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integrated omics

Peilin Jia, Xiangning Chen, Wei Xie, Kenneth S Kendler, Zhongming Zhao
Numerous high-throughput omics studies have been conducted in schizophrenia, providing an accumulated catalog of susceptible variants and genes. The results from these studies, however, are highly heterogeneous. The variants and genes nominated by different omics studies often have limited overlap with each other. There is thus a pressing need for integrative analysis to unify the different types of data and provide a convergent view of schizophrenia candidate genes (SZgenes). In this study, we collected a comprehensive, multidimensional dataset, including 7819 brain-expressed genes...
June 20, 2018: Schizophrenia Bulletin
Jan Baumann, Mostafa Kokabee, Jason Wong, Rakshika Balasubramaniyam, Yan Sun, Douglas S Conklin
Recent work has shown that HER2/neu-positive breast cancer cells rely on a unique Warburg-like metabolism for survival and aggressive behavior. These cells are dependent on fatty acid (FA) synthesis, show markedly increased levels of stored fats and disruption of the synthetic process results in apoptosis. In this study, we used global metabolite profiling and a multi-omics network analysis approach to model the metabolic changes in this physiology under palmitate-supplemented growth conditions to gain insights into the molecular mechanism and its relevance to disease prevention and treatment...
June 5, 2018: Oncotarget
Gokhan Yildiz
Hepatocellular carcinoma (HCC) is the most common type of liver cancer and the third-leading cause of malignancy-associated mortality worldwide. HCC cells are highly resistant to chemotherapeutic agents. Therefore, there are currently only two US Food and Drug Administration-approved drugs available for the treatment of HCC. The objective of the present study was to analyze the results of previously published high-throughput drug screening, and in vitro genomic and transcriptomic data from HCC cell lines, and to integrate the obtained results to define the underlying molecular mechanisms of drug sensitivity and resistance in HCC cells...
July 2018: Oncology Letters
Y H Yu, L Doucette-Stamm, J Rogus, K Moss, R Y L Zee, B Steffensen, P M Ridker, J E Buring, S Offenbacher, K Kornman, D I Chasman
Periodontal disease (PD) shares common risk factors with cardiovascular disease. Our hypothesis was that having a family history of myocardial infarction (FamHxMI) may be a novel risk factor for PD. Risk assessment based on FamHxMI, conditional on smoking status, was examined given the strong influence of smoking on PD. Exploratory analysis with inflammatory biomarkers and genetic determinants was conducted to understand potential mechanistic links. The Women's Genome Health Study (WGHS) is a prospective cohort of US female health care professionals who provided blood samples at baseline in the Women's Health Study, a 2 × 2 factorial clinical trial investigating vitamin E and aspirin in the prevention of cardiovascular disease and cancer...
June 1, 2018: Journal of Dental Research
Alexandre Maes, Xavier Martinez, Karen Druart, Benoist Laurent, Sean Guégan, Christophe H Marchand, Stéphane D Lemaire, Marc Baaden
Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins...
June 21, 2018: Journal of Integrative Bioinformatics
Matija Pecak, Peter Korošec, Tanja Kunej
Asthma is a common complex disorder and has been subject to intensive omics research for disease susceptibility and therapeutic innovation. Candidate biomarkers of asthma and its precision treatment demand that they stand the test of multiomics data triangulation before they can be prioritized for clinical applications. We classified the biomarkers of asthma after a search of the literature and based on whether or not a given biomarker candidate is reported in multiple omics platforms and methodologies, using PubMed and Web of Science, we identified omics studies of asthma conducted on diverse platforms using keywords, such as asthma, genomics, metabolomics, and epigenomics...
June 2018: Omics: a Journal of Integrative Biology
Keefe Murphy, Brendan T Murphy, Susie Boyce, Louise Flynn, Sarah Gilgunn, Colm J O'Rourke, Cathy Rooney, Henning Stöckmann, Anna L Walsh, Stephen Finn, Richard J O'Kennedy, John O'Leary, Stephen R Pennington, Antoinette S Perry, Pauline M Rudd, Radka Saldova, Orla Sheils, Denis C Shields, R William Watson
INTRODUCTION: Classifying indolent prostate cancer represents a significant clinical challenge. We investigated whether integrating data from different omic platforms could identify a biomarker panel with improved performance compared to individual platforms alone. METHODS: DNA methylation, transcripts, protein, and glycosylation biomarkers were assessed in a single cohort of patients treated by radical prostatectomy. Novel multi-block statistical data integration approaches were used to deal with missing data and modelled via stepwise multinomial logistic regression, or LASSO...
June 21, 2018: Molecular Oncology
Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle
Multi-omics studies promise the improved characterization of biological processes across molecular layers. However, methods for the unsupervised integration of the resulting heterogeneous data sets are lacking. We present Multi-Omics Factor Analysis (MOFA), a computational method for discovering the principal sources of variation in multi-omics data sets. MOFA infers a set of (hidden) factors that capture biological and technical sources of variability. It disentangles axes of heterogeneity that are shared across multiple modalities and those specific to individual data modalities...
June 20, 2018: Molecular Systems Biology
Fouzia Yeasmin, Tetsushi Yada, Nobuyoshi Akimitsu
Integrative analysis using omics-based technologies results in the identification of a large number of putative short open reading frames (sORFs) with protein-coding capacity within transcripts previously identified as long noncoding RNAs (lncRNAs) or transcripts of unknown function (TUFs). sORFs were previously overlooked because of their diminutive size and the difficulty of identification by bioinformatics analyses. There is now growing evidence of the existence of potentially functional micropeptides produced from sORFs within cells of diverse species...
