Proteogenomics Research Institute for Systems Medicine

San Diego, CA, United States

Proteogenomics Research Institute for Systems Medicine

San Diego, CA, United States
Time filter
Source Type

Halawani D.,McGill University | Tessier S.,University of Montréal | Anzellotti D.,McGill University | Bennett D.A.,Rush University Medical Center | And 4 more authors.
Journal of Neuroscience | Year: 2010

The valosin-containing protein (p97) is a ubiquitin-dependent ATPase that plays central roles in ubiquitin proteasome system (UPS)-mediated protein degradation pathways. p97 has been recently identified as a putative substrate of active Caspase-6 (Casp6) in primary humanneurons. Since Casp6 is activated in mild cognitive impairment (MCI) and Alzheimer's disease (AD) patients' brains, the targeting of p97 by Casp6 may represent an important step that leads to UPS impairment in AD. Here, we show that p97 is a Casp6 substrate in vitro and in vivo. Casp6 cleavage of recombinant p97 generated two N-terminal fragments of 28 and 20 kDa, which were not generated by the other two effector caspases, Caspase-3 and Caspase-7. ATP binding to the D1 ATPase ring of p97 reduced the susceptibility of the N-domain to caspase-mediated proteolysis. Mass spectrometric analysis identified VAPD179 as a Casp6 cleavage site within p97's N-domain. An anti-neoepitope serum immunohistochemically detected p97 cleaved at VAPD179 in the cytoplasm of the cell soma and neurites of hippocampal neurons in MCI and AD. Overexpression of p97 (1-179) fragment, representing p97 cleaved at D179, impaired the degradation of model substrates in the ubiquitin-fusion degradation and the N-end rule pathways, and destabilized endogenous p97. Collectively, these results show that p97 is cleaved by Casp6 in AD and suggest p97 cleavage as an important mechanism for UPS impairment. Copyright © 2010 the authors.

Lopez E.,Hospital 12 Of Octubre | Madero L.,Hospital Infantil Universitario Nino Jesus | Lopez-Pascual J.,Hospital Universitario 12 Of Octubre | Latterich M.,Proteogenomics Research Institute for Systems Medicine
Proteome Science | Year: 2012

Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems, spanning areas of basic biological research, clinical diagnostics, and biomarker discovery directed toward therapeutic applications. Recent advances in protein separation and identification techniques have significantly improved proteomic approaches, leading to enhancement of the depth and breadth of proteome coverage.Proteomic signatures, specific for multiple diseases, including cancer and pre-invasive lesions, are emerging. This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus helping to improve applications of clinical proteomic strategies for translational medicine research. © 2012 Lopez et al.; licensee BioMed Central Ltd.

Dubey R.,University of Southern California | Levin M.D.,Proteogenomics Research Institute for Systems Medicine | Szabo L.Z.,University of Arizona | Laszlo C.F.,University of Arizona | And 5 more authors.
Journal of the American Chemical Society | Year: 2013

Hypoxia is a hallmark of solid tumors, is associated with local invasion, metastatic spread, resistance to chemo-and radiotherapy, and is an independent, negative prognostic factor for a diverse range of malignant neoplasms. The cellular response to hypoxia is primarily mediated by a family of transcription factors, among which hypoxia-inducible factor 1 (HIF1) plays a major role. Under normoxia, the oxygen-sensitive α subunit of HIF1 is rapidly and constitutively degraded but is stabilized and accumulates under hypoxia. Upon nuclear translocation, HIF1 controls the expression of over 100 genes involved in angiogenesis, altered energy metabolism, antiapoptotic, and pro-proliferative mechanisms that promote tumor growth. A designed transcriptional antagonist, dimeric epidithiodiketopiperazine (ETP 2), selectively disrupts the interaction of HIF1α with p300/CBP coactivators and downregulates the expression of hypoxia-inducible genes. ETP 2 was synthesized via a novel homo-oxidative coupling of the aliphatic primary carbons of the dithioacetal precursor. It effectively inhibits HIF1-induced activation of VEGFA, LOX, Glut1, and c-Met genes in a panel of cell lines representing breast and lung cancers. We observed an outstanding antitumor efficacy of both (±)-ETP 2 and meso-ETP 2 in a fully established breast carcinoma model by intravital microscopy. Treatment with either form of ETP 2 (1 mg/kg) resulted in a rapid regression of tumor growth that lasted for up to 14 days. These results suggest that inhibition of HIF1 transcriptional activity by designed dimeric ETPs could offer an innovative approach to cancer therapy with the potential to overcome hypoxia-induced tumor growth and resistance. © 2013 American Chemical Society.

