Faculty Bibliography

ABSTRACT: INTRODUCTION: Multi-marker molecular assays have impacted management of early stage breast cancer, facilitating adjuvant chemotherapy decisions. We generated prognostic models that incorporate protein-based molecular markers and clinico-pathological variables to improve survival prediction. METHODS: We used a quantitative immunofluorescence method to study protein expression of 14 markers included in the Oncotype DX assay on a 638 breast cancer patient cohort with 15-year follow-up. We performed cross-validation analyses to assess performance of multivariate Cox models consisting of these markers and standard clinico-pathological covariates, using an average time-dependent Area Under the Receiver Operating Characteristic curves and compared it to nested Cox models obtained by robust backward selection procedures. RESULTS: A prognostic index derived from of a multivariate Cox regression model incorporating molecular and clinico-pathological covariates (nodal status, tumor size, nuclear grade, and age) is superior to models based on molecular studies alone or clinico-pathological covariates alone. Performance of this composite model can be further improved using feature selection techniques to prune variables. When stratifying patients by Nottingham Prognostic Index (NPI), the most prognostic markers in high and low NPI groups differed. Similarly, for the node-negative, hormone receptor-positive sub-population, we derived a compact model with three clinico-pathological variables and two protein markers that was superior to the full model. CONCLUSIONS: Prognostic models that include both molecular and clinico-pathological covariates can be more accurate than models based on either set of features alone. Furthermore, feature selection can decrease the number of molecular variables needed to predict outcome, potentially resulting in less expensive assays

Purpose: Survival of bone implants depends on biological fixation, and prosthesis loosening can be catastrophic leading to replacement of prostheses. Inflammation and osteoclast-mediated bone resorption in response to wear particles near prostheses contribute to loosening. Because we have demonstrated that adenosine A_2Areceptor activation is anti-inflammatory and prevents osteoclast formation and function we hypothesized that adenosine A_2Areceptor agonists might prevent osteoclast-mediated bone resorption at the site of prosthesis wear in a calvarial model of wear particle-induced bone resorption. Methods: Eighteen C57Bl/6 mice age 6-8 weeks were anesthetized by intraperitoneal injection of ketamine and xylazine and a 1cm midline sagittal incision was made over the calvarium anterior to the line connecting both ears. Six animals received no particles (control), and 12 received 15 ml of polyethylene particle suspension. Of the 12 mice receiving particulate, 6 were injected subcutaneously at the surgical site with 20 ml of 10 muM CGS21680 (A_2Areceptor agonist), and 6 mice were injected with saline 0.9%, beginning immediately after incision closure and continuing every other day until sacrifice. Animals were sacrificed after 14 days and the calvaria were removed, fixed, and prepared for microCT and histological staining with TRAP. Results: Histologic examination of calvaria demonstrated lymphocytic infiltration in both particle-exposed groups. TRAP staining revealed a reduction in osteoclast differentiation after treatment with CGS21680. mCT showed pitting and increased porosity in both particle-exposed groups compared to controls, although in CGS21680-treated mice the reduction in cortical bone was significantly less than in the untreated particle-exposed mice (p<0.01). Control bone volume/trabecular volume was significantly greater (p<0.005) than in either particulate group, however, calvarial bone from CGS21680-treated mice had significantly greater mean bone volume than did the untreated group (p<0.0005). Trabecular thickness was significantly reduced in both CGS21680-treated and untreated particle-exposed groups as compared to control mice (p<0.05). Finally, digital morphometric analysis of microCTs reveals that CGS21680 significantly reduced the area of bone pitting compared to control particle-treated mice (p<0.05). (Table presented) Conclusions: Adenosine A_2Areceptor activation reduces inflammation and bone destruction due to prosthetic wear particles. This observation suggests that delivery of an adenosine A_2Aagonist in the cement may enhance orthopedic implant survival, delaying or eliminating the need for revision arthroplasty surgery

A recent study presents a technique allowing one to image transcription from a single gene copy in live cells, and highlights the dynamic nature of transcriptional regulation.

