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Proteomics and blood biomarkers

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https://www.readbyqxmd.com/read/27911324/proteomics-analysis-of-blood-serums-from-alzheimer-s-disease-patients-using-itraq-labeling-technology
#1
Liming Shen, Liping Liao, Cheng Chen, Yi Guo, Dalin Song, Yong Wang, Youjiao Chen, Kaoyuan Zhang, Ming Ying, Shuiming Li, Qiong Liu, Jiazuan Ni
Alzheimer' disease (AD) is the most common form of dementia affecting up to 6% of the population over the age of 65. In order to discover differentially expressed proteins that might serve as potential biomarkers, the serums from AD patients and healthy controls were compared and analyzed using the proteomics approach of isobaric tagging for relative and absolute quantitation (iTRAQ). For the first time, AD biomarkers in serums are investigated in the Han Chinese population using iTRAQ labeled proteomics strategy...
December 1, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27896965/identification-of-discriminative-imaging-proteomics-associations-in-alzheimer-s-disease-via-a-novel-sparse-correlation-model
#2
Jingwen Yan, Shannon L Risacher, Kwangsik Nho, Andrew J Saykin, L I Shen
Brain imaging and protein expression, from both cerebrospinal fluid and blood plasma, have been found to provide complementary information in predicting the clinical outcomes of Alzheimer's disease (AD). But the underlying associations that contribute to such a complementary relationship have not been previously studied yet. In this work, we will perform an imaging proteomics association analysis to explore how they are related with each other. While traditional association models, such as Sparse Canonical Correlation Analysis (SCCA), can not guarantee the selection of only disease-relevant biomarkers and associations, we propose a novel discriminative SCCA (denoted as DSCCA) model with new penalty terms to account for the disease status information...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896769/depletion-of-highly-abundant-proteins-of-the-human-blood-plasma-applications-in-proteomics-studies-of-psychiatric-disorders
#3
Sheila Garcia, Paulo A Baldasso, Paul C Guest, Daniel Martins-de-Souza
Psychiatric disorders are complex diseases involving exogenous and endogenous factors. Biomarkers for diagnosis or prediction of successful treatment are not existent. In addition, the molecular basis of these diseases is still poorly understood. Blood plasma represents the most complex proteome as it contains subproteomes from several body tissues. However, the high abundance of some little proteins can obscure the analysis of hundreds of low abundance proteins, which are potential biomarkers. Therefore, removal of these high abundance proteins is pivotal in any proteomic study of plasma...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896756/multiplex-biomarker-approaches-in-type-2-diabetes-mellitus-research
#4
Susan E Ozanne, Hassan Rahmoune, Paul C Guest
Type 2 diabetes mellitus is a multifactorial condition resulting in high fasting blood glucose levels. Although its diagnosis is straightforward, there is not one set of biomarkers or drug targets that can be used for classification or personalized treatment of individuals who suffer from this condition. Instead, the application of multiplex methods incorporating a systems biology approach is essential in order to increase our understanding of this disease. This chapter reviews the state of the art in biomarker studies of human type 2 diabetes from a proteomic and metabolomic perspective...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27894246/therapy-related-changes-in-serum-proteome-patterns-of-early-stage-breast-cancer-patients-with-different-outcome
#5
Anna Walaszczyk, Monika Pietrowska, Anna Wojakowska, Agata Abramowicz, Aleksandra Chmura, Barbara Masłyk, Paweł Rodziewicz, Joanna Polańska, Katarzyna Behrendt, Elżbieta Nowicka, Rafał Tarnawski, Piotr Widłak
Adjuvant chemo- and/or radiotherapy is applied in majority of patients treated because of early stage breast cancer even though only a small fraction of them is at high risk of metastasis or recurrence. Hence, knowledge of biomarkers associated with risk of disease progression might help planning of an optimal therapy, and to protect large group of patients from toxicity of unnecessary treatment. Here we aimed to characterize serum proteome of patients diagnosed with early stage breast cancer who either showed no evidence of disease five years after the end of therapy or suffered from metastasis, relapse or second cancer during corresponding follow-up...
