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Proteomics and blood biomarkers

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
Elena Pazos, Manuel Garcia Algar, Cristina Penas, Moritz Nazarenus, Arnau Torruella, Nicolas Pazos-Perez, Luca Guerrini, M Eugenio Vázquez, Eduardo Garcia-Rico, José L Mascareñas, Ramon A Alvarez-Puebla
Blood-based biomarkers (liquid biopsy) offer extremely valua-ble tools for the non-invasive diagnosis and monitoring of tumors. The protein c-MYC, a transcription factor that has been shown to be deregulated in up to 70% of human cancers, can be used as a robust proteomic signature for cancer. Herein, we developed a rapid, highly specific and sensitive SERS assay for the quantification of c-MYC in real blood samples. The sensing scheme relies on the use of specifically designed hybrid plasmonic materials and their bioderivatization with a selective peptidic receptor modified with a SERS transducer...
October 12, 2016: Journal of the American Chemical Society
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
Jon Hazeldine, Peter Hampson, Janet M Lord
As secondary complications remain a significant cause of morbidity and mortality amongst hospitalised trauma patients, the need to develop novel approaches by which to identify patients at risk of adverse outcome is becoming increasingly important. Centred on the idea that patients who experience "poor" outcome post trauma elicit a response to injury that is distinct from those who experience "good" outcome, tailored therapeutics is an emerging concept aimed at improving current treatment regimens by promoting patient-specific therapies...
2016: Burns and trauma
Daniel L Adams, R Katherine Alpaugh, Susan Tsai, Cha-Mei Tang, Steingrimur Stefansson
In tissue biopsies formalin fixed paraffin embedded cancer blocks are micro-sectioned producing multiple semi-identical specimens which are analyzed and subtyped proteomically, and genomically, with numerous biomarkers. In blood based biopsies (BBBs), blood is purified for circulating tumor cells (CTCs) and clinical utility is typically limited to cell enumeration, as only 2-3 positive fluorescent markers and 1 negative marker can be used. As such, increasing the number of subtyping biomarkers on each individual CTC could dramatically enhance the clinical utility of BBBs, allowing in depth interrogation of clinically relevant CTCs...
September 20, 2016: Scientific Reports
Jesús Mateos, Isabel Carneiro, Fernando Corrales, Felix Elortza, Alberto Paradela, Manuel Sánchez Del Pino, Ibon Iloro, Miguel Marcilla, Maria Isabel Mora, Luz Valero, Sergio Ciordia, Verónica Fernández, Maria Antonia Fortuño, Isabel García-Sánchez, Rosario Martínez, Maria Angeles Muñoz, Clara Rodriguez, Nieves Doménech
: Analytical proteomics has experienced exponential progress in the last decade and can be expected to lead research studies on diagnostic and therapeutic biomarkers in the near future. Because the development of this type of analysis requires the use of a large number of human samples with a minimum of quality requirements, our objective was to identify appropriate indicators for quality control of plasma samples stored in biobanks for research in proteomics. To accomplish this, plasma samples from 100 healthy donors were obtained and processed according to the pre-analytical variables of: a) time delay for the first centrifugation of the original blood sample (4 or 24h) and b) number of freeze/thaw cycles (1, 2 or 3) of the processed plasma samples...
September 9, 2016: Journal of Proteomics
Eui Kyung Lee, Young-Jun Shin, Eun Young Park, Nam Deuk Kim, Aree Moon, Seung Jun Kwack, Ji Yeon Son, Sam Kacew, Byung Mu Lee, Ok-Nam Bae, Hyung Sik Kim
Identifying novel biomarkers to detect nephrotoxicity is clinically important. Here, we attempted to identify new biomarkers for mercury-induced nephrotoxicity and compared their sensitivity to that of traditional biomarkers in animal models. Comparative proteomics analysis was performed in kidney tissues of Sprague-Dawley rats after oral treatment with HgCl2 (0.1, 1, or 5 mg/kg/day) for 21 days. Kidney cortex tissues were analyzed by two-dimensional gel electrophoresis/matrix-assisted laser desorption/ionization, and differentially expressed proteins were identified...
August 30, 2016: Archives of Toxicology
Shizhen Qin, Yong Zhou, Li Gray, Ulrike Kusebauch, Laurence McEvoy, Daniel J Antoine, Lucy Hampson, Kevin B Park, David Campbell, Juan Caballero, Gustavo Glusman, Xiaowei Yan, Taek-Kyun Kim, Yue Yuan, Kai Wang, Lee Rowen, Robert L Moritz, Gilbert S Omenn, Munir Pirmohamed, Leroy Hood
Organ-enriched blood proteins, those produced primarily in one organ and secreted or exported to the blood, potentially afford a powerful and specific approach to assessing diseases in their cognate organs. We demonstrate that quantification of organ-enriched proteins in the blood offers a new strategy to find biomarkers for diagnosis and assessment of drug-induced liver injury (and presumably the assessment of other liver diseases). We used selected reaction monitoring (SRM) mass spectrometry to quantify 81 liver-enriched proteins plus three aminotransferases (ALT1, AST1, and AST2) in plasma of C57BL/6J and NOD/ShiLtJ mice exposed to acetaminophen or carbon tetrachloride...
