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Biomarker discovery

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https://www.readbyqxmd.com/read/28444384/e-science-technologies-in-a-workflow-for-personalized-medicine-using-cancer-screening-as-a-case-study
#1
Ola Spjuth, Andreas Karlsson, Mark Clements, Keith Humphreys, Emma Ivansson, Jim Dowling, Martin Eklund, Alexandra Jauhiainen, Kamila Czene, Henrik Grönberg, Pär Sparén, Fredrik Wiklund, Abbas Cheddad, Þorgerður Pálsdóttir, Mattias Rantalainen, Linda Abrahamsson, Erwin Laure, Jan-Eric Litton, Juni Palmgren
Objective: We provide an e-Science perspective on the workflow from risk factor discovery and classification of disease to evaluation of personalized intervention programs. As case studies, we use personalized prostate and breast cancer screenings. Materials and Methods: We describe an e-Science initiative in Sweden, e-Science for Cancer Prevention and Control (eCPC), which supports biomarker discovery and offers decision support for personalized intervention strategies...
April 21, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28443762/prediction-of-therapy-response-in-ovarian-cancer-where-are-we-now
#2
Khalid El Bairi, Mariam Amrani, Abdul Hafeez Kandhro, Said Afqir
Therapy resistance is a major challenge in the management of ovarian cancer (OC). Advances in detection and new technology validation have led to the emergence of biomarkers that can predict responses to available therapies. It is important to identify predictive biomarkers to select resistant and sensitive patients in order to reduce important toxicities, to reduce costs and to increase survival. The discovery of predictive and prognostic biomarkers for monitoring therapy is a developing field and provides promising perspectives in the era of personalized medicine...
April 26, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28442406/anti-amnesic-effect-of-extract-and-alkaloid-fraction-from-aerial-parts-of-peganum-harmala-on-scopolamine-induced-memory-deficits-in-mice
#3
Wei Liu, Yudan Zhu, Yongli Wang, Shenglan Qi, Yuwen Wang, Chao Ma, Shuping Li, Bo Jiang, Xuemei Cheng, Zhengtao Wang, Zhenyu Xuan, Changhong Wang
ETHNOPHARMACOLOGICAL RELEVANCE: Aerial parts of Peganum harmala Linn (APP) is used as traditional medical herb for treatment of forgetfulness in Uighur medicine in China. But, the active ingredients and underlying mechanisms are unclear. AIM OF THE STUDY: The present study was undertaken to investigate the improvement effects of extract and alkaloid fraction from APP on scopolamine-induced cognitive dysfunction and to elucidate their underlying mechanisms of action, and to support its folk use with scientific evidence, and lay a foundation for its further researches...
April 22, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28441039/high-throughput-processing-to-preserve-viable-cells-a-precision-medicine-initiative-cohort-program-workshop
#4
Rebekah S Rasooly, Daniel R Gossett, Marianne K Henderson, Allison Hubel, Stephen N Thibodeau
Conventionally, biobanks supporting clinical research studies have preserved serum, plasma, urine, saliva, a variety of tissue types, and stool. With the emergence of increasingly sophisticated technologies for analyzing single cells, there is growing interest in preserving viable blood cells for future functional studies. The new All of Us Research Program (formerly the Precision Medicine Initiative Cohort Program) biobank plans to house samples from a million or more individuals as part of a cohort with rich phenotypic data and longitudinal follow-up ( www...
April 25, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28440505/detection-of-fetal-epigenetic-biomarkers-through-genome-wide-dna-methylation-study-for-non-invasive-prenatal-diagnosis
#5
Hong-Dan Wang, Lin Liu, Hui-Ru Zhao, Qiao-Fang Hou, Jing-Bin Yan, Wei-Li Shi, Qian-Nan Guo, Li Wang, Shi-Xiu Liao, Bo-Feng Zhu
The discovery of cell-free DNA fetal (cff DNA) in maternal plasma during pregnancy provides a novel perspective for the development of non‑invasive prenatal diagnosis (NIPD). Against the background of maternal DNA, the use of the relatively low concentration of cff DNA is limited in NIPD. Therefore, in order to overcome the complication of the background of maternal DNA and expand the scope of cff DNA application in clinical practice, it is necessary to identify novel universal fetal‑specific DNA markers...