November 28, 2016: Protein and Peptide Letters
https://www.readbyqxmd.com/read/27890796/temporal-profiles-of-plasma-proteome-during-childhood-development
#6
Chih-Wei Liu, Lisa Bramer, Bobbie-Jo Webb-Robertson, Kathleen Waugh, Marian J Rewers, Qibin Zhang
Human blood plasma proteome reflects physiological changes associated with a child's development as well as development of disease states. While age-specific normative values are available for proteins routinely measured in clinical practice, there is paucity of comprehensive longitudinal data regarding changes in human plasma proteome during childhood. We applied TMT-10plex isobaric labeling-based quantitative proteomics to longitudinally profile the plasma proteome in 10 healthy children during their development, each with 9 serial time points from 9months to 15years of age...
November 23, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27887661/biochemical-and-proteomic-analyses-of-the-physiological-response-induced-by-individual-housing-in-gilts-provide-new-potential-stress-markers
#7
Anna Marco-Ramell, Laura Arroyo, Raquel Peña, Raquel Pato, Yolanda Saco, Lorenzo Fraile, Emøke Bendixen, Anna Bassols
BACKGROUND: The objective assessment of animal stress and welfare requires proper laboratory biomarkers. In this work, we have analyzed the changes in serum composition in gilts after switching their housing, from pen to individual stalls, which is generally accepted to cause animal discomfort. RESULTS: Blood and saliva samples were collected a day before and up to four days after changing the housing system. Biochemical analyses showed adaptive changes in lipid and protein metabolism after the housing switch, whereas cortisol and muscular markers showed a large variability between animals...
November 25, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27884852/diagnostic-and-prognostic-biomarkers-in-the-rational-assessment-of-mesothelioma-diaphragm-study-protocol-of-a-prospective-multicentre-observational-study
#8
Selina Tsim, Caroline Kelly, Laura Alexander, Carol McCormick, Fiona Thomson, Rosie Woodward, John E Foster, David B Stobo, Jim Paul, Nick A Maskell, Anthony Chalmers, Kevin G Blyth
INTRODUCTION: Malignant pleural mesothelioma (MPM) is an asbestos-related cancer, which is difficult to diagnose. Thoracoscopy is frequently required but is not widely available. An accurate, non-invasive diagnostic biomarker would allow early specialist referral, limit diagnostic delays and maximise clinical trial access. Current markers offer insufficient sensitivity and are not routinely used. The SOMAmer proteomic classifier and fibulin-3 have recently demonstrated sensitivity and specificity exceeding 90% in retrospective studies...
November 24, 2016: BMJ Open
https://www.readbyqxmd.com/read/27879288/multi-omics-analysis-of-serum-samples-demonstrates-reprogramming-of-organ-functions-via-systemic-calcium-mobilization-and-platelet-activation-in-metastatic-melanoma
#9
Besnik Muqaku, Martin Eisninger, Samuel M Meier, Ammar Tahir, Tobias Prokop, Sebastian Haferkamp, Astrid Slany, Albrecht Reichle, Christopher Gerner
Pathophysiologies of cancer-associated syndroms such as cachexia are poorly understood and no routine biomarkers have been established, yet. Using shotgun proteomics, known marker molecules including PMEL, CRP, SAA and CSPG4 were found deregulated in patients with metastatic melanoma. Targeted analysis of 58 selected proteins with multiple reaction monitoring was applied for independent data verification. In three patients, two of which suffered from cachexia, a tissue damage signature was determined, consisting of nine proteins, PLTP, CD14, TIMP1, S10A8, S10A9, GP1BA, PTPRJ, CD44 and C4A, as well as increased levels of glycine and asparagine, and decreased levels of polyunsaturated phosphatidylcholine concentrations, as determined by targeted metabolomics...
