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https://www.readbyqxmd.com/read/29138271/addressing-the-perfect-storm-biomarkers-in-obesity-and-pathophysiology-of-cardiometabolic-risk
#1
REVIEW
Krasimira Aleksandrova, Dariush Mozaffarian, Tobias Pischon
BACKGROUND: The worldwide rise of obesity has provoked intensified research to better understand its pathophysiology as a means for disease prevention. Several biomarkers that may reflect various pathophysiological pathways that link obesity and cardiometabolic diseases have been identified over the past decades. CONTENT: We summarize research evidence regarding the role of established and novel obesity-related biomarkers, focusing on recent epidemiological evidence for detrimental associations with cardiometabolic diseases including obesity-related cancer...
November 14, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29138111/recent-advances-in-melanoma-research-via-omics-platforms
#2
REVIEW
Carmen Rodríguez-Cerdeira, Alberto Molares-Vila, Miguel Carnero-Gregorio, Alberte Corbalán-Rivas
Melanoma has a high mortality rate and metastatic melanoma is highly resistant to conventional therapies. "Omics" fields such as proteomics and microRNA and exosome studies have provided new knowledge to complement the information generated by genomic studies. This work aimed to review the current status of biomarker discovery for melanoma through multi-"omics" platforms. A few sets of novel microRNAs and proteins are described, some of them with important implications in suppressing melanoma at different stages...
November 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29136207/linkedomics-analyzing-multi-omics-data-within-and-across-32-cancer-types
#3
Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang
The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29133589/precision-oncology-beyond-targeted-therapy-combining-omics-data-with-machine-learning-matches-the-majority-of-cancer-cells-to-effective-therapeutics
#4
Michael Q Ding, Lujia Chen, Gregory F Cooper, Jonathan D Young, Xinghua Lu
Precision oncology involves identifying drugs that will effectively treat a tumor and then prescribing an optimal clinical treatment regimen. However, most first-line chemotherapy drugs do not have biomarkers to guide their application. For molecularly targeted drugs, using the genomic status of a drug target as a therapeutic indicator has limitations. In this study, machine learning methods (e.g., deep learning) were used to identify informative features from genome scale omics data and to train classifiers for predicting the effectiveness of drugs in cancer cell lines...
November 13, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29127996/highlights-in-immune-response-microbiome-and-precision-medicine-in-allergic-disease-and-asthma
#5
EDITORIAL
Milena Sokolowska, Cezmi A Akdis
Several recent key findings in immunology of allergic diseases that have led to a need of reassessment of our current thinking are reviewed in this issue of the journal. Recently developed strong evidence on the role of hygiene hypothesis in protection from allergic disease and its immune mechanisms is reviewed by Ober et al. The authors pointed out immunologic mechanisms of lower prevalence of asthma and allergic sensitization observed among Amish children living on traditional farms with higher endotoxin levels as compared to Hutterite children living on industrialized farms...
October 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/29126224/dbtss-dbkero-for-integrated-analysis-of-transcriptional-regulation
#6
Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki
DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional regulation. In this update, we facilitate interpretations of disease associated genomic variation, using the Japanese population as a model case...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122727/gender-related-metabolomics-and-lipidomics-from-experimental-animal-models-to-clinical-evidence
#7
Matteo Audano, Mariateresa Maldini, Emma De Fabiani, Nico Mitro, Donatella Caruso
Lipidomics and metabolomics have emerged as important tools for the characterization of specific physiological and pathological traits. The selection of the analytical approaches and the choice of a targeted rather than an untargeted strategy in metabolomics find their reasons in the driving hypothesis of the study, sample features and instrumental availability. Moreover, in the last years, -omics approaches have found their application in the study of sex-related dimorphism. In this review, lipidomic and metabolomic analyses are presented in a biomedical perspective...
November 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29113454/modulators-of-redox-metabolism-in-head-and-neck-cancer
#8
Xiaofei Chen, Jade Mims, Xiumei Huang, Naveen Singh, Edward A Motea, Sarah M Planchon, Muhammad Beg, Allen W Tsang, Mercedes Porosnicu, Melissa L Kemp, David A Boothman, Cristina Furdui
SIGNIFICANCE: Head and Neck Squamous Cell Cancer (HNSCC) is a complex disease characterized by high genetic and metabolic heterogeneity. Radiation therapy (RT) alone or combined with systemic chemotherapy is widely used for treatment of HNSCC as definitive treatment or as adjuvant treatment after surgery. Antibodies against Epidermal Growth Factor Receptor (EGFR) are used in definitive or palliative treatment. Recent Advances. Emerging targeted therapies against other proteins of interest as well as programmed cell death protein 1 (PD-1) and programmed death-ligand 1 (PD-L1) immunotherapies are being explored in clinical trials...