April 25, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28440083/systems-metabolomics-for-prediction-of-metabolic-syndrome
#6
Estelle Pujos-Guillot, Marion Brandolini, Mélanie Pétéra, Dhouha Grissa, Charlotte Joly, Bernard Lyan, Eléonore Herquelot, Sébastien Czernichow, Marie Zins, Marcel Goldberg, Blandine Comte
The evolution of human health is a continuum of transitions, involving multifaceted processes at multiple levels and there is an urgent need for integrative biomarkers that can characterize and predict progression towards disease development. The objective of this work was to perform a systems metabolomics approach to predict metabolic syndrome (MetS) development. A case-control design was used within the French occupational GAZEL cohort (n=112 males: discovery study; n=94: replication/validation study). Our integrative strategy was to combine untargeted metabolomics with clinical, sociodemographic and food habit parameters to describe early phenotypes and build multidimensional predictive models...
April 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28438806/emerging-affinity-based-proteomic-technologies-for-large-scale-plasma-profiling-in-cardiovascular-disease
#7
REVIEW
J Gustav Smith, Robert E Gerszten
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets...
April 25, 2017: Circulation
https://www.readbyqxmd.com/read/28438154/network-based-analysis-reveals-novel-gene-signatures-in-peripheral-blood-of-patients-with-chronic-obstructive-pulmonary-disease
#8
Ma'en Obeidat, Yunlong Nie, Virginia Chen, Casey P Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rotzschke, Peter J Castaldi, Craig P Hersh, Nick Fishbane, Raymond T Ng, Bruce McManus, Bruce E Miller, Stephen Rennard, Peter D Paré, Don D Sin
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death and there is a huge unmet clinical need to identify disease biomarkers in peripheral blood. Compared to gene level differential expression approaches to identify gene signatures, network analyses provide a biologically intuitive approach which leverages the co-expression patterns in the transcriptome to identify modules of co-expressed genes. METHODS: A weighted gene co-expression network analysis (WGCNA) was applied to peripheral blood transcriptome from 238 COPD subjects to discover co-expressed gene modules...
April 24, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28437675/whole-blood-sequencing-reveals-circulating-microrna-associations-with-high-risk-traits-in-non-st-segment-elevation-acute-coronary-syndrome
#9
Alice Wang, Lydia Coulter Kwee, Elizabeth Grass, Megan L Neely, Simon G Gregory, Keith A A Fox, Paul W Armstrong, Harvey D White, E Magnus Ohman, Matthew T Roe, Svati H Shah, Mark Y Chan
BACKGROUND AND AIMS: Although circulating microRNA (miRNAs) have emerged as biomarkers predicting mortality in acute coronary syndrome (ACS), more data are needed to understand these mechanisms. Mapping miRNAs to high-risk traits may identify miRNAs involved in pathways conferring risk for poor outcome in ACS. We aim to investigate the relationship between circulating miRNAs and high-risk traits in non-ST-segment elevation acute coronary syndrome (NSTE-ACS). METHODS: Whole-genome miRNA sequencing was performed on RNA extracted from whole blood of 199 patients with NSTE-ACS...
March 30, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28436314/metabolomic-approaches-in-the-discovery-of-potential-urinary-biomarkers-of-drug-induced-liver-injury-dili
#10
Ana Margarida Araújo, Márcia Carvalho, Félix Carvalho, Maria de Lourdes Bastos, Paula Guedes de Pinho
Drug-induced liver injury (DILI) is a major safety issue during drug development, as well as the most common cause for the withdrawal of drugs from the pharmaceutical market. The identification of DILI biomarkers is a labor-intensive area. Conventional biomarkers are not specific and often only appear at significant levels when liver damage is substantial. Therefore, new biomarkers for early identification of hepatotoxicity during the drug discovery process are needed, thus resulting in lower development costs and safer drugs...
