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https://www.readbyqxmd.com/read/28097879/metabolomics-biomarkers-for-tuberculosis-diagnostics-current-status-and-future-objectives
#1
Ilse du Preez, Laneke Luies, Du Toit Loots
Numerous studies have contributed to our current understanding of the complex biology of pulmonary tuberculosis and subsequently provided solutions to its control or eradication. Metabolomics, a newcomer to the Omics research domain, has significantly contributed to this understanding by identifying biomarkers originating from the disease-associated metabolome adaptations of both the microbe and host. These biomarkers have shed light on previously unknown disease mechanisms, many of which have been implemented toward the development of improved diagnostic strategies...
January 18, 2017: Biomarkers in Medicine
https://www.readbyqxmd.com/read/28093659/clinical-and-molecular-relevance-of-mutant-allele-tumor-heterogeneity-in-breast-cancer
#2
Ding Ma, Yi-Zhou Jiang, Xi-Yu Liu, Yi-Rong Liu, Zhi-Ming Shao
PURPOSE: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. METHODS: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment...
January 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28091625/mplex-a-method-for-simultaneous-pathogen-inactivation-and-extraction-of-samples-for-multi-omics-profiling
#3
Kristin E Burnum-Johnson, Jennifer E Kyle, Amie J Eisfeld, Cameron P Casey, Kelly G Stratton, Juan F Gonzalez, Fabien Habyarimana, Nicholas M Negretti, Amy C Sims, Sadhana Chauhan, Larissa B Thackray, Peter J Halfmann, Kevin B Walters, Young-Mo Kim, Erika M Zink, Carrie D Nicora, Karl K Weitz, Bobbie-Jo M Webb-Robertson, Ernesto S Nakayasu, Brian Ahmer, Michael E Konkel, Vladimir Motin, Ralph S Baric, Michael S Diamond, Yoshihiro Kawaoka, Katrina M Waters, Richard D Smith, Thomas O Metz
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements...
January 16, 2017: Analyst
https://www.readbyqxmd.com/read/28079714/radiomic-phenotyping-in-brain-cancer-to-unravel-hidden-information-in-medical-images
#4
Srishti Abrol, Aikaterini Kotrotsou, Ahmed Salem, Pascal O Zinn, Rivka R Colen
Radiomics is a new area of research in the field of imaging with tremendous potential to unravel the hidden information in digital images. The scope of radiology has grown exponentially over the last two decades; since the advent of radiomics, many quantitative imaging features can now be extracted from medical images through high-throughput computing, and these can be converted into mineable data that can help in linking imaging phenotypes with clinical data, genomics, proteomics, and other "omics" information...
January 11, 2017: Topics in Magnetic Resonance Imaging: TMRI
https://www.readbyqxmd.com/read/28077457/systems-biology-derived-biomarkers-to-predict-progression-of-renal-function-decline-in-type-2-diabetes-mellitus
#5
Gert Mayer, Hiddo J L Heerspink, Constantin Aschauer, Andreas Heinzel, Georg Heinze, Alexander Kainz, Judith Sunzenauer, Paul Perco, Dick de Zeeuw, Peter Rossing, Michelle Pena, Rainer Oberbauer
OBJECTIVE: Chronic kidney disease (CKD) in diabetes has a complex molecular and likely multifaceted pathophysiology. We aimed to validate a panel of biomarkers identified using a systems biology approach to predict the individual decline of estimated glomerular filtration rate (eGFR) in a large group of patients with type 2 diabetes mellitus and CKD at various stages. RESEARCH DESIGN AND METHODS: We used publicly available "omics" data to develop a molecular process model of CKD in diabetes and identified a representative parsimonious set of nine molecular biomarkers: chitinase 3-like protein 1, growth hormone 1, hepatocyte growth factor, matrix metalloproteinase (MMP) 2, MMP7, MMP8, MMP13, tyrosine kinase, and tumor necrosis factor receptor-1...
January 11, 2017: Diabetes Care
https://www.readbyqxmd.com/read/28075340/bioactive-nutrients-and-nutrigenomics-in-age-related-diseases
#6
REVIEW
Tania Rescigno, Luigina Micolucci, Mario F Tecce, Anna Capasso
The increased life expectancy and the expansion of the elderly population are stimulating research into aging. Aging may be viewed as a multifactorial process that results from the interaction of genetic and environmental factors, which include lifestyle. Human molecular processes are influenced by physiological pathways as well as exogenous factors, which include the diet. Dietary components have substantive effects on metabolic health; for instance, bioactive molecules capable of selectively modulating specific metabolic pathways affect the development/progression of cardiovascular and neoplastic disease...
