Comparison of LIRADS 5 Image Guided Core Biopsy Derived From Formalin Fixed and Frozen Tissue Cores for Radiogenomics and Radioproteomics Analysis in Well, Moderate and Poorly Differentiated Hepatocellular Carcinoma.

The aim of this pilot study is to evaluate and compare the quality of the genomics and proteomics data obtained from paired Formalin Fixed Paraffin Embedded (FFPE) and frozen (FF) tissue percutaneous core biopsies of Liver Imaging Reporting and Data System 5 (LIRADS 5) hepatocellular carcinoma (HCC) of varying histological grades. The preliminary data identified differentially expressed proteins and genes in poor, moderate and well differentiated HCC biopsies, with a greater efficacy in fresh frozen samples. The data offered valuable insights into the characteristics and suitability of samples for future studies.

Proteogenomics for pediatric brain cancer.

Pediatric central nervous system tumors are the most common tumors in children, it constitute 15%-20% of all malignancies in children and are the leading cause of cancer related deaths in children. Proteogenomics is an emerging field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of biomarkers for diagnosis and therapeutic purposes. Integrative proteogenomics analysis of pediatric tumors identified underlying biological processes and potential treatments as well as the functional effects of somatic mutations and copy number variation driving tumorigenesis.

Proteomics identification of radiation-induced changes of membrane proteins in the rat model of arteriovenous malformation in pursuit of targets for brain AVM molecular therapy.

BACKGROUND: Rapid identification of novel targets and advancement of a vascular targeting strategy requires a comprehensive assessment of AVM endothelial membrane protein changes in response to irradiation. The aim of this study is to provide additional potential target protein molecules for evaluation in animal trials to promote intravascular thrombosis in AVM vessels post radiosurgery. METHODS: We employed in vivo biotinylation methodology that we developed, to label membrane proteins in the rat model of AVM post radiosurgery. Mass spectrometry expression (MSE) analysis was used to identify and quantify surface protein expression between irradiated and non irradiated rats, which mimics a radiosurgical treatment approach. RESULTS: Our proteomics data revealed differentially expressed membrane proteins between irradiated and non irradiated rats, e.g. profilin-1, ESM-1, ion channel proteins, annexin A2 and lumican. CONCLUSION: This work provides additional potential target protein molecules for evaluation in animal trials to promote intravascular thrombosis in AVM vessels post radiosurgery.

Integral membrane proteins: bottom-up, top-down and structural proteomics.

INTRODUCTION: Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information. Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.

Identification of protein targets in cerebral endothelial cells for brain arteriovenous malformation (AVMs) molecular therapies.

BACKGROUND: To develop a new molecular targeted treatment for brain (AVMs), identification of membrane proteins that are localised on the AVM endothelium is crucial. Current treatment methods are surgery and radiosurgery. However, complete occlusion post radiosurgery are achieved within 3 years, while patient remain at risk of haemorrhage. This study aims to identify potential protein targets in AVM endothelial cells that discriminate these vessels from normal vessels; these proteins targets will be investigated for the molecular therapy of brain AVMs to promote rapid thrombosis after radiosurgery. METHODS: We employed in vitro biotinylation that we developed, and mass spectrometry to detect cell surface-exposed proteins in cultures of murine cerebral endothelial cells (bEnd.3). Two forms of mass spectrometry were applied (iTRAQ-MS and MSE) to identify and quantify membrane protein expression at various time-points following irradiation which simulates a radiosurgical treatment approach. Immunocytochemistry was used to confirm the expression of selected membrane proteins. ProteinPilot V4.0 software was used to analyse the iTRAQ-MS data and the MSE data was analysed using ProteinLynx Global Server version 2.5 software. RESULTS: The proteomics data revealed several differentially expressed membrane proteins between irradiated and non-irradiated cells at specific time points, e.g. PECAM-1, cadherin-5, PDI, EPCR and integrins. Immunocytochemistry data confirmed the expression of these proteins. CONCLUSION: Cell surface protein biotinylation and proteomics analysis successfully identified membrane proteins from murine brain endothelial cells in response to irradiation. This work suggests potential target protein molecules for evaluation in animal models of brain-AVM.

