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Clinical Proteomics

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https://www.readbyqxmd.com/read/27895544/mesoporous-silica-chip-enabled-peptide-profiling-as-an-effective-platform-for-controlling-bio-sample-quality-and-optimizing-handling-procedure
#1
Kai Liang, Hongmei Wu, Tony Y Hu, Yan Li
BACKGROUND: High quality clinical samples are critical for meaningful interpretation of data obtained in both basic and translational medicine. More specifically, optimized pre-analysis handling to bio-sample is crucial for avoiding biased analysis in a clinical setting. A universally applicable method for the evaluation of sample quality and pre-analysis handling is therefore in great demand. METHODS: The fingerprint pattern of low molecular weight (LMW) peptides in sera is directly associated with sample quality and handling process...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27895543/proteome-analysis-of-excretory-secretory-proteins-of-entamoeba-histolytica-hm1-imss-via-lc-esi-ms-ms-and-lc-maldi-tof-tof
#2
Jorim Anak Ujang, Soon Hong Kwan, Mohd Nazri Ismail, Boon Huat Lim, Rahmah Noordin, Nurulhasanah Othman
BACKGROUND: Excretory-secretory (ES) proteins of E. histolytica are thought to play important roles in the host invasion, metabolism, and defence. Elucidation of the types and functions of E. histolytica ES proteins can further our understanding of the disease pathogenesis. Thus, the aim of this study is to use proteomics approach to better understand the complex ES proteins of the protozoa. METHODS: E. histolytica ES proteins were prepared by culturing the trophozoites in protein-free medium...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27833472/integrated-glycomic-analysis-of-ovarian-cancer-side-population-cells
#3
Ran Zhao, Xiaoxia Liu, Yisheng Wang, Xiaoxiang Jie, Ruihuan Qin, Wenjun Qin, Mengyu Zhang, Haiyan Tai, Caiting Yang, Lili Li, Peike Peng, Miaomiao Shao, Xingwang Zhang, Hao Wu, Yuanyuan Ruan, Congjian Xu, Shifang Ren, Jianxin Gu
BACKGROUND: Ovarian cancer is the most lethal gynecological malignancy due to its frequent recurrence and drug resistance even after successful initial treatment. Accumulating scientific evidence indicates that subpopulations of cancer cells with stem cell-like properties, such as so-called side population (SP) cells, are primarily responsible for these recurrences. A better understanding of SP cells may provide new clues for detecting and targeting these cancer-initiating cells and ultimately help to eradicate cancer...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27822170/proteomics-in-india-the-clinical-aspect
#4
REVIEW
Somaditya Mukherjee, Arun Bandyopadhyay
Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27799870/proteomic-profiling-of-lung-adenocarcinoma-indicates-heightened-dna-repair-antioxidant-mechanisms-and-identifies-lasp1-as-a-potential-negative-predictor-of-survival
#5
Johannes F Fahrmann, Dmitry Grapov, Brett S Phinney, Carol Stroble, Brian C DeFelice, William Rom, David R Gandara, Yanhong Zhang, Oliver Fiehn, Harvey Pass, Suzanne Miyamoto
BACKGROUND: Lung cancer is the leading cause of cancer mortality in the United States. Non-small cell lung cancer accounts for 85% of all lung cancers for which adenocarcinoma is the most common histological type. Management of lung cancer is hindered by high false-positive rates due to difficulty resolving between benign and malignant tumors. Better molecular analysis comparing malignant and non-malignant tissues will provide important evidence of the underlying biology contributing to tumorigenesis...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27799869/proteomic-profiling-of-retinoblastoma-by-high-resolution-mass-spectrometry
#6
Ravikanth Danda, Kalaivani Ganapathy, Gajanan Sathe, Anil K Madugundu, Sharavan Ramachandran, Uma Maheswari Krishnan, Vikas Khetan, Pukhraj Rishi, T S Keshava Prasad, Akhilesh Pandey, Subramanian Krishnakumar, Harsha Gowda, Sailaja V Elchuri