January 8, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28065164/plasma-proteome-and-metabolome-characterization-of-an-experimental-human-thyrotoxicosis-model
#7
Maik Pietzner, Beatrice Engelmann, Tim Kacprowski, Janine Golchert, Anna-Luise Dirk, Elke Hammer, K Alexander Iwen, Matthias Nauck, Henri Wallaschofski, Dagmar Führer, Thomas F Münte, Nele Friedrich, Uwe Völker, Georg Homuth, Georg Brabant
BACKGROUND: Determinations of thyrotropin (TSH) and free thyroxine (FT4) represent the gold standard in evaluation of thyroid function. To screen for novel peripheral biomarkers of thyroid function and to characterize FT4-associated physiological signatures in human plasma we used an untargeted OMICS approach in a thyrotoxicosis model. METHODS: A sample of 16 healthy young men were treated with levothyroxine for 8 weeks and plasma was sampled before the intake was started as well as at two points during treatment and after its completion, respectively...
January 9, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28063332/metabolomics-a-potential-way-to-know-the-role-of-vitamin-d-on-multiple-sclerosis
#8
REVIEW
Diego Luque-Córdoba, María D Luque de Castro
The literature about the influence of vitamin D on multiple sclerosis (MS) is very controversial, possibly as a result of the way through which the research on the subject has been conducted. The studies developed so far have been focused exclusively on gene expression: the effect of a given vitamin D metabolite on target receptors. The influence of the vitamin D status (either natural or after supplementation) on MS has been studied by measurement of the 25 monohydroxylated metabolite (also known as circulating form), despite the 1,25 dihydroxylated metabolite is considered the active form...
December 29, 2016: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28057301/axgxe-using-flies-to-interrogate-the-complex-etiology-of-neurodegenerative-disease
#9
C Burke, K Trinh, V Nadar, S Sanyal
Progressive and late-onset neurological disorders such as Parkinson's disease and Alzheimer's disease affect up to 50 million people globally-a number postulated to double every 20 years in a continually aging population. While predisposing allelic variants in several genes clearly confer risk, individual age and specific environmental influences are equally important discriminators of disease onset age and progression. However, none of these factors can independently predict disease with significant precision...
2017: Current Topics in Developmental Biology
https://www.readbyqxmd.com/read/28040685/using-knowledge-driven-genomic-interactions-for-multi-omics-data-analysis-metadimensional-models-for-predicting-clinical-outcomes-in-ovarian-carcinoma
#10
Dokyoon Kim, Ruowang Li, Anastasia Lucas, Shefali S Verma, Scott M Dudek, Marylyn D Ritchie
It is common that cancer patients have different molecular signatures even though they have similar clinical features, such as histology, due to the heterogeneity of tumors. To overcome this variability, we previously developed a new approach incorporating prior biological knowledge that identifies knowledge-driven genomic interactions associated with outcomes of interest. However, no systematic approach has been proposed to identify interaction models between pathways based on multi-omics data. Here we have proposed such a novel methodological framework, called metadimensional knowledge-driven genomic interactions (MKGIs)...
December 31, 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28031971/bluepen-biomarkers-llc-integrated-biomarker-solutions
#11
EDITORIAL
Ian A Blair, Clementina Mesaros, Patrick Lilley, Matthew Nunez
BluePen Biomarkers provides a unique comprehensive multi-omics biomarker discovery and validation platform. We can quantify, integrate and analyze genomics, proteomics, metabolomics and lipidomics biomarkers, alongside clinical data, demographics and other phenotypic data. A unique bio-inspired signal processing analytic approach is used that has the proven ability to identify biomarkers in a wide variety of diseases. The resulting biomarkers can be used for diagnosis, prognosis, mechanistic studies and predicting treatment response, in contexts from core research through clinical trials...
June 2016: Future Science OA
https://www.readbyqxmd.com/read/28017698/metabonomics-of-ageing-towards-understanding-metabolism-of-a-long-and-healthy-life
#12
REVIEW
Francois-Pierre J Martin, Ivan Montoliu, Martin Kussmann
Systems biology approaches have been increasingly employed in clinical studies to enhance our understanding of the role of genetics, environmental factors and their interactions on nutritional, health and disease status. Amongst the new omics technologies, metabonomics has emerged as a robust platform to capture metabolic and nutritional requirements by enabling, in a minimally invasive fashion, the monitoring of a wide range of biochemical compounds. Their variations reflect comprehensively the various molecular regulatory processes, which are tightly controlled and under the influence of genetics, diet, gut microbiota and other environmental factors...
December 23, 2016: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28013203/systemic-lupus-erythematosus-biomarkers-the-challenging-quest
#13
Cristina Arriens, Jonathan D Wren, Melissa E Munroe, Chandra Mohan
SLE, a multisystem heterogeneous disease, is characterized by production of antibodies to cellular components, with activation of both the innate and the adaptive immune system. Decades of investigation of blood biomarkers has resulted in incremental improvements in the understanding of SLE. Owing to the heterogeneity of immune dysregulation, no single biomarker has emerged as a surrogate for disease activity or prediction of disease. Beyond identification of surrogate biomarkers, a multitude of clinical trials have sought to inhibit elevated SLE biomarkers for therapeutic benefit...
