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Proteomics and blood biomarkers

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https://www.readbyqxmd.com/read/29045505/surfaceome-profiling-enables-isolation-of-cancer-specific-exosomal-cargo-in-liquid-biopsies-from-pancreatic-cancer-patients
#1
J Castillo, V Bernard, F A San Lucas, K Allenson, M Capello, D U Kim, P Gascoyne, F C Mulu, B M Stephens, J Huang, H Wang, A A Momin, R O Jacamo, M Katz, R Wolff, M Javle, G Varadhachary, I I Wistuba, S Hanash, A Maitra, H Alvarez
Background: Detection of circulating tumor DNA (ctDNA) can be limited due to their relative scarcity in circulation, particularly while patients are actively undergoing therapy. Exosomes provide a vehicle through which cancer-specific material can be enriched from the compendium of circulating non-neoplastic tissue-derived nucleic acids. We performed a comprehensive profiling of the pancreatic ductal adenocarcinoma (PDAC) exosomal "surfaceome" in order to identify surface proteins that will render liquid biopsies amenable to cancer-derived exosome enrichment for downstream molecular profiling...
September 25, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29041828/urine-protein-biomarkers-for-detection-of-cardiovascular-disease-and-their-use-for-the-clinic
#2
Sarah Röthlisberger, Johanna Pedroza-Diaz
Cardiovascular disease (CVD) is the leading noncommunicable disease and main cause of death worldwide. Traditionally, blood has been the sample of choice for biomarker discovery, however, urine has roused great interest in recent years as a source of biomarkers. Sample collection is simple, non-invasive, and there is the possibility of implementing minimal cost tests in primary care settings. Areas covered: In this review, we systematically searched PubMed for proteomic studies of CVD, with the criteria that urine was included as a biological sample...
October 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29028997/serum-quantitative-proteomic-analysis-reveals-soluble-egfr-to-be-a-marker-of-insulin-resistance-in-male-mice-and-humans
#3
Mayu Kyohara, Jun Shirakawa, Tomoko Okuyama, Ayuko Kimura, Yu Togashi, Kazuki Tajima, Hisashi Hirano, Yasuo Terauchi
To identify circulating factors as candidates involved in type 2 diabetes (T2DM), we conducted two different quantitative proteomic analyses: 1) db/db mouse sera were compared with db/+ mouse sera obtained at 4, 8, 12, and 24 weeks of age, and 2) db/db mouse sera from animals treated with liraglutide were compared with sera from animals without liraglutide treatment. 20 and eight proteins were differentially expressed in db/db mouse sera in the first experiment and in db/db mouse sera after liraglutide treatment in the second experiment, respectively...
October 5, 2017: Endocrinology
https://www.readbyqxmd.com/read/29025360/best-practice-of-identification-and-proteomic-analysis-of-extracellular-vesicles-in-human-health-and-disease
#4
Barbara W Sódar, Árpád Kovács, Tamás Visnovitz, Éva Pállinger, Károly Vékey, Gabriella Pocsfalvi, Lilla Turiák, Edit I Buzás
Extracellular vesicles are emerging sources of biomarkers for modern preventive and precision medicine. Extracellular vesicles in body fluids offer a unique opportunity for integrative biomarker approaches due to their complex biocargo that includes proteins, lipids, nucleic acids and metabolites. Mass spectrometry-based proteomics data suggest that a significant portion of human proteins are sorted into extracellular vesicles and amenable for biomarker discovery schemes. Areas covered: this review focuses on key aspects of isolation, quality control and subsequent analysis of blood plasma- and conditioned medium-derived extracellular vesicle proteins, and summarizes the current state-of-the-art in the field...