November 22, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27864139/evening-morning-peroxiredoxin-2-redox-oligomeric-state-changes-in-obstructive-sleep-apnea-red-blood-cells-correlation-with-polysomnographic-and-metabolic-parameters
#10
Amélia Feliciano, Fátima Vaz, Vukosava M Torres, Cristina Valentim-Coelho, Rita Silva, Vesna Prosinecki, Bruno M Alexandre, Ana S Carvalho, Rune Matthiesen, Atul Malhotra, Paula Pinto, Cristina Bárbara, Deborah Penque
We have examined the effects of Obstructive Sleep Apnea (OSA) on red blood cell (RBC) proteome variation at evening/morning day time to uncover new insights into OSA-induced RBC dysfunction that may lead to OSA manifestations. Dysregulated proteins mainly fall in the group of catalytic enzymes, stress response and redox regulators such as peroxiredoxin 2 (PRDX2). Validation assays confirmed that at morning the monomeric/dimeric forms of PRDX2 were more overoxidized in OSA RBC compared to evening samples. Six month of positive airway pressure (PAP) treatment decreased this overoxidation and generated multimeric overoxidized forms associated with chaperone/transduction signaling activity of PRDX2...
November 15, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27849439/liver-proteome-in-diabetes-type-1-rat-model-insulin-dependent-and-independent-changes
#11
Camila Pereira Braga, Cory H T Boone, Ryan A Grove, Dana Adamcova, Ana Angélica Henrique Fernandes, Jiri Adamec, Pedro de Magalhães Padilha
Diabetes mellitus type 1 (DM1) is a major public health problem that continues to burden the healthcare systems worldwide, costing exponentially more as the epidemic grows. Innovative strategies and omics system diagnostics for earlier diagnosis or prognostication of DM1 are essential to prevent secondary complications and alleviate the associated economic burden. In a preclinical study design that involved streptozotocin (STZ)-induced DM1, insulin-treated STZ-induced DM1, and control rats, we characterized the insulin-dependent and -independent changes in protein profiles in liver samples...
November 16, 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27782767/consensus-paper-of-the-wfsbp-task-force-on-biological-markers-criteria-for-biomarkers-and-endophenotypes-of-schizophrenia-part-iii-molecular-mechanisms
#12
Andrea Schmitt, Daniel Martins-de-Souza, Schahram Akbarian, Juliana S Cassoli, Hannelore Ehrenreich, Andre Fischer, Alfred Fonteh, Wagner F Gattaz, Michael Gawlik, Manfred Gerlach, Edna Grünblatt, Tobias Halene, Alkomiet Hasan, Kenij Hashimoto, Yong-Ku Kim, Sophie-Kathrin Kirchner, Johannes Kornhuber, Theo F J Kraus, Berend Malchow, Juliana M Nascimento, Moritz Rossner, Markus Schwarz, Johann Steiner, Leda Talib, Florence Thibaut, Peter Riederer, Peter Falkai
OBJECTIVES: Despite progress in identifying molecular pathophysiological processes in schizophrenia, valid biomarkers are lacking for both the disease and treatment response. METHODS: This comprehensive review summarises recent efforts to identify molecular mechanisms on the level of protein and gene expression and epigenetics, including DNA methylation, histone modifications and micro RNA expression. Furthermore, it summarises recent findings of alterations in lipid mediators and highlights inflammatory processes...
October 26, 2016: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/27780262/the-specific-%C3%AE-1-adrenergic-receptor-antagonist-prazosin-influences-the-urine-proteome
#13
Mindi Zhao, Jianqiang Wu, Youhe Gao
Urine, reflecting many changes in the body, is a better source than blood for biomarker discovery. However, even under physiological conditions, the urine proteome often varies. Understanding how various regulating factors affect urine proteome helps link changes to urine proteome with urinary biomarkers of physiological conditions as well as corresponding diseases. To evaluate the possible impact of α1-adrenergic receptor on urine proteome, this study investigated effects of the specific inhibitor prazosin on the urine proteome in a rat model by using tandem mass tagging and two-dimensional liquid chromatography-tandem mass spectrometry...