Background: Accumulation of immature proteins in the Endoplasmic Reticulum (ER) causes organelle stress that is counteracted by the unfolded protein stress response (UPR). Three pathways compose the UPR and are initiated when Ire1, Perk and Atf6 respectively, are released from heterodimers formed with the ER chaperone BiP. The UPR signals down-regulation of global translation and increased ER-chaperone expression. Ire1 is phosphorylated, activating its nuclease activity, which leads to splicing of the X-box binding protein 1 (Xbp1). The spliced RNA encodes a transcription factor that regulates expression of a subset of genes that comprise one arm of the UPR. Apoptosis is initiated if homeostasis is not re-established following UPR activation. The Ire1 pathway has recently been shown to play arole in the development of vitiligo, while the UPR has been implicated in keratinocyte response to UVB and in drug resistance in melanoma. We therefore investigated the melanocyte response to ER stress induced by chemical ER disruptors and by oxidative stress (the mechanism by which we propose UV exposure perturbs the melanocyte ER). Method: Wild-type mouse melanocytes were treated with thapsigargin, which disrupts the calcium balance in the ER causing UPR induction, and cells harvested at 6, 12 and 24 h. Western blot and microarray analyses were performed and data evaluated to identify pathways activated by thapsigargin treatment. In addition, melanocytes were dosed with compounds that induce oxidative stress. RNA was harvested and evaluated for activation of the UPR by Xbp-1 splicing. Results: IRE1 expression was upregulated within 6 h of treatment with thapsigargin, which promoted splicing of XBP1 mRNA and activation of its transcription factor activity. PERK and its downstream target CHOP were phosphorylated and HA-tagged ATF6 was cleaved within 6-12 h of treatment. Up-regulation of BiP and ER chaperones such as Ero1 and down-regulation of tyrosinase were also observed. In addition, several p53-related pathways were modulated in response to thapsigargin. Induction of oxidative stress was found to induce Xbp1 splicing. Conclusions: The UPR may play an important role in melanocyte response to stress, including response to oxidative stress induced by UV exposure. Dysfunction of this response may contribute to initiation and progression of vitiligo and drug resistance in melanoma

The epsilon4 allele of apolipoprotein E (APOE) is currently the major genetic risk factor identified for Alzheimer's disease (AD). Previous in vivo data from our laboratory has demonstrated that amyloid-beta (Abeta) is rapidly removed from the plasma by the liver and kidney and that the rate of its clearance is affected by ApoE in C57BL/6J and APOE-/- mice. To expand upon these findings, we assessed the peripheral clearance of human synthetic Abeta42 in APOE epsilon2, epsilon3, and epsilon4 knock-in and APOE knock-out mice injected with lipidated recombinant apoE2, E3, and E4 protein. Our results show that APOE does influence the rate at which the mice are able to clear Abeta42 from their bloodstream. Both APOE epsilon4 mice and APOE knock-out mice treated with lipidated recombinant apoE4 demonstrated increased retention of plasma Abeta42 over time compared to APOE epsilon2/APOE knock-out rE2 and APOE epsilon3/APOE knock-out rE3 mice. These findings suggest that the peripheral clearance of Abeta42 is significantly altered by APOE genotype. Given that APOE epsilon4 is a risk factor for AD, then these novel findings provide some insight into the role of ApoE isoforms on the peripheral clearance of Abeta which may impact on clearance from the brain

Although membrane proteins make up 30% of the proteome and are a common target for therapeutic drugs, determination of their atomic structure remains a technical challenge. Electron crystallography represents an alternative to the conventional methods of X-ray diffraction and NMR and relies on the formation of two-dimensional crystals. These crystals are produced by reconstituting purified, detergent-solubilized membrane proteins back into the native environment of a lipid bilayer. This chapter reviews methods for producing two-dimensional crystals and for screening them by negative stain electron microscopy. In addition, we show examples of the different morphologies that are commonly obtained and describe basic image analysis procedures that can be used to evaluate their promise for structure determination by cryoelectron microscopy