October 13, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29019129/dige-analysis-of-proteominer-tm-fractionated-serum-plasma-samples
#5
Sandra Murphy, Paul Dowling
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically difference gel electrophoresis (DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984593/exploring-erythrocytes-as-blood-biomarkers-for-alzheimer-s-disease
#6
Anna Stevenson, Dianne Lopez, Paul Khoo, Rajesh N Kalaria, Elizabeta B Mukaetova-Ladinska
Peripheral biomarkers for dementia are few and far between. Despite research into blood plasma/serum biomarkers for dementia diagnostics, there is a lack of information on erythrocytes and their vast proteomes as potential biomarkers. This review identifies a number of relevant and potentially promising erythrocyte biomarkers for various subtypes of dementia. These include erythrocyte morphology, oxidative stress, and erythrocyte membrane proteins such as the glucose transporter (GLUT-1), amyloid-β, IgG, Hsp90, calpain-1, and band 3 protein...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28974776/associations-between-snps-and-immune-related-circulating-proteins-in-schizophrenia
#7
Man K Chan, Jason D Cooper, Stefanie Heilmann-Heimbach, Josef Frank, Stephanie H Witt, Markus M Nöthen, Johann Steiner, Marcella Rietschel, Sabine Bahn
Genome-wide association studies (GWAS) and proteomic studies have provided convincing evidence implicating alterations in immune/inflammatory processes in schizophrenia. However, despite the convergence of evidence, direct links between the genetic and proteomic findings are still lacking for schizophrenia. We investigated associations between single nucleotide polymorphisms (SNPs) from the custom-made PsychArray and the expression levels of 190 multiplex immunoassay profiled serum proteins in 149 schizophrenia patients and 198 matched controls...
October 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28974115/application-of-proteomics-to-graft-versus-host-disease-from-biomarker-discovery-to-potential-clinical-applications
#8
Richard B Presland
Graft-versus-host disease (GVHD) is a frequent and potentially life-threatening complication that occurs in many patients who undergo hematopoietic stem cell transplantation. In an effort to develop blood and tissue-based biochemical assays for GVHD diagnosis, high throughput proteomic platforms have been widely utilized for the identification and validation of disease biomarkers for both acute and chronic GVHD. Areas covered: This article reviews biomarker research findings on acute and chronic GVHD ascertained by studying peripheral blood, urine and saliva that gives biological information on systemic or localized disease...
October 4, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28973020/dynamic-adaptation-of-myocardial-proteome-during-heart-failure-development
#9
Julia Rüdebusch, Alexander Benkner, Axel Poesch, Marcus Dörr, Uwe Völker, Karina Grube, Elke Hammer, Stephan B Felix
Heart failure (HF) development is characterized by huge structural changes that are crucial for disease progression. Analysis of time dependent global proteomic adaptations during HF progression offers the potential to gain deeper insights in the disease development and identify new biomarker candidates. Therefore, hearts of TAC (transverse aortic constriction) and sham mice were examined by cardiac MRI on either day 4, 14, 21, 28, 42, and 56 after surgery (n = 6 per group/time point). At each time point, proteomes of the left (LV) and right ventricles (RV) of TAC and sham mice were analyzed by mass spectrometry (MS)...
2017: PloS One
https://www.readbyqxmd.com/read/28951502/revisiting-biomarker-discovery-by-plasma%C3%A2-proteomics
#10
REVIEW
Philipp E Geyer, Lesca M Holdt, Daniel Teupser, Matthias Mann
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth...
September 26, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28912895/mass-spectrometry-assisted-gel-based-proteomics-in-cancer-biomarker-discovery-approaches-and-application
#11
REVIEW
Rongrong Huang, Zhongsi Chen, Lei He, Nongyue He, Zhijiang Xi, Zhiyang Li, Yan Deng, Xin Zeng
There is a critical need for the discovery of novel biomarkers for early detection and targeted therapy of cancer, a major cause of deaths worldwide. In this respect, proteomic technologies, such as mass spectrometry (MS), enable the identification of pathologically significant proteins in various types of samples. MS is capable of high-throughput profiling of complex biological samples including blood, tissues, urine, milk, and cells. MS-assisted proteomics has contributed to the development of cancer biomarkers that may form the foundation for new clinical tests...