April 24, 2017: Critical Reviews in Toxicology
https://www.readbyqxmd.com/read/28436239/clinical-applications-of-quantitative-proteomics-using-targeted-and-untargeted-data-independent-acquisition-techniques
#11
Jesse G Meyer, Birgit Schilling
While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered: This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e...
April 24, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28436162/the-path-forward-2015-international-children-s-tumor-foundation-conference-on-neurofibromatosis-type-1-type-2-and-schwannomatosis
#12
Jaishri O Blakeley, Annette Bakker, Anne Barker, Wade Clapp, Rosalie Ferner, Michael J Fisher, Marco Giovannini, David H Gutmann, Matthias A Karajannis, Joseph L Kissil, Eric Legius, Alison C Lloyd, Roger J Packer, Vijaya Ramesh, Vincent M Riccardi, David A Stevenson, Nicole J Ullrich, Meena Upadhyaya, Anat Stemmer-Rachamimov
The Annual Children's Tumor Foundation International Neurofibromatosis Meeting is the premier venue for connecting discovery, translational and clinical scientists who are focused on neurofibromatosis types 1 and 2 (NF1 and NF2) and schwannomatosis (SWN). The meeting also features rare tumors such as glioma, meningioma, sarcoma, and neuroblastoma that occur both within these syndromes and spontaneously; associated with somatic mutations in NF1, NF2, and SWN. The meeting addresses both state of the field for current clinical care as well as emerging preclinical models fueling discovery of new therapeutic targets and discovery science initiatives investigating mechanisms of tumorigenesis...
April 24, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28434677/the-microbiome-of-the-prostate-tumor-microenvironment
#13
Ilaria Cavarretta, Roberto Ferrarese, Walter Cazzaniga, Diego Saita, Roberta Lucianò, Elisa R Ceresola, Irene Locatelli, Laura Visconti, Giovanni Lavorgna, Alberto Briganti, Manuela Nebuloni, Claudio Doglioni, Massimo Clementi, Francesco Montorsi, Filippo Canducci, Andrea Salonia
BACKGROUND: The advent of molecular-based methods of identification and characterization of complex microbial populations has led to a new era of microbial discovery. A detailed and comprehensive analysis of the microbial ecosystem of the pathologic and healthy prostate tissues has not been yet reported. OBJECTIVES: To characterize the microbiome possibly associated to the pathologic prostate microenvironment. DESIGN, SETTING, AND PARTICIPANTS: The microbiome profile of tumor, peri-tumor, and nontumor tissues was assessed on 16 radical prostatectomy-specimens...
April 20, 2017: European Urology
https://www.readbyqxmd.com/read/28434587/aligning-physiology-with-psychology-translational-neuroscience-in-neuropsychiatric-drug-discovery
#14
REVIEW
Robert A McArthur
This review presents an overview of some of the pre-clinical and clinical issues that have contributed to the failures of potential novel neuropsychiatric drugs, which have prompted a re-examination of the role of animal models of neuropsychiatric disorders. Advances both in basic neuroscience and technology have driven the development of animal models of aspects of neuropsychiatric disorders. Genetics and environmental factors have been the primary contributors to the development of new animal models. Neuroimaging has contributed to the search for biomarkers by which neuropsychiatric disorders may be identified and differentiated, its progression monitored and that the effects of therapy assessed...
May 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28434291/the-importance-of-pre-clinical-studies-in-animal-models-of-ttr-amyloidosis-for-the-discovery-of-novel-patient-disease-biomarkers
#15
N P Gonçalves, D Martins, M J Saraiva
No abstract text is available yet for this article.
March 2017: Amyloid: the International Journal of Experimental and Clinical Investigation
https://www.readbyqxmd.com/read/28434268/ubiquitin-c-terminal-hydrolase-l1-uch-l1-as-a-therapeutic-and-diagnostic-target-in-neurodegeneration-neurotrauma-and-neuro-injuries
#16
Kevin K Wang, Zhihui Yang, George Sarkis, Isabel Torres, Vijaya Raghavan
Since its discovery as a major CNS-abundant protein 25 years ago, Ubiquitin C-terminal hydrolase-L1 (UCH-L1) has emerged as an important enzyme in regulating brain protein metabolism, by coupling to the proteasome pathway of protein degradation. Areas covered: UCH-L1 is implicated in both familial and sporadic Parkinson disease and other chronic neurodegenerative diseases. Also, UCH-L1 has been recently emerging as a biofluid-based biomarker for various forms of acute neurotrauma and CNS injury. Expert opinion: The loss of UCH-L1 activity coupled with the gain of proteinopathy function are linked to neurodegeneration such as Parkinsonism and Alzheimer's disease...
