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https://www.readbyqxmd.com/read/29448284/-the-keyrole-of-multiomics-in-the-predictive-preventive-and-personalised-medical-approach-towards-glaucoma-management
#1
Olga Golubnitschaja
Glaucoma is the second leading cause of blindness, with altogether about 70 million patients registered worldwide. These facts prompt us to reconsider currently applied concepts in overall glaucoma management. Innovative strategies of predictive, preventive and personalised medicine (PPPM) are expected to considerably improve disease prevention and personalised treatment. The comprehensive PPPM measures include the application of individualised patient profiles, "phenotyping", molecular characterisation of the pre-lesions and disease stages, innovative screening programs, patient stratification, early and predictive diagnosis, targeted prevention, and the creation of personalised treatment algorithms...
February 2018: Klinische Monatsblätter Für Augenheilkunde
https://www.readbyqxmd.com/read/29417741/how-can-omic-science-be-improved
#2
Kai Simons
One of the promises of multiomic analysis was to transform the clinical diagnostics to deliver much more exact phenotyping of disease states. However, despite enormous investments, the transformation of clinical routine has not taken place. There are many reasons for this lack of success but one is the failure to deliver quantitative and reproducible data. This failure is not only impeding progress in clinical phenotyping but also in the application of omic science in systems biology. The focus in this Viewpoint will be on lipidomics but the lessons learned are generally applicable...
February 8, 2018: Proteomics
https://www.readbyqxmd.com/read/29369067/evidence-establishing-a-link-between-prenatal-and-early-life-stress-and-asthma-development
#3
Maria José Rosa, Alison G Lee, Rosalind J Wright
PURPOSE OF REVIEW: The objective of this review is to provide an update on our evolving understanding of the effects of stress in pregnancy and during early development on the onset of asthma-related phenotypes across childhood, adolescence, and into early adulthood. RECENT FINDINGS: Accumulating evidence over the past 2 decades has established that prenatal and early-life psychological stress and stress correlates (e.g., maternal anxiety or depression) increase the risk for childhood respiratory disorders...
January 23, 2018: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29365031/unravelling-triple-negative-breast-cancer-molecular-heterogeneity-using-an-integrative-multiomic-analysis
#4
Y Bareche, D Venet, M Ignatiadis, P Aftimos, M Piccart, F Rothe, C Sotiriou
Background: Recent efforts of genome-wide gene expression profiling analyses have improved our understanding of the biological complexity and diversity of triple negative breast cancers (TNBCs) reporting, at least 6 different molecular subtypes of TNBC namely Basal-like 1 (BL1), basal-like 2 (BL2), immunomodulatory (IM), mesenchymal (M), mesenchymal stem-like (MSL) and luminal androgen receptor (LAR). However, little is known regarding the potential driving molecular events within each subtype, their difference in survival and response to therapy...
January 22, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29359109/proteome-and-metabolome-of-subretinal-fluid-in-central-serous-chorioretinopathy-and-rhegmatogenous-retinal-detachment-a-pilot-case-study
#5
Laura Kowalczuk, Alexandre Matet, Marianne Dor, Nasim Bararpour, Alejandra Daruich, Ali Dirani, Francine Behar-Cohen, Aurélien Thomas, Natacha Turck
Purpose: To investigate the molecular composition of subretinal fluid (SRF) in central serous chorioretinopathy (CSCR) and rhegmatogenous retinal detachment (RRD) using proteomics and metabolomics. Methods: SRF was obtained from one patient with severe nonresolving bullous CSCR requiring surgical subretinal fibrin removal, and two patients with long-standing RRD. Proteins were trypsin-digested, labeled with Tandem-Mass-Tag and fractionated according to their isoelectric point for identification and quantification by tandem mass spectrometry...
January 2018: Translational Vision Science & Technology
https://www.readbyqxmd.com/read/29343144/cell-surface-proteomics-for-the-identification-of-novel-therapeutic-targets-in-cancer
#6
Laura Kuhlmann, Emma Cummins, Ismael Samudio, Thomas Kislinger
Cancer is the second most common cause of death worldwide and its heterogeneity complicates therapy. Standard cytotoxic regiments disrupt rapidly dividing cells, regardless of their neoplastic status. The introduction of less toxic targeted therapies has partially contributed to the observed decrease in cancer-related mortality. Cell-surface proteins represent attractive targets for therapy, due to their easily-accessible localization and their involvement in essential signaling pathways, often dysregulated in cancer...