2017: Theranostics
https://www.readbyqxmd.com/read/28912679/proteomic-differences-in-blood-plasma-associated-with-antidepressant-treatment-response
#12
Christoph W Turck, Paul C Guest, Giuseppina Maccarrone, Marcus Ising, Stefan Kloiber, Susanne Lucae, Florian Holsboer, Daniel Martins-de-Souza
The current inability of clinical psychiatry to objectively select the most appropriate treatment is a major factor contributing to the severity and clinical burden of major depressive disorder (MDD). Here, we have attempted to identify plasma protein signatures in 39 MDD patients to predict response over a 6-week treatment period with antidepressants. LC-MS/MS analysis showed that differences in the levels of 29 proteins at baseline were found in the group with a favorable treatment outcome. Most of these proteins were components of metabolism or immune response pathways as well as multiple components of the coagulation cascade...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28876640/gene-and-protein-expression-profiling-of-pancreatic-tumours-reveal-dysregulated-pathways-and-novel-potential-biomarker
#13
E N Nweke, M N Ntwasa, M B Brand, J D Devar, M D Smith, G P Candy
BACKGROUND: Pancreatic cancer (PDAC) is a deadly type of cancer with almost an equal amount of new cases and deaths observed yearly. It accounts for about 7% of cancer-related deaths worldwide. In many multi-racial societies including South Africa, the black population has the highest incidence rate. Less than 5% of PDAC patients live up to 5 years. The lack of specific and sensitive diagnostic PDAC biomarkers is strongly responsible for this poor statistic. The discovery of differentially expressed genes and proteins associated with PDAC is crucial to elucidating this condition and may lead to biomarker finding and further understanding of the disease...
June 2017: South African Journal of Surgery. Suid-Afrikaanse Tydskrif Vir Chirurgie
https://www.readbyqxmd.com/read/28869421/a-systemic-view-on-the-distribution-of-diet-derived-methanol-and-hepatic-acetone-in-mice
#14
Martin Kistler, Andreea Muntean, Vera Hoellriegl, Georg Matuschek, Ralf Zimmermann, Christoph Hoeschen, Martin Hrabe de Angelis, Jan Rozman
Volatile organic compounds (VOCs) from breath can successfully be used to diagnose disease-specific pathological alterations in metabolism. However, the exact origin and underlying biochemical pathways that could be mapped to VOC signatures are mainly unknown. There is a knowledge gap regarding the contribution of tissues, organs, the gut microbiome, and exogenous factors to the "sum signal" from breath samples. Animal models for human disease such as mutant mice provide the possibility to reproduce genetic predisposition to disease, thereby allowing the in-depth analysis of metabolic and biochemical functions...
September 4, 2017: Journal of Breath Research
https://www.readbyqxmd.com/read/28860968/differential-peripheral-proteomic-biosignature-of-fluoxetine-response-in-a-mouse-model-of-anxiety-depression
#15
Indira Mendez-David, Céline Boursier, Valérie Domergue, Romain Colle, Bruno Falissard, Emmanuelle Corruble, Alain M Gardier, Jean-Philippe Guilloux, Denis J David
The incorporation of peripheral biomarkers in the treatment of major depressive disorders (MDD) could improve the efficiency of treatments and increase remission rate. Peripheral blood mononuclear cells (PBMCs) represent an attractive biological substrate allowing the identification of a drug response signature. Using a proteomic approach with high-resolution mass spectrometry, the present study aimed to identify a biosignature of antidepressant response (fluoxetine, a Selective Serotonin Reuptake Inhibitor) in PBMCs in a mouse model of anxiety/depression...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28860483/selective-lrrk2-kinase-inhibition-reduces-phosphorylation-of-endogenous-rab10-and-rab12-in-human-peripheral-mononuclear-blood-cells
#16
Kenneth Thirstrup, Justus C Dächsel, Felix S Oppermann, Douglas S Williamson, Garrick P Smith, Karina Fog, Kenneth V Christensen
