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Biomarker discovery

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https://www.readbyqxmd.com/read/28340480/using-uhplc-q-trap-ms-as-a-complementary-technique-to-in-depth-mine-uplc-q-tof-ms-data-for-identifying-modified-nucleosides-in-urine
#1
Zhiwei Lu, Qing Wang, Meiling Wang, Shuang Fu, Qingqing Zhang, Zhixin Zhang, Huizhen Zhao, Yuehong Liu, Zhenhai Huang, Ziye Xie, Honghong Yu, Xiaoyan Gao
Modified nucleosides, metabolites of RNA, are potential biomarkers of cancer before the appearance of morphological abnormalities. It is of great significance to comprehensively detect and identify nucleosides in human urine for discovery of cancer biomarkers. However, the lower abundance, the greater polarity and the matrix effects make it difficult to detect urinary nucleosides. In this paper, an integrated method consisted of sample preparation followed by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS) detection and primary identification, then ultra-high performance liquid chromatography coupled with hybrid triple quadrupole linear ion trap mass spectrometer (UHPLC Q-Trap/MS) further identification and validation were introduced...
March 12, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28340378/current-fda-approved-treatments-for-non-small-cell-lung-cancer-and-potential-biomarkers-for-its-detection
#2
REVIEW
Karla A Ruiz-Ceja, Yolanda I Chirino
BACKGROUND: Lung cancer is the leading worldwide cancer with almost 1.5 million deaths every year. Some drugs for lung cancer treatment have been available on the market for decades, but novel drugs have emerged promising better outcomes, especially for Non-Small Cell Lung Cancer (NSCLC), which represents 75% of lung cancer cases. However, how much do drugs have evolved for NSCLC treatment? Are they sharing the same mechanism of action? AIM: In this review we analyzed how the approved drugs by Federal Drug Agency for NSCLC have advanced in the last four decades identifying shared mechanism of action of medicines against NSCLC treatment and some of the potential biomarkers for early detection...
March 21, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28339517/omics-studies-their-use-in-diagnosis-and-reclassification-of-sle-and-other-systemic-autoimmune-diseases
#3
Maria Teruel, Chris Chamberlain, Marta E Alarcón-Riquelme
Omics studies of systemic autoimmune diseases (SADs) in general, and SLE in particular, have delivered isolated information from transcriptome, epigenome, genome, cytokine and metabolome analyses. Such analyses have resulted in the identification of disease susceptibility genes and the description of IFN expression signatures, allowing extensive insight into the mechanisms of disease and the development of new therapies. Access to such technologies allows the recognition of patterns of disease at a pathway level, thereby, to reclassify SLE and other SADs and to develop new therapeutics from a personalized perspective...
October 19, 2016: Rheumatology
https://www.readbyqxmd.com/read/28335509/novel-diagnostic-and-predictive-biomarkers-in-pancreatic-adenocarcinoma
#4
REVIEW
John C Chang, Madappa Kundranda
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease for a multitude of reasons including very late diagnosis. This in part is due to the lack of understanding of the biological behavior of PDAC and the ineffective screening for this disease. Significant efforts have been dedicated to finding the appropriate serum and imaging biomarkers to help early detection and predict response to treatment of PDAC. Carbohydrate antigen 19-9 (CA 19-9) has been the most validated serum marker and has the highest positive predictive value as a stand-alone marker...
March 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334324/understanding-the-genetic-landscape-of-small-cell-carcinoma-of-the-urinary-bladder-and-implications-for-diagnosis-prognosis-and-treatment-a-review
#5
Erik J Kouba, Liang Cheng
Importance: Small cell carcinoma of the urinary bladder is a rare and aggressive neuroendocrine tumor of the urinary bladder. Although research has been performed since the first case was reported in 1981, most of our understanding of the disease treatments has been extrapolated from small cell carcinoma of the lung. However, current data on patient survival have been stagnant. Observations: With the advent of advanced molecular diagnostic methods, a new potential for understanding the origin and treatment of small cell carcinoma of the urinary bladder has become evident...
