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Providence, RI, United States

Meitner P.A.,Center for Cancer Research Development | Resnick M.B.,The Miriam Hospital
Methods in Molecular Biology | Year: 2011

Expression array analysis of epithelial mRNA to identify biomarkers of premalignant and malignant conditions in the gastrointestinal (GI) tract is an area of intense study. Archived formalin-fixed paraffin-embedded (FFPE) tissues documenting these changes are readily available and should be a valuable resource for retrospective analysis. Laser capture microdissection of defined areas of epithelial cells at different stages of neoplastic progression is described together with methods for prequalification of RNA in FFPE tissue blocks selected for analysis. Paradise reagents specifically designed for isolation and amplification of RNA from FFPE archival tissue specimens are used to prepare probes for the human X3P microarray from Affymetrix. © 2011 Springer Science+Business Media, LLC. Source

Josic D.,Center for Cancer Research Development | Josic D.,Brown University | Josic D.,University of Rijeka | Breen L.,Center for Cancer Research Development | And 5 more authors.
Electrophoresis | Year: 2012

Sample displacement chromatography (SDC) in reversed-phase and ion-exchange modes was introduced approximately 20 years ago. This method was first used for the preparative purification of peptides and proteins. Recently, SDC in ion-exchange mode was also successfully used for enrichment of low-abundance proteins from human plasma. In this paper, the use of SDC for the separation of plasma proteins in hydrophobic interaction mode is demonstrated. By use of two or more columns coupled in series during sample application, and subsequent elution of detached columns in parallel, additional separation of bound proteins was achieved. Further low-abundance, physiologically active proteins could be highly enriched and detected by ESI-MS/MS. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Rucevic M.,Center for Cancer Research Development | Rucevic M.,Ruder Boskovic Institute | Rucevic M.,Massachusetts Institute of Technology | Rosenquist T.,State University of New York at Stony Brook | And 6 more authors.
Journal of Proteomics | Year: 2012

Strong indications have been presented that dietary poisoning with aristolochic acids (AA) is responsible for Endemic Nephropathy (EN) and AA associated cancer of the upper urinary tract (UUTC). Our recent investigation showed drastic urinary proteome changes in AA treated mice. This study was designed to identify proteome changes associated with AA nephrotoxicity in experimental animal model. The DBA and C57BL mice, which differ in AA sensitivity, were exposed to AA for 4. days. The strategy for urinary, plasma and kidney tissue proteome study of AA exposed and control mice integrated gel-based and in-solution tryptic digestion combined with LC-ESI-MS/MS. To maximize proteome coverage, plasma fractionation scheme was developed and MS compatible sequential tissue extraction procedure was established. Proteomic analyses of urinary, plasma and kidney tissue tryptic digests resulted in identification of several cytoskeletal proteins, as well as proteins involved in kidney development and inflammatory response, that are differentially expressed in both AA exposed and control mice. These proteins are consistent with renal pathogenesis of endotoxicity and cancer. This proteomic strategy could be effectively translated for unbiased discovery of potential biomarkers for EN and associated UUTC in humans. At the same time, these results highlight the significance of AA exposure with EN. This article is part of a Special Issue entitled: Integrated omics. © 2012. Source

Rucevic M.,Center for Cancer Research Development | Rucevic M.,Ruder Boskovic Institute | Hixson D.,Center for Cancer Research Development | Hixson D.,Brown University | And 3 more authors.
Electrophoresis | Year: 2011

Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Cao L.,Center for Cancer Research Development | Clifton J.G.,Brown University | Reutter W.,Charite - Medical University of Berlin | Josic D.,Brown University | Josic D.,University of Rijeka
Analytical Chemistry | Year: 2013

The gel-based proteomic analysis of plasma membranes from rat liver and chemically induced, malignant hepatocellular carcinoma Morris hepatoma 7777 was systematically optimized to yield the maximum number of proteins containing transmembrane domains (TMDs). Incorporation of plasma membrane proteins into a polyacrylamide "tube gel" followed by in-gel digestion of "tube gel" pieces significantly improved detection by electrospray ionization-liquid chromatography-tandem mass spectrometry. Removal of less hydrophobic proteins by washing isolated plasma membranes with 0.1 M sodium carbonate enables detection of a higher number of hydrophobic proteins containing TMDs in both tissues. Subsequent treatment of plasma membranes by a proteolytic enzyme (trypsin) causes the loss of some of the proteins that are detected after washing with sodium carbonate, but it enables the detection of other hydrophobic proteins containing TMDs. Introduction of mass spectrometers with higher sensitivity, higher mass resolution and mass accuracy, and a faster scan rate significantly improved detection of membrane proteins, but the improved sample preparation is still useful and enables detection of additional hydrophobic proteins. Proteolytic predigestion of plasma membranes enables detection of additional hydrophobic proteins and better sequence coverage of TMD-containing proteins in plasma membranes from both tissues. © 2013 American Chemical Society. Source

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