2016: PloS One
https://www.readbyqxmd.com/read/27778251/biomarkers-of-diabetic-retinopathy
#14
Daniel Shu Wei Ting, Kara-Anne Tan, Val Phua, Gavin Siew Wei Tan, Chee Wai Wong, Tien Yin Wong
Diabetic retinopathy (DR), a leading cause of acquired vision loss, is a microvascular complication of diabetes. While traditional risk factors for diabetic retinopathy including longer duration of diabetes, poor blood glucose control, and dyslipidemia are helpful in stratifying patient's risk for developing retinopathy, many patients without these traditional risk factors develop DR; furthermore, there are persons with long diabetes duration who do not develop DR. Thus, identifying biomarkers to predict DR or to determine therapeutic response is important...
December 2016: Current Diabetes Reports
https://www.readbyqxmd.com/read/27777179/thiol-oxidation-and-di-tyrosine-formation-in-human-plasma-proteins-induced-by-inflammatory-concentrations-of-hypochlorous-acid
#15
Graziano Colombo, Marco Clerici, Alessandra Altomare, Francesco Rusconi, Daniela Giustarini, Nicola Portinaro, Maria Lisa Garavaglia, Ranieri Rossi, Isabella Dalle-Donne, Aldo Milzani
: In this study, we assessed the oxidative damage occurring in plasma proteins when human blood was exposed to inflammatory concentrations of hypochlorous acid (HOCl). We used specific thiol labelling and Western blot analyses to determine protein thiol oxidation, as well as analytical gel filtration HPLC coupled to fluorescence detection to explore formation of high molecular weight (HMW) protein aggregates. Thiol-containing proteins oxidized by HOCl were identified by redox proteomics...
October 21, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27774271/circulating-biomarker-responses-to-medical-management-vs-mechanical-circulatory-support-in-severe-inotrope-dependent-acute-heart-failure
#16
Anna J Meredith, Darlene L Y Dai, Virginia Chen, Zsuzsanna Hollander, Raymond Ng, Annemarie Kaan, Scott Tebbutt, Krishnan Ramanathan, Anson Cheung, Bruce M McManus
BACKGROUND: Severe inotrope-dependent acute heart failure (AHF) is associated with poor clinical outcomes. There are currently no well-defined blood biomarkers of response to treatment that can guide management or identify recovery in this patient population. In the present study, we characterized the levels of novel and emerging circulating biomarkers of heart failure in patients with AHF over the first 30 days of medical management or mechanical circulatory support (MCS). We hypothesized a shared a plasma proteomic treatment response would be identifiable in both patient groups, representing reversal of the AHF phenotype...
June 2016: ESC Heart Failure
https://www.readbyqxmd.com/read/27771981/blood-biomarker-discovery-in-drug-free-schizophrenia-the-contribution-of-proteomics-and-multiplex-immunoassays
#17
Sophie Sabherwal, Jane A English, Melanie Föcking, Gerard Cagney, David R Cotter
Recent evidence supports an association between systemic abnormalities and the pathology of psychotic disorders which has led to the search for peripheral blood-based biomarkers. Areas covered: Here, we summarize blood biomarker findings in schizophrenia from the literature identified by two methods currently driving biomarker discovery in the human proteome; mass spectrometry and multiplex immunoassay. From a total of 14 studies in the serum or plasma of drug-free schizophrenia patients; 47 proteins were found to be significantly altered twice or more, in the same direction...
November 11, 2016: Expert Review of 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
#18
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/27731990/sers-surface-selection-rules-for-the-proteomic-liquid-biopsy-in-real-samples-efficient-detection-of-the-oncoprotein-c-myc
#19
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
https://www.readbyqxmd.com/read/27708557/plasma-degradome-affected-by-variable-storage-of-human-blood
#20
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
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