March 23, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28333763/inflammatory-status-and-lung-function-predict-mortality-in-lung-cancer-screening-participants
#6
Ugo Pastorino, Daniele Morelli, Alfonso Marchianò, Stefano Sestini, Paola Suatoni, Francesca Taverna, Mattia Boeri, Gabriella Sozzi, Anna Cantarutti, Giovanni Corrao
Low-dose computed tomography (LDCT) screening trials have based their risk selection algorithm on age and tobacco exposure, but never on pulmonary risk-related biomarkers. In the present study, the baseline inflammatory status, measured by C-reactive protein (CRP) level, and lung function, measured by forced expiratory volume in 1 s (FEV1), were tested as independent predictors of all-cause mortality in LDCT-screening participants. Between 2000 and 2010, 4413 volunteers were enrolled in two LDCT-screening trials, with evaluable baseline CRP and FEV1 values: 2037 were included in the discovery set and 2376 were included in the validation set...
March 23, 2017: European Journal of Cancer Prevention
https://www.readbyqxmd.com/read/28331847/learning-parsimonious-classification-rules-from-gene-expression-data-using-bayesian-networks-with-local-structure
#7
Jonathan Lyle Lustgarten, Jeya Balaji Balasubramanian, Shyam Visweswaran, Vanathi Gopalakrishnan
The comprehensibility of good predictive models learned from high-dimensional gene expression data is attractive because it can lead to biomarker discovery. Several good classifiers provide comparable predictive performance but differ in their abilities to summarize the observed data. We extend a Bayesian Rule Learning (BRL-GSS) algorithm, previously shown to be a significantly better predictor than other classical approaches in this domain. It searches a space of Bayesian networks using a decision tree representation of its parameters with global constraints, and infers a set of IF-THEN rules...
March 2017: Data (Basel)
https://www.readbyqxmd.com/read/28331811/proteomic-analysis-of-bronchoalveolar-lavage-fluid-balf-from-lung-cancer-patients-using-label-free-mass-spectrometry
#8
Abduladim Hmmier, Michael Emmet O'Brien, Vincent Lynch, Martin Clynes, Ross Morgan, Paul Dowling
BACKGROUND: Lung cancer is the leading cause of cancer-related mortality in both men and women throughout the world. The need to detect lung cancer at an early, potentially curable stage, is essential and may reduce mortality by 20%. The aim of this study was to identify distinct proteomic profiles in bronchoalveolar fluid (BALF) and plasma that are able to discriminate individuals with benign disease from those with non-small cell lung cancer (NSCLC). METHODS: Using label-free mass spectrometry analysis of BALF during discovery-phase analysis, a significant number of proteins were found to have different abundance levels when comparing control to adenocarcinoma (AD) or squamous cell lung carcinoma (SqCC)...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/28330821/beyond-precision-surgery-molecularly-motivated-precision-care-for-gastric-cancer
#9
REVIEW
Y Y Choi, J-H Cheong
Gastric cancer is one of the leading causes of cancer-related deaths worldwide. Despite the high disease prevalence, gastric cancer research has not gained much attention. Recently, genome-scale technology has made it possible to explore the characteristics of gastric cancer at the molecular level. Accordingly, gastric cancer can be classified into molecular subtypes that convey more detailed information of tumor than histopathological characteristics, and these subtypes are associated with clinical outcomes...
March 1, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28330782/preparative-two-dimensional-separations-involving-liquid-liquid-chromatography
#10
Léa Marlot, Karine Faure
The increasing performances of analytical techniques, especially two-dimensional liquid chromatography hyphenated with highly sensitive detectors, allow discovery of new targeted compounds in highly complex samples, whether biomarkers in environmental effluents, natural metabolomes in natural products or unknown impurities in synthetic chemical process. While structural identification can usually be achieved through mass spectrometry and databases, it can be useful to confirm the potential structure via NMR analysis and/or to obtain standard reference material for quantitative purposes, incentive for the production of μg to mg of new target compounds...