Genetic variation in the leucine-rich repeat kinase 2 (LRRK2) gene is associated with risk of familial and sporadic Parkinson's disease (PD). To support clinical development of LRRK2 inhibitors as disease-modifying treatment in PD biomarkers for kinase activity, target engagement and kinase inhibition are prerequisite tools. In a combined proteomics and phosphoproteomics study on human peripheral mononuclear blood cells (PBMCs) treated with the LRRK2 inhibitor Lu AF58786 a number of putative biomarkers were identified...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28843803/downregulation-of-apolipoprotein-e-and-apolipoprotein-j-in-moyamoya-disease-a-proteome-analysis-of-cerebrospinal-fluid
#17
Daina Kashiwazaki, Haruto Uchino, Satoshi Kuroda
BACKGROUND AND PURPOSE: Genetic factors are closely involved in the etiology of moyamoya disease (MMD). However, its postgenomic mechanisms are still unknown. This study was aimed to identify specific biomarkers in the cerebrospinal fluid (CSF) of patients with MMD, using quantitative proteome technique. METHODS: This study included 10 patients with MMD and 4 controls. The CSF was collected without blood contamination during surgery. A comparative 2-dimensional gel electrophoresis study (2D-PAGE) was performed...
August 23, 2017: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/28821634/lipidomic-and-proteomic-analysis-of-exosomes-from-mouse-cortical-collecting-duct-cells
#18
Viet D Dang, Kishore Kumar Jella, Ragy R T Ragheb, Nancy D Denslow, Abdel A Alli
Exosomes are endosome-derived nanovesicles that are involved in cellular communication and signaling. Exosomes are produced by epithelial cells and are found in biologic fluids including blood and urine. The packaged material within exosomes includes proteins and lipids, but the molecular comparison within exosome subtypes is largely unknown. The purpose of this study was to investigate differences between exosomes derived from the apical plasma membrane and basolateral plasma membrane of polarized murine cortical collecting duct principal cells...
August 16, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28816095/new-astroglial-injury-defined-biomarkers-for-neurotrauma-assessment
#19
Julia Halford, Sean Shen, Kyohei Itamura, Jaclynn Levine, Albert C Chong, Gregg Czerwieniec, Thomas C Glenn, David A Hovda, Paul Vespa, Ross Bullock, W Dalton Dietrich, Stefania Mondello, Joseph A Loo, Ina-Beate Wanner
Traumatic brain injury (TBI) is an expanding public health epidemic with pathophysiology that is difficult to diagnose and thus treat. TBI biomarkers should assess patients across severities and reveal pathophysiology, but currently, their kinetics and specificity are unclear. No single ideal TBI biomarker exists. We identified new candidates from a TBI CSF proteome by selecting trauma-released, astrocyte-enriched proteins including aldolase C (ALDOC), its 38kD breakdown product (BDP), brain lipid binding protein (BLBP), astrocytic phosphoprotein (PEA15), glutamine synthetase (GS) and new 18-25kD-GFAP-BDPs...
October 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28808996/preparation-and-immunoaffinity-depletion-of-fresh-frozen-tissue-homogenates-for-mass-spectrometry-based-proteomics-in-the-context-of-drug-target-biomarker-discovery
#20
DaRue A Prieto, King C Chan, Donald J Johann, Xiaoying Ye, Gordon Whitely, Josip Blonder
The discovery of novel drug targets and biomarkers via mass spectrometry (MS)-based proteomic analysis of clinical specimens has proven to be challenging. The wide dynamic range of protein concentration in clinical specimens and the high background/noise originating from highly abundant proteins in tissue homogenates and serum/plasma encompass two major analytical obstacles. Immunoaffinity depletion of highly abundant blood-derived proteins from serum/plasma is a well-established approach adopted by numerous researchers; however, the utilization of this technique for immunodepletion of tissue homogenates obtained from fresh frozen clinical specimens is lacking...
2017: Methods in Molecular Biology
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