Zebrafish has emerged in the past 5 years as a model for the study of sleep and wake behaviors. Experimental evidence has shown that periods of behavioral quiescence in zebrafish larvae and adults are sleep-like states, as these rest bouts are regulated by the circadian cycle, are associated with decreases in arousal, and are increased following rest deprivation. Furthermore, zebrafish share with mammals a hypocretin/orexin system that promotes wakefulness, and drugs that alter mammalian sleep have similar effects on zebrafish rest. In this chapter, we review the zebrafish sleep literature and describe a long-term, high-throughput monitoring system for observing sleep and wake behaviors in larval zebrafish.

OBJECTIVES: Alzheimer's disease (AD) is the leading cause of dementia and the most common form of amyloidosis in humans. Extensive extracellular deposition of amyloid-beta (Abeta), a 40-42 amino acid degradation product of APP, is considered a hallmark feature of AD. Our attention is focused on the highly heterogeneous biochemical nature of the brain Abeta species. METHODS AND POPULATION: We have fractionated water-soluble, detergent-soluble and formic acid-solube Abeta species from transgenic mouse models of amyloid deposition and AD cases. Subsequently, we applied a combination of biochemical techniques including immunoprecipitation followed by identification of Abeta fragments with a novel highly sensitive matrixassisted laser desorption/ionization time-of-flight mass spectrometry technique. RESULTS: Our biochemical data on the Abeta species present in sporadic and familial AD cases and in transgenic mouse models highlight the presence of similar N- and C-terminally truncated fragments-likely reflecting the ability of multiple proteases to degrade Abeta in situ- and several post-translational modifications with still unclear roles in the amyloidogenesis mechanism. Notably, not all the brain Abeta peptides have identical solubility properties. SIGNIFICANCE OF STUDY: In view of these findings and the growing evidence that an imbalance between Abeta production and clearance plays a major role in the process of Abeta deposition, we hypothesize that certain truncated and post-translationally modified Abeta fragments have a distinct and opposite role in clearance and fibrillization mechanisms and that the spectrum and abundance of these species vary according to the magnitude of the amyloid load

Endocytic alterations are one of the earliest changes to occur in Alzheimer's disease (AD), and are hypothesized to be involved in the selective vulnerability of specific neuronal populations during the progression of AD. Previous microarray and real-time quantitative PCR experiments revealed an upregulation of the early endosomal effector rab5 and the late endosome constituent rab7 in the hippocampus of people with mild cognitive impairment (MCI) and AD. To assess whether these select rab GTPase gene expression changes are reflected in protein levels within selectively vulnerable brain regions (basal forebrain, frontal cortex, and hippocampus) and relatively spared areas (cerebellum and striatum), we performed immunoblot analysis using antibodies directed against rab5 and rab7 on postmortem human brain tissue harvested from cases with a premortem clinical diagnosis of no cognitive impairment (NCI), MCI, and AD. Results indicate selective upregulation of both rab5 and rab7 levels within basal forebrain, frontal cortex, and hippocampus in MCI and AD, which also correlated with Braak staging. In contrast, no differences in protein levels were found in the less vulnerable cerebellum and striatum. These regional immunoblot assays are consistent with single cell gene expression data, and provide protein-based evidence for endosomal markers contributing to the vulnerability of cell types within selective brain regions during the progression of AD

Mass spectrometry is a method of choice for quantifying low-abundance proteins and peptides in many biological studies. Here, we describe a range of computational aspects of protein and peptide quantitation, including methods for finding and integrating mass spectrometric peptide peaks, and detecting interference to obtain a robust measure of the amount of proteins present in samples