March 18, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28328968/c-reactive-protein-and-n-terminal-prohormone-brain-natriuretic-peptide-as-biomarkers-in-acute-exacerbations-of-copd-leading-to-hospitalizations
#11
Yu-Wei Roy Chen, Virginia Chen, Zsuzsanna Hollander, Jonathon A Leipsic, Cameron J Hague, Mari L DeMarco, J Mark FitzGerald, Bruce M McManus, Raymond T Ng, Don D Sin
There are currently no accepted and validated blood tests available for diagnosing acute exacerbations of chronic obstructive pulmonary disease (AECOPD). In this study, we sought to determine the discriminatory power of blood C-reactive protein (CRP) and N-terminal prohormone brain natriuretic peptide (NT-proBNP) in the diagnosis of AECOPD requiring hospitalizations. The study cohort consisted of 468 patients recruited in the COPD Rapid Transition Program who were hospitalized with a primary diagnosis of AECOPD, and 110 stable COPD patients who served as controls...
2017: PloS One
https://www.readbyqxmd.com/read/28327523/methodological-challenges-in-protein-microarray-and-immunohistochemistry-for-the-discovery-of-novel-autoantibodies-in-paediatric-acute-disseminated-encephalomyelitis
#12
Patrick Peschl, Melanie Ramberger, Romana Höftberger, Karin Jöhrer, Matthias Baumann, Kevin Rostásy, Markus Reindl
Acute disseminated encephalomyelitis (ADEM) is a rare autoimmune-mediated demyelinating disease affecting mainly children and young adults. Differentiation to multiple sclerosis is not always possible, due to overlapping clinical symptoms and recurrent and multiphasic forms. Until now, immunoglobulins reactive to myelin oligodendrocyte glycoprotein (MOG antibodies) have been found in a subset of patients with ADEM. However, there are still patients lacking autoantibodies, necessitating the identification of new autoantibodies as biomarkers in those patients...
March 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28325740/proximal-tubulopathy-prime-mover-and-key-therapeutic-target-in-diabetic-kidney-disease
#13
Richard E Gilbert
The current view of diabetic kidney disease, based on meticulously acquired ultrastructural morphometry and the utility of measuring plasma creatinine and urinary albumin, has been almost entirely focused on the glomerulus. While clearly of great importance, changes in the glomerulus are not the major determinant of renal prognosis in diabetes and may not be the primary event in the development of diabetic kidney disease either. Indeed, advances in biomarker discovery and a greater appreciation of tubulointerstitial histopathology and the role of tubular hypoxia in the pathogenesis of chronic kidney disease have given us pause to reconsider the current "glomerulocentric" paradigm and focus attention on the proximal tubule that by virtue of the high energy requirements and reliance on aerobic metabolism render it particularly susceptible to the derangements of the diabetic state...
April 2017: Diabetes
https://www.readbyqxmd.com/read/28325368/chagas-disease-diagnostic-applications-present-knowledge-and-future-steps
#14
V Balouz, F Agüero, C A Buscaglia
Chagas disease, caused by the protozoan Trypanosoma cruzi, is a lifelong and debilitating illness of major significance throughout Latin America and an emergent threat to global public health. Being a neglected disease, the vast majority of Chagasic patients have limited access to proper diagnosis and treatment, and there is only a marginal investment into R&D for drug and vaccine development. In this context, identification of novel biomarkers able to transcend the current limits of diagnostic methods surfaces as a main priority in Chagas disease applied research...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28325298/relevance-of-fusion-genes-in-pediatric-cancers-toward-precision-medicine
#15
REVIEW
Célia Dupain, Anne Catherine Harttrampf, Giorgia Urbinati, Birgit Geoerger, Liliane Massaad-Massade
Pediatric cancers differ from adult tumors, especially by their very low mutational rate. Therefore, their etiology could be explained in part by other oncogenic mechanisms such as chromosomal rearrangements, supporting the possible implication of fusion genes in the development of pediatric cancers. Fusion genes result from chromosomal rearrangements leading to the juxtaposition of two genes. Consequently, an abnormal activation of one or both genes is observed. The detection of fusion genes has generated great interest in basic cancer research and in the clinical setting, since these genes can lead to better comprehension of the biological mechanisms of tumorigenesis and they can also be used as therapeutic targets and diagnostic or prognostic biomarkers...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28325210/breast-cancer-immunology-and-immunotherapy-current-status-and-future-perspectives