BACKGROUND: Retinoblastoma is an ocular neoplastic cancer caused primarily due to the mutation/deletion of RB1 gene. Due to the rarity of the disease very limited information is available on molecular changes in primary retinoblastoma. High throughput analysis of retinoblastoma transcriptome is available however the proteomic landscape of retinoblastoma remains unexplored. In the present study we used high resolution mass spectrometry-based quantitative proteomics to identify proteins associated with pathogenesis of retinoblastoma...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27799868/antibody-based-proteomics-to-identify-an-apoptosis-signature-for-early-recurrence-of-hepatocellular-carcinoma
#7
Noriaki Morofuji, Hidenori Ojima, Nobuyoshi Hiraoka, Takuji Okusaka, Minoru Esaki, Satoshi Nara, Kazuaki Shimada, Yoshiro Kishi, Tadashi Kondo
BACKGROUND: Early recurrence after surgical resection is a hallmark of poor prognosis in hepatocellular carcinoma (HCC). To determine the proteomic background of early recurrence of HCC, we focused on apoptosis-related proteins. METHODS: Surgically resected tumor tissues were obtained from 80 patients, including HCC tumor tissues, non-tumor tissues, and normal liver tissues. These samples were grouped in the discovery and validation sample sets. The expression level of 192 apoptosis-related proteins was monitored using 247 commercially available antibodies and western blotting...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27795698/implementation-and-evaluation-of-amyloidosis-subtyping-by-laser-capture-microdissection-and-tandem-mass-spectrometry
#8
Peter Mollee, Samuel Boros, Dorothy Loo, Jayde E Ruelcke, Vanessa A Lakis, Kim-Anh Lê Cao, Patricia Renaut, Michelle M Hill
BACKGROUND: Correct identification of the amyloidosis-causing protein is crucial for clinical management. Recently the Mayo Clinic reported laser-capture microdissection (LCM) with liquid chromatography-coupled tandem mass spectrometry (MS/MS) as a new diagnostic tool for amyloid diagnosis. Here, we report an independent implementation of this proteomic diagnostics method at the Princess Alexandra Hospital Amyloidosis Centre in Brisbane, Australia. RESULTS: From 2010 to 2014, 138 biopsies received from 35 different organ sites were analysed by LCM-MS/MS using Congo Red staining to visualise amyloid deposits...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27761105/fibrinogen-alpha-c-chain-5-9%C3%A2-kda-fragment-fic5-9-a-biomarker-for-various-pathological-conditions-is-produced-in-post-blood-collection-by-fibrinolysis-and-coagulation-factors
#9
Wataru Kikuchi, Motoi Nishimura, Takahisa Kuga, Sachio Tsuchida, Tatsuya Saito, Mamoru Satoh, Kenta Noda, Yoshio Kodera, Takeshi Tomonaga, Fumio Nomura
BACKGROUND: Fibrinogen alpha C chain 5.9 kDa fragment (FIC5.9) is a new serum biomarker for chronic hepatitis that was discovered by proteomics analysis. Previous studies have shown that FIC5.9 is derived from the C-terminal region of fibrinogen alpha chain and the serum levels of FIC5.9 decrease in chronic hepatitis. It also have been reported that FIC5.9 cannot be detected in the blood stream of the systemic circulation and it is released from fibrinogen during blood clotting in collecting tube...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27757071/n-glycosylation-proteome-enrichment-analysis-in-kidney-reveals-differences-between-diabetic-mouse-models
#10
Leena Liljedahl, Maiken Højgaard Pedersen, Jenny Norlin, James N McGuire, Peter James
BACKGROUND: Diabetic nephropathy (DN) is a late complication in both type 1 diabetes mellitus (T1DM) and T2DM. Already at an early stage of DN morphological changes occur at the cell surface and in the extracellular matrix where the majority of the proteins carry N-linked glycosylations. These glycosylated proteins are highly important in cell adhesion and cell-matrix processes but not much is known about how they change in DN or whether the distinct etiology of T1DM and T2DM could have an effect on their abundances...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27713681/mass-spectrometry-based-approaches-to-targeted-quantitative-proteomics-in-cardiovascular-disease
#11
Clementina Mesaros, Ian A Blair
