DNA methyl transferases (DNMT1 and 3b), xeroderma pigmentosum complementation group A (XPA), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), increased phosphatase activity and enhanced sensitivity to 5-azacytidine (5-azaC)-mediated toxicity, relative to controls.ConclusionsEctopic expression of ERK alone is sufficient to promote phenotypic conversion of C10 cells associated with altered DNMT expression patterns and sensitivity to DNMT inhibitor. This model may have applications for predicting sensitivity to DNMT inhibitors.

Modulation of JB6 mouse epidermal cell transformation response by the prostaglandin F2α receptor

Prostaglandin F2α (PGF2α) modulates clonal selection processes in the mouse skin model of carcinogenesis. In this study we investigated whether JB6 mouse epidermal cells expressed a functional PGF2α receptor (FP) coupled with a cell‐transformation response. Treatment of JB6 cells with an FP agonist (fluprostenol) potently (pM‐nM) increased anchorage‐dependent and anchorage‐independent growth. Inositol phospholipid accumulation and extracellular signal–regulated kinase (Erk) activity were increased in cells treated with FP agonists, consistent with established FP‐related signal transduction. FP mRNA was detected by reverse transcription–polymerase chain reaction, and the average specific [3H]PGF2α binding was 8.25 ± 0.95 fmol/mg protein. Erk activity and colony size were increased by cotreatment of JB6 cells with epidermal growth factor (EGF) and fluprostenol to a greater extent than with either treatment alone, whereas the cotreatment effect on colony number appeared to be simply additive. Collectively, our data indicated that JB6 cells expressed a functional FP coupled with transformation‐related signal transduction and the regulation of clonal selection processes. Erk activity appears to be a convergence point in the EGF and FP pathways. The data raise the possibility that the FP contributes to clonal selection processes but probably plays a more important role as a response modifier.

Impaired osteoblast differentiation in annexin A2- And -A5-deficient cells

Annexins are a class of calcium-binding proteins with diverse functions in the regulation of lipid rafts, inflammation, fibrinolysis, transcriptional programming and ion transport. Within bone, they are well-characterized as components of mineralizing matrix vesicles, although little else is known as to their function during osteogenesis. We employed shRNA to generate annexin A2 (AnxA2)- or annexin A5 (AnxA5)-knockdown pre-osteoblasts, and determined whether proliferation or osteogenic differentiation was altered in knockdown cells, compared to pSiren (Si) controls. We report that DNA content, a marker of proliferation, was significantly reduced in both AnxA2 and AnxA5 knockdown cells. Alkaline phosphatase expression and activity were also suppressed in AnxA2- or AnxA5-knockdown after 14 days of culture. The pattern of osteogenic gene expression was altered in knockdown cells, with Col1a1 expressed more rapidly in knock-down cells, compared to pSiren. In contrast, Runx2, Ibsp, and Bglap all revealed decreased expression after 14 days of culture. In both AnxA2- and AnxA5-knockdown, interleukin-induced STAT6 signaling was markedly attenuated compared to pSiren controls. These data suggest that AnxA2 and AnxA5 can influence bone formation via regulation of osteoprogenitor proliferation, differentiation, and responsiveness to cytokines in addition to their well-studied function in matrix vesicles.

Cellular dichotomy between anchorage-independent growth responses to bFGF and TPA reflects molecular switch in commitment to carcinogenesis

We have investigated gene expression patterns underlying reversible and irreversible anchorage‐independent growth (AIG) phenotypes to identify more sensitive markers of cell transformation for studies directed at interrogating carcinogenesis responses. In JB6 mouse epidermal cells, basic fibroblast growth factor (bFGF) induces an unusually efficient and reversible AIG response, relative to 12‐O‐tetradecanoyl phorbol‐13‐acetate (TPA)‐induced AIG which is irreversible. The reversible and irreversible AIG phenotypes are characterized by largely nonoverlapping global gene expression profiles. However, a subset of differentially expressed genes were identified as common to reversible and irreversible AIG phenotypes, including genes regulated in a reciprocal fashion. Hepatic leukemia factor (HLF) and D‐site albumin promoter‐binding protein (DBP) were increased in both bFGF and TPA soft agar colonies and selected for functional validation. Ectopic expression of human HLF and DBP in JB6 cells resulted in a marked increase in TPA‐ and bFGF‐regulated AIG responses. HLF and DBP expression were increased in soft agar colonies arising from JB6 cells exposed to gamma radiation and in a human basal cell carcinoma tumor tissue, relative to paired nontumor tissue. Subsequent biological network analysis suggests that many of the differentially expressed genes that are common to bFGF‐ and TPA‐dependent AIG are regulated by c‐Myc, SP‐1, and HNF‐4 transcription factors. Collectively, we have identified a potential molecular switch that mediates the transition from reversible to irreversible AIG.