#16
L de la Cruz-Merino, M Chiesa, R Caballero, F Rojo, N Palazón, F H Carrasco, V Sánchez-Margalet
Cancer immunology has gained renewed interest in the past few years due to emerging findings on mechanisms involved in tumoral immune evasion. Indisputably, immune edition is currently considered a critical hallmark of cancer. Basic research has revealed new targets which can be modulated in the clinical setting with new compounds and strategies. As recent evidence confirms, breast cancer (BC) is a complex and heterogeneous disease in which host immune responses play a substantial role. T-infiltrating lymphocytes measurement is suggested as a powerful new tool necessary to predict early BC evolution, especially in HER2-positive and triple negative subtypes...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28324303/subtypes-of-parkinson-s-disease-what-do-they-tell-us-about-disease-progression
#17
REVIEW
Seyed-Mohammad Fereshtehnejad, Ronald B Postuma
Parkinson's disease is a widely heterogeneous disorder with a broad list of motor and nonmotor manifestations. Identifying subtypes of Parkinson's disease is one of the top clinical and research priorities. This review aims to summarize the most valid conventional and recent subtyping solutions that have been introduced so far and to update our current knowledge with recent discoveries on the association between subtypes and disease progression. We also discuss the challenges of subtyping in the context of Parkinson's disease, stability of the subtypes over time, and potential clinical implications...
April 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28323150/systematic-expression-profiling-analysis-mines-dys-regulated-modules-in-active-tuberculosis-based-on-re-weighted-protein-protein-interaction-network-and-attract-algorithm
#18
Ying Sun, Yan Weng, Ying Zhang, Xiang Yan, Lei Guo, Jia Wang, Xin Song, Ying Yuan, Fu-Ye Chang, Chun-Ling Wang
About 90% of tuberculosis (TB) patients latently infected with Mycobacterium tuberculosis (Mtb) show no symptoms, yet have a 10% chance in lifetime to progress active TB. Nevertheless, current diagnosis approaches need improvement in efficiency and sensitivity. The objective of this work was to detect potential signatures for active TB to further improve the understanding of the biological roles of functional modules involved in this disease. First, targeted networks of active TB and control groups were established via re-weighting protein-protein interaction (PPI) networks using Pearson's correlation coefficient (PCC)...
March 17, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28321148/circulating-mir-132-3p-as-a-candidate-diagnostic-biomarker-for-malignant-mesothelioma
#19
Daniel G Weber, Katarzyna Gawrych, Swaantje Casjens, Alexander Brik, Martin Lehnert, Dirk Taeger, Beate Pesch, Jens Kollmeier, Torsten T Bauer, Georg Johnen, Thomas Brüning
The use of circulating microRNAs as biomarkers has opened new opportunities for diagnosis of cancer because microRNAs exhibit tumor-specific expression profiles. The aim of this study was the identification of circulating microRNAs in human plasma as potential biomarkers for the diagnosis of malignant mesothelioma. For discovery, TaqMan Low Density Array Human MicroRNA Cards were used to analyze 377 microRNAs in plasma samples from 21 mesothelioma patients and 21 asbestos-exposed controls. For verification, individual TaqMan microRNA assays were used for quantitative real-time PCR in plasma samples from 22 mesothelioma patients and 44 asbestos-exposed controls...
2017: Disease Markers
https://www.readbyqxmd.com/read/28319050/extracellular-matrix-proteomics-identifies-molecular-signature-of-symptomatic-carotid-plaques
#20
Sarah R Langley, Karin Willeit, Athanasios Didangelos, Ljubica Perisic Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gerard Pasterkamp, Alun H Davies, Claudia Monaco, Ulf Hedin, Catherine M Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
BACKGROUND: The identification of patients with high-risk atherosclerotic plaques prior to the manifestation of clinical events remains challenging. Recent findings question histology- and imaging-based definitions of the "vulnerable plaque," necessitating an improved approach for predicting onset of symptoms. METHODS: We performed a proteomics comparison of the vascular extracellular matrix and associated molecules in human carotid endarterectomy specimens from 6 symptomatic versus 6 asymptomatic patients to identify a protein signature for high-risk atherosclerotic plaques...
March 20, 2017: Journal of Clinical Investigation
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