October 7, 2016: Journal of Proteome Research
Ayodele A Alaiya, Mahmoud Aljurf, Zakia Shinwari, Fahad Almohareb, Hafiz Malhan, Hazzaa Alzahrani, Tarek Owaidah, Jonathan Fox, Fahad Alsharif, Said Y Mohamed, Walid Rasheed, Ghuzayel Aldawsari, Amr Hanbali, Syed Osman Ahmed, Naeem Chaudhri
There is unmet need for prediction of treatment response for chronic myeloid leukemia (CML) patients. The present study aims to identify disease-specific/disease-associated protein biomarkers detectable in bone marrow and peripheral blood for objective prediction of individual's best treatment options and prognostic monitoring of CML patients. Bone marrow plasma (BMP) and peripheral blood plasma (PBP) samples from newly-diagnosed chronic-phase CML patients were subjected to expression-proteomics using quantitative two-dimensional gel electrophoresis (2-DE) and label-free liquid chromatography tandem mass spectrometry (LC-MS/MS)...
September 2016: International Journal of Oncology
Li Chen, Mingshu Mo, Guangning Li, Luan Cen, Lei Wei, Yousheng Xiao, Xiang Chen, Shaomin Li, Xinling Yang, Shaogang Qu, Pingyi Xu
Parkinson's disease (PD) is referring to the multi-systemic α-synucleinopathy with Lewy bodies deposited in midbrain. In ageing, the environmental and genetic factors work together and overactive major histocompatibility complex pathway to regulate immune reactions in central nerve system which resulting in neural degeneration, especially in dopaminergic neurons. As a series of biomarkers, the human leukocyte antigen genes with its related proteomics play cortical roles on the antigen presentation of major histocompatibility complex molecules to stimulate the differentiation of T lymphocytes and i-proteasome activities under their immune response to the PD-related environmental alteration and genetic variation...
2016: Translational Neurodegeneration
Maria-Jose Martinez-Bravo, Casper J E Wahlund, Khaleda Rahman Qazi, Robert Moulder, Ana Lukic, Olof Rådmark, Riitta Lahesmaa, Johan Grunewald, Anders Eklund, Susanne Gabrielsson
BACKGROUND: Sarcoidosis is an inflammatory granulomatous disorder characterized by accumulation of TH1-type CD4(+) T cells and immune effector cells within affected organs, most frequently the lungs. Exosomes are extracellular vesicles conveying intercellular communication with possible diagnostic and therapeutic applications. OBJECTIVES: We aimed to provide an understanding of the proinflammatory role of bronchoalveolar lavage fluid (BALF) exosomes in patients with sarcoidosis and to find candidates for disease biomarkers...
August 23, 2016: Journal of Allergy and Clinical Immunology
Ali T Khan, Richard J B Dobson, Martina Sattlecker, Steven J Kiddle
OBJECTIVE: Peripheral protein biomarkers of Alzheimer's disease (AD) may help identify novel treatment avenues by allowing early diagnosis, recruitment to clinical trials, and treatment initiation. The purpose of this review was to determine which proteins have been found to be differentially expressed in the AD brain and whether these proteins are also found within the blood of AD patients. METHODS: A two-stage approach was conducted. The first stage involved conducting a systematic search to identify discovery-based brain proteomic studies of AD...
June 2016: Annals of Clinical and Translational Neurology
Lasse Folkersen, Boel Brynedal, Lina Marcela Diaz-Gallo, Daniel Ramsköld, Klementy Shchetynsky, Helga Westerlind, Yvonne Sundström, Danika Schepis, Aase Hensvold, Nancy Vivar, Maija-Leena Eloranta, Lars Rönnblom, Søren Brunak, Vivianne Malmström, Anca Catrina, Ulrik Gw Moerch, Lars Klareskog, Leonid Padyukov, Louise Berg
OBJECTIVE: In rheumatoid arthritis (RA) several recent efforts have sought to discover means of predicting which patients would benefit from treatment. However, results have been discrepant with few successful replications. Our objective was to build a biobank with DNA, RNA and protein measurements to test the claim that the current state-of-the-art precision medicine will benefit RA patients. METHODS: We collected 451 blood samples from 61 healthy individuals and 185 RA patients initiating treatment, before treatment initiation and at a 3 month follow-up time...
August 15, 2016: Molecular Medicine
Meredith C Henderson, Alan B Hollingsworth, Kelly Gordon, Michael Silver, Rao Mulpuri, Elias Letsios, David E Reese
Despite significant advances in breast imaging, the ability to accurately detect Breast Cancer (BC) remains a challenge. With the discovery of key biomarkers and protein signatures for BC, proteomic technologies are currently poised to serve as an ideal diagnostic adjunct to imaging. Research studies have shown that breast tumors are associated with systemic changes in levels of both serum protein biomarkers (SPB) and tumor associated autoantibodies (TAAb). However, the independent contribution of SPB and TAAb expression data for identifying BC relative to a combinatorial SPB and TAAb approach has not been fully investigated...
