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Proteomics and blood biomarkers

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https://www.readbyqxmd.com/read/28101531/osteopontin-is-a-blood-biomarker-for-microglial-activation-and-brain-injury-in-experimental-hypoxic-ischemic-encephalopathy
#1
Yikun Li, Eric B Dammer, Xiaohui Zhang-Brotzge, Scott Chen, Duc M Duong, Nicholas T Seyfried, Chia-Yi Kuan, Yu-Yo Sun
Clinical management of neonatal hypoxic-ischemic encephalopathy (HIE) suffers from the lack of reliable surrogate marker tests. Proteomic analysis may identify such biomarkers in blood, but there has been no proof-of-principle evidence to support this approach. Here we performed in-gel trypsin digestion of plasma proteins from four groups of 10-d-old mice [untouched and 24 h after low-dose lipopolysaccharide (LPS) exposure, hypoxia-ischemia (HI), or LPS/HI injury; n = 3 in each group) followed by liquid chromatography-tandem mass spectrometry and bioinformatics analysis to search for HI- and LPS/HI-associated brain injury biomarkers...
January 2017: ENeuro
https://www.readbyqxmd.com/read/28067231/multiomics-reveal-non-alcoholic-fatty-liver-disease-in-rats-following-chronic-exposure-to-an-ultra-low-dose-of-roundup-herbicide
#2
Robin Mesnage, George Renney, Gilles-Eric Séralini, Malcolm Ward, Michael N Antoniou
The impairment of liver function by low environmentally relevant doses of glyphosate-based herbicides (GBH) is still a debatable and unresolved matter. Previously we have shown that rats administered for 2 years with 0.1 ppb (50 ng/L glyphosate equivalent dilution; 4 ng/kg body weight/day daily intake) of a Roundup GBH formulation showed signs of enhanced liver injury as indicated by anatomorphological, blood/urine biochemical changes and transcriptome profiling. Here we present a multiomic study combining metabolome and proteome liver analyses to obtain further insight into the Roundup-induced pathology...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28062797/targeted-proteomics-for-multiplexed-verification-of-markers-of-colorectal-tumorigenesis
#3
Anuli Christiana Uzozie, Nathalie Selevsek, Asa Wahlander, Paolo Nanni, Jonas Grossmann, Achim Weber, Federico Buffoli, Giancarlo Marra
Targeted proteomic methods can accelerate the verification of multiple tumor marker candidates in large series of patient samples. We utilized the targeted approach known as selected / multiple reaction monitoring (SRM/MRM) to verify potential protein markers of colorectal adenoma identified by our group in previous transcriptomic and quantitative shotgun proteomic studies of a large cohort of precancerous colorectal lesions. We developed SRM assays to reproducibly detect and quantify 25 (62.5%) of the 40 selected proteins in an independent series of precancerous and cancerous tissue samples (19 adenoma/normal mucosa pairs; 17 adenocarcinoma/normal mucosa pairs)...
January 4, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27965111/sialylated-fetuin-a-as-a-candidate-predictive-biomarker-for-successful-grass-pollen-allergen-immunotherapy
#4
Noémie Caillot, Julien Bouley, Karine Jain, Sandrine Mariano, Sonia Luce, Stéphane Horiot, Sabi Airouche, Chloé Beuraud, Christian Beauvallet, Philippe Devillier, Sylvie Chollet-Martin, Christine Kellenberger, Laurent Mascarell, Henri Chabre, Thierry Batard, Emmanuel Nony, Vincent Lombardi, Véronique Baron-Bodo, Philippe Moingeon
BACKGROUND: Eligibility to immunotherapy is based on the determination of IgE reactivity to a specific allergen by skin prick or in vitro testing. Biomarkers predicting the likelihood of clinical improvement during immunotherapy would significantly improve patient selection. METHODS: Proteins were differentially assessed by 2D-DiGE and label-free mass spectrometry in pre-treatment sera obtained from clinical responders and non-responders within a cohort of 82 grass pollen allergic patients receiving sublingual immunotherapy or placebo...