November 7, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29111762/metabolomics-and-lipidomics-profiling-of-a-combined-mitochondrial-plus-endoplasmic-reticulum-fraction-of-human-fibroblasts-a-robust-tool-for-clinical-studies
#9
Charlotte Veyrat-Durebex, Cinzia Bocca, Stéphanie Chupin, Judith Kouassi Nzoughet, Gilles Simard, Guy Lenaers, Pascal Reynier, Hélène Blasco
Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles' functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29111012/advancing-stroke-genomic-research-in-the-age-of-trans-omics-big-data-science-emerging-priorities-and-opportunities
#10
REVIEW
Mayowa Owolabi, Emmanuel Peprah, Huichun Xu, Rufus Akinyemi, Hemant K Tiwari, Marguerite R Irvin, Kolawole Wasiu Wahab, Donna K Arnett, Bruce Ovbiagele
BACKGROUND: We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science. METHODS: Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017. RESULTS: We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use...
November 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/29110777/the-use-of-cerebrospinal-fluid-in-biomarker-studies
#11
C E Teunissen, C Verheul, E A J Willemse
Cerebrospinal fluid (CSF) is an extremely useful matrix for biomarker research for several purposes, such as diagnosis, prognosis, monitoring, and identification of prominent leads in pathways of neurologic diseases. Such biomarkers can be identified based on a priori hypotheses around prominent protein changes, but also by applying -omics technologies. Proteomics is widely used, but metabolomics and transcriptomics are rapidly revealing their potential for CSF studies. The basis of such studies is the availability of high-quality biobanks...
2017: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29110627/the-impact-of-translational-research-in-breast-cancer-care-can-we-improve-the-therapeutic-scenario
#12
Francesco Perri, Giuseppe Buono, Francesco Schettini, Grazia Arpino, Roberto Bianco, Carmen Criscitiello, Sabino De Placido, Mario Giuliano
Traditionally, breast cancer (BC) is divided into different immunohistochemically (IHC)-defined subtypes, according to the expression of hormone receptors and overexpression/amplification of human epidermal growth factor receptor 2 (HER2), with crucial therapeutic implications. In the last few years, the definition of different BC molecular subgroups within the IHC-defined subtypes and the identification of the important role that molecular heterogeneity can play in tumor progression and treatment resistance have inspired the search for personalized therapeutic approaches...
November 2, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/29109301/personalized-medicine-a-modern-approach-for-the-diagnosis-and-management-of-hypertension
#13
REVIEW
Carmine Savoia, Massimo Volpe, Guido Grassi, Claudio Borghi, Enrico Agabiti Rosei, Rhian M Touyz
The main goal of treating hypertension is to reduce blood pressure to physiological levels and thereby prevent risk of cardiovascular disease and hypertension-associated target organ damage. Despite reductions in major risk factors and the availability of a plethora of effective antihypertensive drugs, the control of blood pressure to target values is still poor due to multiple factors including apparent drug resistance and lack of adherence. An explanation for this problem is related to the current reductionist and 'trial-and-error' approach in the management of hypertension, as we may oversimplify the complex nature of the disease and not pay enough attention to the heterogeneity of the pathophysiology and clinical presentation of the disorder...
November 15, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/29106475/quantitative-serum-nuclear-magnetic-resonance-metabolomics-in-large-scale-epidemiology-a-primer-on-omic-technologies
#14
Peter Würtz, Antti J Kangas, Pasi Soininen, Debbie A Lawlor, George Davey Smith, Mika Ala-Korpela
Detailed metabolic profiling in large-scale epidemiologic studies has uncovered novel biomarkers for cardiometabolic diseases and clarified the molecular associations of established risk factors. A quantitative metabolomics platform based on nuclear magnetic resonance spectroscopy has found widespread use, already profiling over 400,000 blood samples. Over 200 metabolic measures are quantified per sample; in addition to many biomarkers routinely used in epidemiology, the method simultaneously provides fine-grained lipoprotein subclass profiling and quantification of circulating fatty acids, amino acids, gluconeogenesis-related metabolites, and many other molecules from multiple metabolic pathways...