April 24, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28434075/associations-of-self-reported-smoking-cotinine-levels-and-epigenetic-smoking-indicators-with-oxidative-stress-among-older-adults-a-population-based-study
#17
Xu Gao, Xīn Gào, Yan Zhang, Lutz Philipp Breitling, Ben Schöttker, Hermann Brenner
Tobacco smoking and oxidative stress (OS) are both related to a wide spectrum of adverse age-related health outcomes, but their association is not yet well-established. We examined the associations of self-reported smoking indicators, serum cotinine levels and smoking-related DNA methylation biomarkers with two urinary proxy markers of OS, 8-isoprostane (8-iso) and 8-hydroxy-2'-deoxyguanosine (8-oxodG), in two independent subsets of older adults recruited in Germany (discovery set: n = 978, validation set: n = 531)...
April 22, 2017: European Journal of Epidemiology
https://www.readbyqxmd.com/read/28433920/proteomic-analysis-of-sockeye-salmon-serum-as-a-tool-for-biomarker-discovery-and-new-insight-into-the-sublethal-toxicity-of-diluted-bitumen
#18
Sarah L Alderman, Laura A Dindia, Christopher J Kennedy, Anthony P Farrell, Todd E Gillis
Pipelines carrying diluted bitumen (dilbit) from Canada's oil sands traverse North America, including the freshwater habitat of Pacific salmon, posing a risk of environmental release and aquatic exposure. Swimming performance is impacted in juvenile sockeye (Oncorhynchus nerka) exposed to dilbit; therefore biomarkers of dilbit exposure will be valuable for monitoring at-risk salmon stocks. This study characterized changes in the serum proteome of sockeye exposed to a sub-lethal and environmentally relevant concentration of dilbit using isobaric tags for relative and absolute quantitation (iTRAQ), and included a range of experimental conditions to permit identification of biomarkers that are robust across time (1 and 4wk) and exercise level (at rest and following a swim test)...
April 12, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28430874/developmental-sall2-transcription-factor-a-new-player-in-cancer
#19
Viviana E Hermosilla, Matias I Hepp, David Escobar, Carlos Farlas, Elizabeth N Riffo, Ariel F Castro, Roxana Pincheira
SALL2, also known as Spalt-like transcription factor 2, is a member of the SALL family of transcription factors involved in development and conserved through evolution. Since its identification in 1996, findings indicate that SALL2 plays a role in neurogenesis, neuronal differentiation and eye development. Consistently, SALL2 deficiency associates with neural tube defects and coloboma, a congenital eye disease. Relevant to cancer, clinical studies indicate that SALL2 is deregulated in various cancers, and is a specific biomarker for Synovial Sarcoma...
April 18, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28429560/is-there-a-role-for-newer-biomarkers-in-chronic-kidney-disease-mineral-and-bone-disorder-management
#20
Sven-Jean Tan, Michael Mx Cai
The current management of Chronic Kidney Disease-Mineral Bone Disorder (CKD-MBD) relies largely on clinical judgement and assessment of biochemical parameters including serum calcium, phosphate and intact parathyroid hormone concentrations. In the past two decades, there has been a leap in the understanding of the pathophysiology of CKD-MBD, leading to the discovery of novel biomarkers. The potential utility of these markers in this clinical setting is an area of intense investigation. In the absence of any guidelines aiding the clinician's understanding and application of these markers, we summarise the current available literature surrounding fibroblast growth factor-23, α-Klotho, sclerostin and serum calcification propensity testing and their respective assays in the context of CKD-MBD management...
March 2017: Nephrology
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