December 10, 2016: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/27943336/verification-of-protein-biomarkers-for-the-identification-of-biological-stains-by-quadrupole-time-of-flight-mass-spectrometry
#5
Kevin M Legg, Roger Powell, Nichole Reisdorph, Rick Reisdorph, Phillip B Danielson
Advances in proteomics technology over the past decade offer forensic serologists a greatly improved opportunity to accurately characterize the tissue source from which a DNA has been developed. Such information can provide critical context to evidence and can help to prioritize downstream DNA analysis. Previous proteome studies compiled panels of "candidate biomarkers" specific to each of six body fluids (i.e. peripheral blood, menstrual fluid, vaginal fluid, seminal fluid, urine and saliva). Here, a multiplex Quadrupole Time-of-flight assay has been developed in order to verify the tissue/body fluid specificity the 23 protein biomarkers that comprise these panels and the consistency with which they can be detected across a samples population of fifty humans...
December 12, 2016: Electrophoresis
https://www.readbyqxmd.com/read/27943101/salivary-biomarkers-in-cancer-detection
#6
REVIEW
Xiaoqian Wang, Karolina Elżbieta Kaczor-Urbanowicz, David T W Wong
Cancer is the second most common cause of death in the USA. Its symptoms are often not specific and absent, until the tumors have already metastasized. Therefore, there is an urgent demand for developing rapid, highly accurate and noninvasive tools for cancer screening, early detection, diagnostics, staging and prognostics. Saliva as a multi-constituent oral fluid comprises secretions from the major and minor salivary glands, extensively supplied by blood. Molecules such as DNAs, RNAs, proteins, metabolites, and microbiota, present in blood, could be also found in saliva...
January 2017: Medical Oncology
https://www.readbyqxmd.com/read/27931010/impact-and-influence-of-omics-technology-on-hyper-tension-studies
#7
REVIEW
Alzenira Costa, Octavio Luiz Franco
BACKGROUND: Hypertension is an important risk factor for cardiovascular diseases. Pathophysiology and molecular mechanisms involved in hypertension regulation are not very well known. Recently, high-throughput Next-Generation Sequencing (NGS) technology has identified hundreds of gene loci associated with multiple cardiovascular pathologies, including blood pressure (BP), generating new expectations in hypertension studies, revealing new pathways and genetic mechanisms underlying BP regulation...
February 1, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/27924632/low-level-expression-of-sod1-in-peripheral-blood-samples-of-patients-diagnosed-with-primary-open-angle-glaucoma
#8
Licelly Canizales, Laura Rodriguez, Carlos Rivera, Alexander Martinez, Fabián Mendez, Andres Castillo
AIM: Glaucoma is a multifactorial disease of retinal ganglion cells, with low prognosis. For that reason, the identification of biomarkers in peripheral blood samples for diagnostics and treatment of the disease is needed. To establish mRNA expression level of several oxidative stress biomarkers reported in aqueous humor of patients with primary open-angle glaucoma (POAG). MATERIALS & METHODS: The mRNA expression levels of eight genes from 15 patients diagnosed with POAG and 11 control subjects were analyzed using an RT(2) Custom Profiler PCR Array...
December 2016: Biomarkers in Medicine
https://www.readbyqxmd.com/read/27911324/proteomics-analysis-of-blood-serums-from-alzheimer-s-disease-patients-using-itraq-labeling-technology
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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...
January 30, 2017: 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
#15
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
#16
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
#17
Besnik Muqaku, Martin Eisinger, Samuel M Meier, Ammar Tahir, Tobias Pukrop, Sebastian Haferkamp, Astrid Slany, Albrecht Reichle, Christopher Gerner
Pathophysiologies of cancer-associated syndromes 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...
January 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27864139/evening-and-morning-peroxiredoxin-2-redox-oligomeric-state-changes-in-obstructive-sleep-apnea-red-blood-cells-correlation-with-polysomnographic-and-metabolic-parameters
#18
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...
February 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27849439/liver-proteome-in-diabetes-type-1-rat-model-insulin-dependent-and-independent-changes
#19
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...
December 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
#20
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
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