Mass spectrometry-based proteomics methodology has become an important tool in elucidating some of the underlying mechanisms involved in cardiovascular disease. The present review provides details on selected important protein targets where highly selective and specific mass spectrometry-based approaches have led to important new findings and provided new mechanistic information. The role of six proteins involved in the etiology of cardiovascular disease (acetylated platelet cyclooxygenase-1, serum apolipoprotein A1, apolipoprotein C-III, serum C-reactive protein, serum high mobility group box-1 protein, insulin-like growth factor I) and their quantification has been discussed...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27708557/plasma-degradome-affected-by-variable-storage-of-human-blood
#12
Maria Kaisar, Leon F A van Dullemen, Marie-Laëtitia Thézénas, M Zeeshan Akhtar, Honglei Huang, Sandrine Rendel, Philip D Charles, Roman Fischer, Rutger J Ploeg, Benedikt M Kessler
BACKGROUND: The successful application of-omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio banks. Mining the plasma proteome holds promise to improve our understanding of disease mechanisms and may represent a source of biomarkers. However, a major confounding factor for defining disease-specific proteomic signatures in plasma is the variation in handling and processing of clinical samples leading to protein degradation...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27708556/precision-medicine-from-pharmacogenomics-to-pharmacoproteomics
#13
Allison B Chambliss, Daniel W Chan
Disease progression and drug response may vary significantly from patient to patient. Fortunately, the rapid development of high-throughput 'omics' technologies has allowed for the identification of potential biomarkers that may aid in the understanding of the heterogeneities in disease development and treatment outcomes. However, mechanistic gaps remain when the genome or the proteome are investigated independently in response to drug treatment. In this article, we discuss the current status of pharmacogenomics in precision medicine and highlight the needs for concordant analysis at the proteome and metabolome levels via the more recently-evolved fields of pharmacoproteomics, toxicoproteomics, and pharmacometabolomics...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27688741/increased-sialylation-of-site-specific-o-glycoforms-of-hemopexin-in-liver-disease
#14
Miloslav Sanda, Julius Benicky, Jing Wu, Yiwen Wang, Kepher Makambi, Jaeil Ahn, Coleman I Smith, Peng Zhao, Lihua Zhang, Radoslav Goldman
BACKGROUND: Non-invasive monitoring of liver disease remains an important health issue. Liver secreted glycoproteins reflect pathophysiological states of the organ and represent a rational target for serologic monitoring. In this study, we describe sialylated O-glycoforms of liver-secreted hemopexin (HPX) and quantify them as a ratio of disialylated to monosialylated form (S-HPX). METHODS: We measured S-HPX in serum of participants of the HALT-C trial using a LC-MS/MS-MRM assay...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27651752/adapting-extracellular-matrix-proteomics-for-clinical-studies-on-cardiac-remodeling-post-myocardial-infarction
#15
REVIEW
Merry L Lindsey, Michael E Hall, Romain Harmancey, Yonggang Ma
Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of cardiac wound healing responses that involve stimulation of robust inflammation to clear necrotic myocytes and tissue debris and induction of extracellular matrix (ECM) protein synthesis to generate a scar. Proteomic strategies provide us with a means to index the ECM proteins expressed in the LV, quantify amounts, determine functions, and explore interactions. This review will focus on the efforts taken in the proteomics research field that have expanded our understanding of post-MI LV remodeling, concentrating on the strengths and limitations of different proteomic approaches to glean information that is specific to ECM turnover in the post-MI setting...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27597813/development-of-a-liquid-chromatography-high-resolution-mass-spectrometry-method-for-the-quantitation-of-viral-envelope-glycoprotein-in-ebola-virus-like-particle-vaccine-preparations
#16
Lisa H Cazares, Michael D Ward, Ernst E Brueggemann, Tara Kenny, Paul Demond, Christopher R Mahone, Karen A O Martins, Jonathan E Nuss, Trevor Glaros, Sina Bavari