2016: PloS One
Caroline Solazzo, Blandine Courel, Jacques Connan, Bart E van Dongen, Holly Barden, Kirsty Penkman, Sheila Taylor, Beatrice Demarchi, Pierre Adam, Philippe Schaeffer, Arie Nissenbaum, Ofer Bar-Yosef, Michael Buckley
Mortuary practices in human evolution record cognitive, social changes and technological innovations. The Neolithic Revolution in the Levant was a watershed in this domain that has long fascinated the archaeological community. Plaster modelled skulls are well known at Jericho and several other Neolithic sites, and in Nahal Hemar cave (Israel, ca. 8200 -7300 cal. BC) excavations yielded six unique human skulls covered with a black organic coating applied in a net pattern evoking a headdress. This small cave was used as storage for paraphernalia in the semi-arid area of the Judean desert and the dry conditions preserved other artefacts such as baskets coated with a similar dark substance...
2016: Scientific Reports
Frank Kolbinger, Christian Loesche, Marie-Anne Valentin, Xiaoyu Jiang, Yi Cheng, Philip Jarvis, Thomas Peters, Claudio Calonder, Gerard Bruin, Florine Polus, Birgit Aigner, David M Lee, Manfred Bodenlenz, Frank Sinner, Thomas Rudolf Pieber, Dhavalkumar D Patel
BACKGROUND: IL-17A is a key driver of human autoimmune diseases, particularly psoriasis. OBJECTIVE: We sought to determine the role of IL-17A in psoriasis pathogenesis, and to identify a robust, measurable biomarker of IL-17A-driven pathology. METHODS: We studied 8 healthy and 8 psoriasis subjects before and after administration of secukinumab, a fully human anti-IL-17A mAb, and utilized a combination of classical techniques and a novel skin microperfusion assay to evaluate the expression of 170 proteins in blood, non-lesional skin and lesional skin...
August 5, 2016: Journal of Allergy and Clinical Immunology
Julien Peltier, Jean-Pierre Roperch, Stéphane Audebert, Jean-Paul Borg, Luc Camoin
UNLABELLED: Colorectal cancer (CRC) remains a major cause of cancer related-death in developed countries. The mortality risk is correlated with the stage of CRC determined at the primary diagnosis and early diagnosis is associated with enhanced survival rate. Currently, only faecal occult blood tests are used to screen for CRC. Consequently, there is an incentive to identify specific markers of CRC. We used quantitative proteomic analysis of serum samples to characterize protein profiles in adenoma, CRC and healthy control samples...
October 4, 2016: Journal of Proteomics
Shanna L Ashley, Meng Xia, Susan Murray, David N O'Dwyer, Ethan Grant, Eric S White, Kevin R Flaherty, Fernando J Martinez, Bethany B Moore
RATIONALE: Biomarkers in easily accessible compartments like peripheral blood that can predict disease progression in idiopathic pulmonary fibrosis (IPF) would be clinically useful regarding clinical trial participation or treatment decisions for patients. In this study, we used unbiased proteomics to identify relevant disease progression biomarkers in IPF. METHODS: Plasma from IPF patients was measured using an 1129 analyte slow off-rate modified aptamer (SOMAmer) array, and patient outcomes were followed over the next 80 weeks...
2016: PloS One
Melinda Rezeli, Olof Gidlöf, Mikael Evander, Paulina Bryl-Górecka, Ramasri Sathanoori, Patrik Gilje, Krzysztof Pawłowski, Péter Horvatovich, David Erlinge, György Marko-Varga, Thomas Laurell
Extracellular vesicles (ECVs), including microparticles and exosomes, are submicrometer membrane vesicles released by diverse cell types upon activation or stress. Circulating ECVs are potential reservoirs of disease biomarkers, and the complexity of these vesicles is significantly lower compared to their source, blood plasma, which makes ECV-based biomarker studies more promising. Proteomic profiling of ECVs is important not only to discover new diagnostic or prognostic markers but also to understand their roles in biological function...
September 6, 2016: Analytical Chemistry
Tetsushi Yamamoto, Mitsuhiro Kudo, Wei-Xia Peng, Hideyuki Takata, Hideki Takakura, Kiyoshi Teduka, Takenori Fujii, Kuniko Mitamura, Atsushi Taga, Eiji Uchida, Zenya Naito
Colorectal cancer (CRC) is one of the most common cancers worldwide, and many patients are already at an advanced stage when they are diagnosed. Therefore, novel biomarkers for early detection of colorectal cancer are required. In this study, we performed a global shotgun proteomic analysis using formalin-fixed and paraffin-embedded (FFPE) CRC tissue. We identified 84 candidate proteins whose expression levels were differentially expressed in cancer and non-cancer regions. A label-free semiquantitative method based on spectral counting and gene ontology (GO) analysis led to a total of 21 candidate proteins that could potentially be detected in blood...
July 28, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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