Radiosurgery Alters the Endothelial Surface Proteome: Externalized Intracellular Molecules as Potential Vascular Targets in Irradiated Brain Arteriovenous Malformations.

Stereotactic radiosurgery (SRS) is an established treatment for brain arteriovenous malformations (AVMs) that drives blood vessel closure through cellular proliferation, thrombosis and fibrosis, but is limited by a delay to occlusion of 2-3 years and a maximum treatable size of 3 cm. In this current study we used SRS as a priming tool to elicit novel protein expression on the endothelium of irradiated AVM vessels, and these proteins were then targeted with prothrombotic conjugates to induce rapid thrombosis and vessel closure. SRS-induced protein changes on the endothelium in an animal model of AVM were examined using in vivo biotin labeling of surface-accessible proteins and comparative proteomics. LC-MS/MS using SWATH acquisition label-free mass spectrometry identified 280 proteins in biotin-enriched fractions. The abundance of 56 proteins increased after irradiation of the rat arteriovenous fistula (20 Gy, ≥1.5-fold). A large proportion of intracellular proteins were present in this subset: 29 mitochondrial and 9 cytoskeletal. Three of these proteins were chosen for further validation based on previously published evidence for surface localization and a role in autoimmune stimulation: cardiac troponin I (TNNI3); manganese superoxide dismutase (SOD2); and the E2 subunit of the pyruvate dehydrogenase complex (PDCE2). Immunostaining of AVM vessels confirmed an increase in abundance of PDCE2 across the vessel wall, but not a measurable increase in TNNI3 or SOD2. All three proteins co-localized with the endothelium after irradiation, however, more detailed subcellular distribution could not be accurately established. In vitro, radiation-stimulated surface translocation of all three proteins was confirmed in nonpermeabilized brain endothelial cells using immunocytochemistry. Total protein abundance increased modestly after irradiation for PDCE2 and SOD2 but decreased for TNNI3, suggesting that radiation primarily affects subcellular distribution rather than protein levels. The novel identification of these proteins as surface exposed in response to radiation raises important questions about their potential role in radiation-induced inflammation, fibrosis and autoimmunity, but may also provide unique candidates for vascular targeting in brain AVMs and other vascular tissues.

Proteomics Analysis of Brain Meningiomas in Pursuit of Novel Biomarkers of the Aggressive Behavior.

The aim of this pilot study was to evaluate the use of advanced proteomics techniques to identify novel protein markers that contribute to the transformation of benign meningiomas to more aggressive and malignant subtypes. Multiplex peptide stable isotope dimethyl labelling and nano-LCMS was used to identify and quantify the differentially expressed proteins in WHO Grade I, II and III meningioma tissues. The proteins identified will help elucidate the process of transformation to malignancy and may contribute to improved diagnosis and treatment of these aggressive tumors.

Proteomic clues to the identification of QX disease-resistance biomarkers in selectively bred Sydney rock oysters, Saccostrea glomerata.

The Sydney rock oyster, Saccostrea glomerata, is susceptible to infection by the protozoan parasite, Marteilia sydneyi, the causative agent of QX disease. M. sydneyi infection peaks during summer when QX disease can cause up to 95% mortality. The current study takes a proteomic approach using 2-dimensional electrophoresis and mass spectrometry to identify markers of QX disease resistance among Sydney rock oysters. Proteome maps were developed for QX disease-resistant and -susceptible oysters. Six proteins in those maps were clearly associated with resistance and so were characterized by mass spectrometry. Two of the proteins (p9 and p11) were homologous to superoxide dismutase-like molecules from the Pacific oyster, Crassostrea gigas, and the Eastern oyster, Crassostrea virginica. The remaining S. glomerata proteins had no obvious similarities to known molecules in sequence databases. p9 and p11 are currently being investigated as potential markers for the selective breeding of QX disease-resistant oysters.