Signal pathway profiling of prostate cancer using reverse phase protein arrays

Reverse phase protein arrays represent a new proteomics microarray technology with which to study the fluctuating state of the proteome in minute quantities of cells. The activation status of cell signaling pathways controls cellular fate and deregulation of these pathways underpins carcinogenesis. Changes in pathway activation that occur between early stage prostatic epithelial lesions, prostatic stroma and the extracellular matrix can be analyzed by obtaining pure populations of cell types by laser capture microdissection (LCM) and analyzing the relative states of several key phosphorylation points within the cellular circuitry. We have applied reverse phase protein array technology to analyze the status of key points in cell signaling involved in pro-survival, mitogenic, apoptotic and growth regulation pathways in the progression from normal prostate epithelium to invasive prostate cancer. Using multiplexed reverse phase protein arrays coupled with LCM, the states of signaling changes during disease progression from prostate cancer study sets were analyzed. Focused analysis of phospho-specific endpoints revealed changes in cellular signaling events through disease progression and between patients. We have used a new protein array technology to study specific molecular pathways believed to be important in cell survival and progression from normal epithelium to invasive carcinoma directly from human tissue specimens. With the advent of molecular targeted therapeutics, the identification, characterization and monitoring of the signaling events within actual human biopsies will be critical for patient-tailored therapy.     

Does Auxin Play a Role in the Release of Apical Dominance by Shoot Inversion in Ipomoea nil?

According to the auxin-inhibition hypothesis of apical dominance,apically produced auxin moves down the stem and inhibits axillarybud outgrowth, either directly or indirectly. This hypothesishas been examined further by monitoring changes in basipetalauxin transport and endogenous auxin concentration in Ipomoeanil caused by shoot inversion, a stimulus that releases apicaldominance. The results indicate that inversion reduces auxintransport in the main stem. In upright shoots of intact plants,a 16-h pretreatment with [³H]IAA 4 cm below the apex resultsin downward movement of label and accumulation in nodes, especiallythe cotyledonary node. Label does not accumulate in the lateralbuds. GC-MS determinations of endogenous free auxin level inthe fourth node, where a lateral bud grows out following inversionof the upper part of the shoot, show no changes at 3 and 8 hafter inversion, the range of times for inversion-induced budrelease, or at 24 h, when bud outgrowth is continuing. However,inversion did cause a just-detectable decrease (approx. 10%)in the IAA level of the shoot's elongation region. Althoughauxin transport in segments of the main stem is partially inhibitedby inversion over a period shorter than the latent time of budrelease, thus providing a means for the expected depletion ofauxin in the fourth node, no depletion could be detected there.These results suggest that either a decrease in IAA level inthe main stem is not causal of bud release or that the decreasedIAA pool responsible for bud release is compartmented and cannotbe measured in whole-tissue extracts.Copyright 1993, 1999 AcademicPress Apical dominance, auxin content, auxin transport, axillary bud release, GC-MS, Ipomoea nil, Pharbitis nil, shoot inversion     

Gonadal regeneration in masculinized female or steroid-treated rainbow trout (Oncorhynchus mykiss)

In salmonids, the development of an indifferent gonad into a testis or an ovary is normally determined chromosomally but can be reversed or changed by the administration of exogenous steroids during specific times in embryonic development. Because the gonads of sexually mature rainbow trout (RBT) are capable of regeneration following surgical removal and since regeneration of some tissue involves dedifferentiation, the objective of this experiment was to determine if the phenotypic sex of RBT gonads could be reversed during the regenerative process. In experiment 1, male RBT were surgically gonadectomized (Gx) or left intact and subsequently treated with estradiol-17beta, a steroid that feminizes male RBT embryos. All Gx males regenerated testicular tissue regardless of treatment. Likewise, the gonads of sham-operated, intact fish treated with exogenous estrogen showed no evidence of sex-reversal. In experiment 2, testes from masculinized females (XX genotype; male phenotype) were surgically removed. In all cases, only testicular tissue was regenerated in the masculinized females. Taken together, these results are consistent with the conclusion that gonads of salmonid fishes are not susceptible to sex-reversing stimuli during the regenerative process and that gonadal regeneration in salmonids is a result of cellular proliferation of the remaining gonadal remnant.     

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds

Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the biochemical associations between the taxonomic and metabolomic profiles of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Biochemical association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment.     

Identification of direct target engagement biomarkers for kinase-targeted therapeutics

Pharmacodynamic (PD) biomarkers are an increasingly valuable tool for decision-making and prioritization of lead compounds during preclinical and clinical studies as they link drug-target inhibition in cells with biological activity. They are of particular importance for novel, first-in-class mechanisms, where the ability of a targeted therapeutic to impact disease outcome is often unknown. By definition, proximal PD biomarkers aim to measure the interaction of a drug with its biological target. For kinase drug discovery, protein substrate phosphorylation sites represent candidate PD biomarkers. However, substrate phosphorylation is often controlled by input from multiple converging pathways complicating assessment of how potently a small molecule drug hits its target based on substrate phoshorylation measurements alone. Here, we report the use of quantitative, differential mass-spectrometry to identify and monitor novel drug-regulated phosphorylation sites on target kinases. Autophosphorylation sites constitute clinically validated biomarkers for select protein tyrosine kinase inhibitors. The present study extends this principle to phosphorylation sites in serine/threonine kinases looking beyond the T-loop autophosphorylation site. Specifically, for the 3'-phosphoinositide-dependent protein kinase 1 (PDK1), two phospho-residues p-PDK1(Ser410) and p-PDK1(Thr513) are modulated by small-molecule PDK1 inhibitors, and their degree of dephosphorylation correlates with inhibitor potency. We note that classical, ATP-competitive PDK1 inhibitors do not modulate PDK1 T-loop phosphorylation (p-PDK1(Ser241)), highlighting the value of an unbiased approach to identify drug target-regulated phosphorylation sites as these are complementary to pathway PD biomarkers. Finally, we extend our analysis to another protein Ser/Thr kinase, highlighting a broader utility of our approach for identification of kinase drug-target engagement biomarkers.     

CMV-Independent Lysis of Glioblastoma by Ex Vivo Expanded/Activated Vδ1+ γδ T Cells

Vδ2^neg γδ T cells, of which Vδ1+ γδ T cells are by far the largest subset, are important effectors against CMV infection. Malignant gliomas often contain CMV genetic material and proteins, and evidence exists that CMV infection may be associated with initiation and/or progression of glioblastoma multiforme (GBM). We sought to determine if Vδ1+ γδ T cells were cytotoxic to GBM and the extent to which their cytotoxicity was CMV dependent. We examined the cytotoxic effect of ex vivo expanded/activated Vδ1+ γδ T cells from healthy CMV seropositive and CMV seronegative donors on unmanipulated and CMV-infected established GBM cell lines and cell lines developed from short- term culture of primary tumors. Expanded/activated Vδ1+ T cells killed CMV-negative U251, U87, and U373 GBM cell lines and two primary tumor explants regardless of the serologic status of the donor. Experimental CMV infection did not increase Vδ1+ T cell - mediated cytotoxicity and in some cases the cell lines were more resistant to lysis when infected with CMV. Flow cytometry analysis of CMV-infected cell lines revealed down-regulation of the NKG2D ligands ULBP-2, and ULBP-3 as well as MICA/B in CMV-infected cells. These studies show that ex vivo expanded/activated Vδ1+ γδ T cells readily recognize and kill established GBM cell lines and primary tumor-derived GBM cells regardless of whether CMV infection is present, however, CMV may enhance the resistance GBM cell lines to innate recognition possibly contributing to the poor immunogenicity of GBM.