BACKGROUND: Ebola virus like particles (EBOV VLPs, eVLPs), are produced by expressing the viral transmembrane glycoprotein (GP) and structural matrix protein VP40 in mammalian cells. When expressed, these proteins self-assemble and bud from 'host' cells displaying morphology similar to infectious virions. Several studies have shown that rodents and non-human primates vaccinated with eVLPs are protected from lethal EBOV challenge. The mucin-like domain of envelope glycoprotein GP1 serves as the major target for a productive humoral immune response...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27528862/a-proteomic-evaluation-of-urinary-changes-associated-with-cardiopulmonary-bypass
#17
Ravi C Dwivedi, Mario Navarrete, Nora Choi, Victor Spicer, Claudio Rigatto, Rakesh C Arora, Oleg Krokhin, Julie Ho, John A Wilkins
BACKGROUND: The urinary proteome of patients undergoing cardiopulmonary bypass (CPB) may provide important insights into systemic and renal changes associated with the procedure. Such information may ultimately provide a basis to differentiate changes or properties associated with the development of acute kidney injury. While mass spectrometry (MS) analysis offers the potential for in-depth compositional analysis it is often limited in coverage and relative quantitation capacity. The aim of this study was to develop a process flow for the preparation and comparison of the intraoperative urinary proteome...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27499720/quantification-of-angiotensin-ii-regulated-proteins-in-urine-of-patients-with-polycystic-and-other-chronic-kidney-diseases-by-selected-reaction-monitoring
#18
Ana Konvalinka, Ihor Batruch, Tomas Tokar, Apostolos Dimitromanolakis, Shelby Reid, Xuewen Song, York Pei, Andrei P Drabovich, Eleftherios P Diamandis, Igor Jurisica, James W Scholey
BACKGROUND: Angiotensin-II (Ang II) mediates progression of autosomal-dominant polycystic kidney disease (ADPKD) and other chronic kidney diseases (CKD). However, markers of kidney Ang II activity are lacking. We previously defined 83 Ang II-regulated proteins in vitro, which reflected kidney Ang II activity in vivo. METHODS: In this study, we developed selected reaction monitoring (SRM) assays for quantification of Ang II-regulated proteins in urine of ADPKD and CKD patients...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27429603/identification-of-potential-protein-biomarkers-for-early-detection-of-pregnancy-in-cow-urine-using-2d-dige-and-label-free-quantitation
#19
Preeti Rawat, Shveta Bathla, Rubina Baithalu, Munna Lal Yadav, Sudarshan Kumar, Syed Azamal Ali, Anurag Tiwari, Masoud Lotfan, Jasmine Naru, Manoj Jena, Pradip Behere, Ashok K Balhara, Rajesh Vashisth, Inderjeet Singh, Ajay Dang, Jai K Kaushik, Tushar K Mohanty, Ashok K Mohanty
BACKGROUND: An early, reliable and noninvasive method of early pregnancy diagnosis is prerequisite for efficient reproductive management in dairy industry. The early detection of pregnancy also help in to reduce the calving interval and rebreeding time which is beneficial for industries as well as farmers. The aim of this work is to identify potential biomarker for pregnancy detection at earlier stages (16-25 days). To achieve this goal we performed DIGE and LFQ for identification of protein which has significant differential expression during pregnancy...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27382363/quantitative-proteomic-analysis-of-histone-modifications-in-decitabine-sensitive-and-resistant-leukemia-cell-lines
#20
Chunchao Zhang, Jinfeng Suo, Hiroyuki Katayama, Yue Wei, Guillermo Garcia-Manero, Samir Hanash
BACKGROUND: The refractory nature of many cancers remains the main health challenge over the past century. The epigenetic drug, decitabine (DAC), represents one of the most promising therapeutic agents in cancers particularly in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). However, its ambiguous anti-tumor mechanism and the unpredictable drug-resistant nature in some population compromise its application in cancer therapy. In crosstalk with DNA methylation, histone post-translational modifications (PTMs) are the key players in modulating the downstream epigenetic status of tumor suppressor genes...
2016: Clinical Proteomics
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