2018: Frontiers in Genetics
Giulia M Sancesario, Sergio Bernardini
Recent progresses in high-throughput technologies have led to a new scenario in investigating pathologies, named the "Omics era", which integrate the opportunity to collect large amounts of data and information at the molecular and protein levels together with the development of novel computational and statistical tools that are able to analyze and filter such data. Subsequently, advances in genotyping arrays, next generation sequencing, mass spectrometry technology, and bioinformatics allowed for the simultaneous large-scale study of thousands of genes (genomics), epigenetics factors (epigenomics), RNA (transcriptomics), metabolites (metabolomics) and proteins(proteomics), with the possibility of integrating multiple types of omics data ("multi -omics")...
June 16, 2018: Clinical Biochemistry
Muneer A Malla, Anamika Dubey, Shweta Yadav, Ashwani Kumar, Abeer Hashem, Elsayed Fathi Abd Allah
Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution...
2018: Frontiers in Microbiology
Elizabeth M Kennedy, George N Goehring, Michael H Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K Smith, Karen N Conneely
BACKGROUND: Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. RESULTS: We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells...
June 19, 2018: BMC Genomics
Denis M Nyaga, Mark H Vickers, Craig Jefferies, Jo K Perry, Justin M O'Sullivan
Type 1 diabetes mellitus (T1D) is a complex autoimmune disorder characterised by loss of the insulin-producing pancreatic beta cells in genetically predisposed individuals, ultimately resulting in insulin deficiency and hyperglycaemia. T1D is most common among children and young adults, and the incidence is on the rise across the world. The aetiology of T1D is hypothesized to involve genetic and environmental factors that result in the T-cell mediated destruction of pancreatic beta cells. There is a strong genetic risk to T1D; with genome-wide association studies (GWAS) identifying over 60 susceptibility regions within the human genome which are marked by single nucleotide polymorphisms (SNPs)...
June 15, 2018: Molecular and Cellular Endocrinology
Nicholas Ceglia, Yu Liu, Siwei Chen, Forest Agostinelli, Kristin Eckel-Mahan, Paolo Sassone-Corsi, Pierre Baldi
Circadian rhythms play a fundamental role at all levels of biological organization. Understanding the mechanisms and implications of circadian oscillations continues to be the focus of intense research. However, there has been no comprehensive and integrated way for accessing and mining all circadian omic datasets. The latest release of CircadiOmics ( fills this gap for providing the most comprehensive web server for studying circadian data. The newly updated version contains high-throughput 227 omic datasets corresponding to over 74 million measurements sampled over 24 h cycles...
June 15, 2018: Nucleic Acids Research
Kévin Vervier, Jacob J Michaelson
Motivation: Model-based estimates of general deleteriousness, like CADD, DANN or PolyPhen, have become indispensable tools in the interpretation of genetic variants. However, these approaches say little about the tissues in which the effects of deleterious variants will be most meaningful. Tissue-specific annotations have been recently inferred for dozens of tissues/cell types from large collections of cross-tissue epigenomic data, and have demonstrated sensitivity in predicting affected tissues in complex traits...
April 18, 2018: Bioinformatics
Carrie D Nicora, Kristin E Burnum-Johnson, Ernesto S Nakayasu, Cameron P Casey, Richard A White, Taniya Roy Chowdhury, Jennifer E Kyle, Young-Mo Kim, Richard D Smith, Thomas O Metz, Janet K Jansson, Erin S Baker
Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges, since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required...
May 30, 2018: Journal of Visualized Experiments: JoVE
Zachary Kornberg, Jonathan Chou, Felix Y Feng, Charles J Ryan
Data from recent high-throughput studies analyzing local and advanced prostate cancer have revealed an incredible amount of biological diversity, which has led to the classification of distinct molecular tumor subtypes. While integrating prostate cancer genomics with clinical medicine is still at its infancy, new approaches to treat prostate cancer are well underway and being studied. With the recognition that DNA damage repair (DDR) mutations play an important role in the pathogenesis of this disease, clinicians can begin to utilize genomic information in complex treatment decisions for prostate cancer patients...
May 2018: Annals of Translational Medicine
Catarina R Marques
Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose...
2018: Frontiers in Microbiology
Pooja Jha, Molly T McDevitt, Rahul Gupta, Pedro M Quiros, Evan G Williams, Karim Gariani, Maroun B Sleiman, Leo Diserens, Adam Jochem, Arne Ulbrich, Joshua J Coon, Johan Auwerx, David J Pagliarini
The genetics of individual lipid species and their relevance in disease is largely unresolved. We profiled a subset of storage, signaling, membrane, and mitochondrial liver lipids across 385 mice from 47 strains of the BXD mouse population fed chow or high-fat diet and integrated these data with complementary multi-omics datasets. We identified several lipid species and lipid clusters with specific phenotypic and molecular signatures and, in particular, cardiolipin species with signatures of healthy and fatty liver...
June 7, 2018: Cell Systems
Leen J Luyten, Nelly D Saenen, Bram G Janssen, Karen Vrijens, Michelle Plusquin, Harry A Roels, Florence Debacq-Chainiaux, Tim S Nawrot
BACKGROUND: Fetal development is a crucial window of susceptibility in which exposure-related alterations can be induced on the molecular level, leading to potential changes in metabolism and development. The placenta serves as a gatekeeper between mother and fetus, and is in contact with environmental stressors throughout pregnancy. This makes the placenta as a temporary organ an informative non-invasive matrix suitable to investigate omics-related aberrations in association with in utero exposures such as ambient air pollution...
June 13, 2018: Environmental Research
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