Chrastina A.,Proteogenomics Research Institute for Systems Medicine | Schnitzer J.E.,Proteogenomics Research Institute for Systems Medicine
Experimental Lung Research | Year: 2012

Pulmonary infarction is a life-threatening lung injury that requires rapid and accurate diagnosis for proper treatment. Targetable and reproducible small-animal models that would allow experimental development and preclinical evaluation of diagnostic methods for detecting pulmonary infarction are critically missing. The authors report here a novel procedure to selectively induce pulmonary infarction by photodestructive laser-light irradiation in a targeted location within a specific lung compartment after administration of a photosensitizer. Histopathological analysis of the illuminated lung tissue revealed massive hemorrhage and vascular occlusion after acute injury localized to the site of irradiation. Collapse of alveolar structure, neutrophil influx, and necrosis were subsequently observed. Computed tomography (CT) scans showed evidence of abnormal density and airspace consolidation in the irradiated area of the lung, but not elsewhere in the lung compartment. Perfusion imaging using 99mTc-labeled macroaggregated albumin by single-photon emission computed tomography revealed diminished scintigraphic signal in the opaque area of infarcted lung tissue. The histological changes, CT findings, and perfusion characteristics of pulmonary infarction are mimicked using laser-irradiated, photosensitizer-mediated photodestruction to selectively induce chronic lung injury in a localized area. This small-animal model can be easily and readily used for targeted induction of pulmonary infarction in a designated area of lung compartment and offers the potential for use in evaluating novel diagnostic and therapeutic methods. © 2011 Informa Healthcare USA, Inc.

Chrastina A.,Proteogenomics Research Institute for Systems Medicine | Pokreisz P.,Catholic University of Leuven | Schnitzer J.E.,Proteogenomics Research Institute for Systems Medicine
American Journal of Physiology - Heart and Circulatory Physiology | Year: 2014

We describe a novel model of myocardial infarction (MI) in rats induced by percutaneous transthoracic low-energy laser-targeted photodynamic irradiation. The procedure does not require thoracotomy and represents a minimally invasive alternative to existing surgical models. Target cardiac area to be photodynamically irradiated was triangulated from the thoracic X-ray scans. The acute phase of MI was histopathologically characterized by the presence of extensive vascular occlusion, hemorrhage, loss of transversal striations, neutrophilic infiltration, and necrotic changes of cardiomyocytes. Consequently, damaged myocardium was replaced with fibrovascular and granulation tissue. The fibrotic scar in the infarcted area was detected by computer tomography imaging. Cardiac troponin I (cTnI), a specific marker of myocardial injury, was significantly elevated at 6 h (41 ± 6 ng/ml, n 4, P<0.05 vs. baseline) and returned to baseline after 72 h. Triphenyltetrazolium chloride staining revealed transmural anterolateral infarcts targeting 25 ± 3% of the left ventricle at day 1 with a decrease to 20 ± 3% at day 40 (n 6 for each group, P <0.01 vs. day 1). Electrocardiography (ECG) showed significant ST-segment elevation in the acute phase with subsequent development of a pathological Q wave and premature ventricular contractions in the chronic phase of MI. Vectorcardiogram analysis of spatiotemporal electrical signal transduction revealed changes in inscription direction, QRS loop morphology, and redistribution in quadrant areas. The photodynamically induced MI in n 51 rats was associated with 12% total mortality. Histological findings, ECG abnormalities, and elevated cTnI levels confirmed the photosensitizer-dependent induction of MI after laser irradiation. This novel rodent model of MI might provide a platform to evaluate new diagnostic or therapeutic interventions. © 2014 the American Physiological Society.