January 18, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29328921/tomato-multiomics-reveals-consequences-of-crop-domestication-and-improvement
#7
James Giovannoni
Genome-scale analyses of variation, gene expression, and metabolite accumulation in ancestral, early domesticates, and modern tomatoes by Zhu et al. identify genes underlying fruit chemistry and demonstrate that alleles affecting metabolic quality have been bred into modern varieties as a result of linkage drag. Similar metabolic hitchhikers are likely ubiquitous in other domesticated species.
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29312565/dissect-new-mechanistic-insights-for-geniposide-efficacy-on-the-hepatoprotection-using-multiomics-approach
#8
Shi Qiu, Aihua Zhang, Tianlei Zhang, Hui Sun, Yu Guan, Guangli Yan, Xijun Wang
A multi-omics approach could yield in-depth mechanistic insights. Here, we performed an integrated analysis of miRNAome, proteome and metabolome, aimed to investigate the underlying mechanism of active product geniposide in ethanol-induced apoptosis. We found that integrative meta-analysis identified 28 miRNAs, 20 proteins and 7 metabolites significantly differentially expressed, respectively. Further analysis identified geniposide extensively regulated multiple metabolism pathways and the most important related pathway was citrate cycle (TCA cycle)...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29199496/recent-trends-on-the-role-of-epigenomics-metabolomics-and-noncoding-rnas-in-rationalizing-mood-stabilizing-treatment
#9
Claudia Pisanu, Theodora Katsila, George P Patrinos, Alessio Squassina
Mood stabilizers are the cornerstone in treatment of mood disorders, but their use is characterized by high interindividual variability. This feature has stimulated intensive research to identify predictive biomarkers of response and disentangle the molecular bases of their clinical efficacy. Nevertheless, findings from studies conducted so far have only explained a small proportion of the observed variability, suggesting that factors other than DNA variants could be involved. A growing body of research has been focusing on the role of epigenetics and metabolomics in response to mood stabilizers, especially lithium salts...
January 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29187204/experimental-design-and-quantitative-analysis-of-microbial-community-multiomics
#10
REVIEW
Himel Mallick, Siyuan Ma, Eric A Franzosa, Tommi Vatanen, Xochitl C Morgan, Curtis Huttenhower
Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data...
November 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/29186684/pancreatic-adenocarcinoma-therapeutic-targets-revealed-by-tumor-stroma-cross-talk-analyses-in-patient-derived-xenografts
#11
Rémy Nicolle, Yuna Blum, Laetitia Marisa, Celine Loncle, Odile Gayet, Vincent Moutardier, Olivier Turrini, Marc Giovannini, Benjamin Bian, Martin Bigonnet, Marion Rubis, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Aurélie Maignan, Gwen Lomberk, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Jonathan Garnier, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Julie Roques, Ezequiel Calvo, Fabienne Guillaumond, Sophie Vasseur, Raul Urrutia, Aurélien de Reyniès, Nelson Dusetti, Juan Iovanna
Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC) xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively). Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk...
November 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/29174548/the-role-of-transforming-growth-factor-%C3%AE-in-human-hepatocarcinogenesis-mechanistic-and-therapeutic-implications-from-an-integrative-multiomics-approach
#12
EDITORIAL
Jens U Marquardt
No abstract text is available yet for this article.
November 21, 2017: Gastroenterology
https://www.readbyqxmd.com/read/29132754/the-engineering-potential-of-rhodosporidium-toruloides-as-a-workhorse-for-biotechnological-applications
#13
REVIEW
Young-Kyoung Park, Jean-Marc Nicaud, Rodrigo Ledesma-Amaro
Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism...