November 1, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29106465/a-strategy-for-multimodal-data-integration-application-to-biomarkers-identification-in-spinocerebellar-ataxia
#15
Imene Garali, Isaac M Adanyeguh, Farid Ichou, Vincent Perlbarg, Alexandre Seyer, Benoit Colsch, Ivan Moszer, Vincent Guillemot, Alexandra Durr, Fanny Mochel, Arthur Tenenhaus
The growing number of modalities (e.g. multi-omics, imaging and clinical data) characterizing a given disease provides physicians and statisticians with complementary facets reflecting the disease process but emphasizes the need for novel statistical methods of data analysis able to unify these views. Such data sets are indeed intrinsically structured in blocks, where each block represents a set of variables observed on a group of individuals. Therefore, classical statistical tools cannot be applied without altering their organization, with the risk of information loss...
July 3, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29103195/maternal-sepsis-in-the-era-of-genomic-medicine
#16
REVIEW
C Kouskouti, N Evangelatos, A Brand, F Kainer
PURPOSE: Maternal sepsis remains one of the leading causes of direct and indirect maternal mortality both in high- and low-income environments. In the last two decades, systems biology approaches, based on '-omics' technologies, have started revolutionizing the diagnosis and management of the septic syndrome. The scope of this narrative review is to present an overview of the basic '-omics' technologies, exemplified by cases relevant to maternal sepsis. METHODS: Narrative review of the new '-omics' technologies based on a detailed review of the literature...
November 4, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/29103096/a-decade-of-genetic-and-metabolomic-contributions-to-type-2-diabetes-risk-prediction
#17
REVIEW
Jordi Merino, Miriam S Udler, Aaron Leong, James B Meigs
PURPOSE OF REVIEW: The purpose of this review was to summarize and reflect on advances over the past decade in human genetic and metabolomic discovery with particular focus on their contributions to type 2 diabetes (T2D) risk prediction. RECENT FINDINGS: In the past 10 years, a combination of advances in genotyping efficiency, metabolomic profiling, bioinformatics approaches, and international collaboration have moved T2D genetics and metabolomics from a state of frustration to an abundance of new knowledge...
November 4, 2017: Current Diabetes Reports
https://www.readbyqxmd.com/read/29101939/pharmacogenomics-precision-medicine-and-drug-response
#18
REVIEW
Richard M Weinshilboum, Liewei Wang
Pharmacogenomics is the use of genomic and other "omic" information to individualize drug selection and drug use to avoid adverse drug reactions and to maximize drug efficacy. The science underlying pharmacogenomics has evolved rapidly over the 50 years since it was first suggested that genetics might influence drug response phenotypes. That process has occurred in parallel with advances in DNA sequencing and other molecular technologies, with striking increases in our understanding of the human genome. There are now many validated examples of the clinical utility of pharmacogenomics, and this type of clinical genomic information is increasingly being generated in clinical laboratories, incorporated into electronic health records, and used to "tailor" or individualize drug therapy...
November 2017: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/29101330/translational-utility-of-a-hierarchical-classification-strategy-in-biomolecular-data-analytics
#19
Dieter Galea, Paolo Inglese, Lidia Cammack, Nicole Strittmatter, Monica Rebec, Reza Mirnezami, Ivan Laponogov, James Kinross, Jeremy Nicholson, Zoltan Takats, Kirill A Veselkov
Hierarchical classification (HC) stratifies and classifies data from broad classes into more specific classes. Unlike commonly used data classification strategies, this enables the probabilistic prediction of unknown classes at different levels, minimizing the burden of incomplete databases. Despite these advantages, its translational application in biomedical sciences has been limited. We describe and demonstrate the implementation of a HC approach for "omics-driven" classification of 15 bacterial species at various taxonomic levels achieving 90-100% accuracy, and 9 cancer types into morphological types and 35 subtypes with 99% and 76% accuracy, respectively...
November 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29095697/harmonization-in-laboratory-medicine-more-than-clinical-chemistry
#20
REVIEW
Mario Plebani
The goal of harmonizing laboratory information is to contribute to quality in patient care, ultimately improving upon patient outcomes and safety. The main focus of harmonization and standardization initiatives has been on analytical processes within the laboratory walls, clinical chemistry tests in particular. However, two major evidences obtained in recent years show that harmonization should be promoted not only in the analytical phase but also in all steps of the testing process, encompassing the entire field of laboratory medicine, including innovative areas (e...
November 2, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
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