Chrastina A.,Proteogenomics Research Institute for Systems Medicine | Schnitzer J.E.,Proteogenomics Research Institute for Systems Medicine
International Journal of Nanomedicine | Year: 2010

Silver nanoparticles are increasingly finding applications in medicine; however, little is known about their in vivo tissue distribution. Here, we have developed a rapid method for radiolabeling of silver nanoparticles with iodine-125 in order to track in vivo tissue uptake of silver nanoparticles after systemic administration by biodistribution analysis and single-photon emission computerized tomography (SPECT) imaging. Poly(N-vinyl-2 -pyrrolidone)-capped silver nanoparticles with an average size of 12 nm were labeled by chemisorption of iodine-125 with a >80% yield of radiolabeling efficiency. Radiolabeled silver nanoparticles were intravenously injected in Balb/c mice, and the in vivo distribution pattern of these nanoparticles was evaluated by noninvasive whole-body SPECT imaging, which revealed uptake of the nanoparticles in the liver and spleen. Biodistribution analysis confirmed predominant accumulation of the silver nanoparticles in the spleen (41.5%ID/g) and liver (24.5%ID/g) at 24 h. Extensive uptake in the tissues of the reticuloendothelial system suggests that further investigation of silver nanoparticle interaction with hepatic and splenic tissues at the cellular level is critical for evaluation of the in vivo effects and potential toxicity of silver nanoparticles. This method enables rapid iodine-125 radiolabeling of silver nanoparticles with a specific activity sufficient for in vivo imaging and biodistribution analysis. © 2010 Chrastina and Schnitzer, publisher and licensee Dove Medical Press Ltd.

Yi M.,Proteogenomics Research Institute for Systems Medicine
PLoS ONE | Year: 2012

Annexin A1 is a multi functional molecule which is involved in inflammation, innate and adaptive immune systems, tumor progression and metastasis. We have previously showed the impaired tumor growth, metastasis, angiogenesis and wound healing in annexin A1 knockout mice. While tumor is a piece of heterogeneous mass including not only malignant tumor cells but also the stroma, the importance of the tumor stroma for tumor progression and metastasis is becoming increasingly clear. The tumor stroma is comprised by various components including extracellular matrix and non-malignant cells in the tumor, such as endothelial cells, fibroblasts, immune cells, inflammatory cells. Based on our previous finding of pro-angiogenic functions for annexin A1 in vascular endothelial cell sprouting, wound healing, tumor growth and metastasis, and the previously known properties for annexin A1 in immune cells and inflammation, this study hypothesized that annexin A1 is a key functional player in tumor development, linking the various components in tumor stroma by its actions in endothelial cells and immune cells. Using systems analysis programs commercially available, this paper further compared the gene expression between tumors from annexin A1 wild type mice and annexin A1 knockout mice and found a list of genes that significantly changed in the tumor stroma that lacked annexin A1. This revealed annexin A1 to be an effective regulator in tumor stroma and suggested a mechanism that annexin A1 affects tumor development and metastasis through interaction with the various components in the microenvironment surrounding the tumor cells. © 2012 Ming Yi.

Griffin N.M.,Proteogenomics Research Institute for Systems Medicine | Schnitzer J.E.,Proteogenomics Research Institute for Systems Medicine
Molecular and Cellular Proteomics | Year: 2011