November 10, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/29092936/software-for-the-integration-of-multiomics-experiments-in-bioconductor
#14
Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Phil Chapman, Sean R Davis, David Gomez-Cabrero, Aedin C Culhane, Benjamin Haibe-Kains, Kasper D Hansen, Hanish Kodali, Marie S Louis, Arvind S Mer, Markus Riester, Martin Morgan, Vince Carey, Levi Waldron
Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29080867/-multiomics-study-of-hepg2-cell-line-proteome
#15
E V Poverennaya, O I Kiseleva, E A Ponomarenko, S N Naryzhny, V G Zgoda, A V Lisitsa
Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29069414/the-biostudies-database-one-stop-shop-for-all-data-supporting-a-life-sciences-study
#16
Ugis Sarkans, Mikhail Gostev, Awais Athar, Ehsan Behrangi, Olga Melnichuk, Ahmed Ali, Jasmine Minguet, Juan Camillo Rada, Catherine Snow, Andrew Tikhonov, Alvis Brazma, Johanna McEntyre
BioStudies ( www.ebi.ac.uk/biostudies ) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication. BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces. The actual data can be stored either in BioStudies or remotely, or both. BioStudies imports supplementary data from Europe PMC, and is a resource for authors and publishers for packaging data during the manuscript preparation process...
October 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29049012/transcriptome-profiling-uncovers-potential-common-mechanisms-in-fetal-trisomies-18-and-21
#17
Marija Volk, Aleš Maver, Alenka Hodžić, Luca Lovrečić, Borut Peterlin
Human trisomies have recently been investigated using transcriptomics approaches to identify the gene expression (GE) signatures characteristic of each of these specific aneuploidy conditions. We hypothesized that the viability of cells with gross genomic imbalances might be associated with the activation of resilience mechanisms that are common to different trisomies and that are reflected by specific shared GE patterns. We report in this article our microarray GE analyses of amniocytes from fetuses with viable trisomy conditions, trisomy 21 or trisomy 18, to detect such common expression signatures...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29042495/impact-of-dietary-resistant-starch-on-the-human-gut-microbiome-metaproteome-and-metabolome
#18
Tanja V Maier, Marianna Lucio, Lang Ho Lee, Nathan C VerBerkmoes, Colin J Brislawn, Jörg Bernhardt, Regina Lamendella, Jason E McDermott, Nathalie Bergeron, Silke S Heinzmann, James T Morton, Antonio González, Gail Ackermann, Rob Knight, Katharina Riedel, Ronald M Krauss, Philippe Schmitt-Kopplin, Janet K Jansson
Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of "omics" approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29023486/the-sea-cucumber-genome-provides-insights-into-morphological-evolution-and-visceral-regeneration
#19
Xiaojun Zhang, Lina Sun, Jianbo Yuan, Yamin Sun, Yi Gao, Libin Zhang, Shihao Li, Hui Dai, Jean-François Hamel, Chengzhang Liu, Yang Yu, Shilin Liu, Wenchao Lin, Kaimin Guo, Songjun Jin, Peng Xu, Kenneth B Storey, Pin Huan, Tao Zhang, Yi Zhou, Jiquan Zhang, Chenggang Lin, Xiaoni Li, Lili Xing, Da Huo, Mingzhe Sun, Lei Wang, Annie Mercier, Fuhua Li, Hongsheng Yang, Jianhai Xiang
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers...
October 2017: PLoS Biology
https://www.readbyqxmd.com/read/28973931/systems-level-identification-of-pka-dependent-signaling-in-epithelial-cells
#20
Kiyoshi Isobe, Hyun Jun Jung, Chin-Rang Yang, J'Neka Claxton, Pablo Sandoval, Maurice B Burg, Viswanathan Raghuram, Mark A Knepper
G protein stimulatory α-subunit (Gαs)-coupled heptahelical receptors regulate cell processes largely through activation of protein kinase A (PKA). To identify signaling processes downstream of PKA, we deleted both PKA catalytic subunits using CRISPR-Cas9, followed by a "multiomic" analysis in mouse kidney epithelial cells expressing the Gαs-coupled V2 vasopressin receptor. RNA-seq (sequencing)-based transcriptomics and SILAC (stable isotope labeling of amino acids in cell culture)-based quantitative proteomics revealed a complete loss of expression of the water-channel gene Aqp2 in PKA knockout cells...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
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