December 24, 2016: Rheumatology
https://www.readbyqxmd.com/read/28011753/a-review-on-machine-learning-principles-for-multi-view-biological-data-integration
#14
Yifeng Li, Fang-Xiang Wu, Alioune Ngom
Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association...
December 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28008139/identifying-the-clonal-origin-of-synchronous-multifocal-tumors-in-the-hepatobiliary-and-pancreatic-system-using-multi-omic-platforms
#15
Weiqin Jiang, Yongfeng Ding, Yifei Shen, Longjiang Fan, Linfu Zhou, Zhi Li, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Weijia Fang, Weilin Wang
Synchronous multifocal tumors often pose a diagnostic challenge for oncologists. The purpose of this study was to determine the clonal origin and metastatic relationship of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms. DNA samples were extracted from three masses harvested from a 50-year-old Han Chinese male patient who suffered from synchronous multifocal tumors in the pancreatic tail, upper biliary duct, and omentum at the time of diagnosis. The clonal origin of these samples was tested using two platforms: next-generation sequencing (NGS) of 390 key genes harboring cancer-relevant actionable mutations and whole-genome copy number variation (CNV) chip analysis...
December 19, 2016: Oncotarget
https://www.readbyqxmd.com/read/28007145/genetics-and-genomics-of-single-gene-cardiovascular-diseases-common-hereditary-cardiomyopathies-as-prototypes-of%C3%A2-single-gene-disorders
#16
REVIEW
Ali J Marian, Eva van Rooij, Robert Roberts
This is the first of 2 review papers on genetics and genomics appearing as part of the series on "omics." Genomics pertains to all components of an organism's genes, whereas genetics involves analysis of a specific gene or genes in the context of heredity. The paper provides introductory comments, describes the basis of human genetic diversity, and addresses the phenotypic consequences of genetic variants. Rare variants with large effect sizes are responsible for single-gene disorders, whereas complex polygenic diseases are typically due to multiple genetic variants, each exerting a modest effect size...
December 27, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28005952/microrna-and-transcription-factor-gene-regulatory-network-analysis-reveals-key-regulatory-elements-associated-with-prostate-cancer-progression
#17
Mehdi Sadeghi, Bijan Ranjbar, Mohamad Reza Ganjalikhany, Faiz M Khan, Ulf Schmitz, Olaf Wolkenhauer, Shailendra K Gupta
Technological and methodological advances in multi-omics data generation and integration approaches help elucidate genetic features of complex biological traits and diseases such as prostate cancer. Due to its heterogeneity, the identification of key functional components involved in the regulation and progression of prostate cancer is a methodological challenge. In this study, we identified key regulatory interactions responsible for primary to metastasis transitions in prostate cancer using network inference approaches by integrating patient derived transcriptomic and miRomics data into gene/miRNA/transcription factor regulatory networks...
2016: PloS One
https://www.readbyqxmd.com/read/27997969/studying-the-microbiome-omics-made-accessible
#18
Paul W O'Toole, Burkhardt Flemer
The term microbiome refers to the collection of microbes or microbial genes in a specified location or clinical sample. Identifying micro-organisms has historically relied upon bacteriological culture, which is time consuming and difficult to effectively implement. The recent adaptation of culture-independent techniques for profiling microbial communities, allied with next-generation massively parallel DNA sequencing, allows clinician scientists to determine the entire microbial content of a specimen to a forensic level of detail within 48 hours...
September 2016: Seminars in Liver Disease
https://www.readbyqxmd.com/read/27997814/proteomics-in-cardiovascular-disease-recent-progress-and-clinical-implication-and-implementation
#19
Marika Mokou, Vasiliki Lygirou, Antonia Vlahou, Harald Mischak
Although multiple efforts have been initiated to shed light into the molecular mechanisms underlying cardiovascular disease, it still remains one of the major causes of death worldwide. Proteomic approaches are unequivocally powerful tools that may provide deeper understanding into the molecular mechanisms associated with cardiovascular disease and improve its management. Areas covered: Cardiovascular proteomics is an emerging field and significant progress has been made during the past few years with the aim of defining novel candidate biomarkers and obtaining insight into molecular pathophysiology...
February 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27995389/equipping-physiologists-with-an-informatics-tool-chest-toward-an-integerated-mitochondrial-phenome
#20
Anders Olav Garlid, Jennifer S Polson, Keith D Garlid, Henning Hermjakob, Peipei Ping
Understanding the complex involvement of mitochondrial biology in disease development often requires the acquisition, analysis, and integration of large-scale molecular and phenotypic data. An increasing number of bioinformatics tools are currently employed to aid in mitochondrial investigations, most notably in predicting or corroborating the spatial and temporal dynamics of mitochondrial molecules, in retrieving structural data of mitochondrial components, and in aggregating as well as transforming mitochondrial centric biomedical knowledge...
December 20, 2016: Handbook of Experimental Pharmacology
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