Plasma membranes form a critical biological interface between the inside of every cell and its external environment. Their roles in multiple key cellular functions make them important drug targets. However the protein composition of plasma membranes in general is poorly defined as the inherent properties of lipid embedded proteins, such as their hydrophobicity, low abundance, poor solubility and resistance to digestion and extraction makes them difficult to isolate, solubilize, and identify on a large scale by traditional mass spectrometry methods. Here we describe some of the significant advances that have occurred over the past ten years to address these challenges including: i) the development of new and improved membrane isolation techniques via either subfractionation or direct labeling and isolation of plasma membranes from cells and tissues; ii) modification of mass spectrometry methods to adapt to the hydrophobic nature of membrane proteins and peptides; iii) improvements to digestion protocols to compensate for the shortage of trypsin cleavage sites in lipid-embedded proteins, particularly multi-spanning proteins, and iv) the development of numerous bioinformatics tools which allow not only the identification and quantification of proteins, but also the prediction of membrane protein topology, membrane post-translational modifications and subcellular localization. This review emphasis the importance and difficulty of defining cells in proper patho- and physiological context to maintain the in vivo reality. We focus on how key technological challenges associated with the isolation and identification of cell surface proteins in tissues using mass spectrometry are being addressed in order to identify and quantify a comprehensive plasma membrane for drug and target discovery efforts. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Chrastina A.,Proteogenomics Research Institute for Systems Medicine | Massey K.A.,Proteogenomics Research Institute for Systems Medicine | Schnitzer J.E.,Proteogenomics Research Institute for Systems Medicine
Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology | Year: 2011

Nanoparticles have been investigated as promising nanocarriers for delivery of imaging and therapeutic agents for several decades, but have met with limited success. Although enormous progress in the fields of nanotechnology and nanoscience has been achieved, basic discoveries have not yet translated into effective targeted therapies. Nanoparticles can potentially improve the pharmacokinetics and pharmacodynamics of drugs; however, the complexity of in vivo systems imposes multiple barriers that severely inhibit efficiency and have to be overcome to fully exploit the theoretical potential of nanoparticles. Here, we address two major challenges to effective systemic nanodelivery. Both limited penetration across the vascular endothelium and uptake by the reticuloendothelial system (RES) substantially impede effectiveness of nanoparticle delivery into tissues. Although the design of nanoparticles with extended circulation half-life is essential, it is not sufficient for effective penetration of nanoparticles across the formidable barrier formed by the vascular endothelium. Current nanodelivery systems rely on passive transvascular exchange and tissue accumulation. They require high dosages to create large concentration gradients that drive nanoparticles passively across the blood-tissue interface. However, passive accumulation has resulted in only a fractional dosage of nanoparticles penetrating into target tissue. This inevitably diminishes therapeutic efficacy and aggravates potential side effects. Although there are multiple ways to augment passive delivery, active delivery of targeted nanoparticles across the vascular endothelium could significantly increase the therapeutic index and decrease side effects of nanoparticle-based drug delivery systems. Use of active transendothelial transport pathways, such as caveolae, may provide an effective solution to both target and deliver nanoparticles. © 2011 John Wiley & Sons, Inc..

Schnitzer J.E.,Proteogenomics Research Institute for Systems Medicine
Recent Results in Cancer Research | Year: 2010

All blood vessels are lined by a layer of endothelial cells that help to control vascular permeability. The luminal surface of vascular endothelial cells is studded with transport vesicles called caveolae that are directly in contact with the blood and can transport molecules into and across the endothelium. The vasculature within distinct tissue types expresses a unique array of proteins that can be used to target intravenously injected antibodies directly to that tissue. When the tissuespecific proteins are concentrated in caveolae, the antibodies can be rapidly pumped out of the blood and into the tissue. Tumors appear to be a distinct tissue type with their own unique marker proteins. Targeting accessible proteins at the surface of tumor vasculature with radiolabeled antibodies destroys tumors and drastically increases animal survival. One day, it may be possible to specifically pump targeted molecules into tumors. This could increase therapeutic efficacy and decrease side effects because most of the drug would accumulate specifically in the tumor. Thus, targeting caveolae may provide a universal portal to pump drugs, imaging agents, and gene vectors out of the blood and into underlying tissue. © 2010 Springer-Verlag Berlin Heidelberg.

Loading Proteogenomics Research Institute for Systems Medicine collaborators
Loading Proteogenomics Research Institute for Systems Medicine collaborators