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https://www.readbyqxmd.com/read/29663340/molecular-signatures-in-hepatocellular-carcinoma-a-step-toward-rationally-designed-cancer-therapy
#1
REVIEW
Derek J Erstad, Bryan C Fuchs, Kenneth K Tanabe
Molecular characterization of hepatocellular carcinoma (HCC) has greatly improved our understanding of disease pathogenesis. Mutational analysis, RNA and microRNA expression profiling, and epigenetic characterization have revealed common aberrations in oncogenes and tumor suppressors that correlate with disease biology and serve as a guide for the rational design of targeted therapies. These approaches have also led to the discovery of novel targets, including mutations in isocitrate dehydrogenase and chromatin remodeling enzymes...
April 17, 2018: Cancer
https://www.readbyqxmd.com/read/29617661/integrated-genomic-analysis-of-the-ubiquitin-pathway-across-cancer-types
#2
Zhongqi Ge, Jake S Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, Hu Chen, Yutong Sun, Fan Yao, Jun Li, Huiwen Zhang, Jianfang Liu, Craig D Shriver, Hai Hu, Helen Piwnica-Worms, Li Ma, Han Liang
Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29556549/a-microbial-perspective-on-the-grand-challenges-in-comparative-animal-physiology
#3
Kevin D Kohl
Interactions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). In this perspective, I discuss how the field of host-microbe interactions can be used to address topics that have been identified as grand challenges in comparative animal physiology: (i) horizontal integration of physiological processes across organisms, (ii) vertical integration of physiological processes across organizational levels within organisms, and (iii) temporal integration of physiological processes during evolutionary change...
March 2018: MSystems
https://www.readbyqxmd.com/read/29536452/applications-of-single-cell-sequencing-for-multiomics
#4
Yungang Xu, Xiaobo Zhou
Single-cell sequencing interrogates the sequence or chromatin information from individual cells with advanced next-generation sequencing technologies. It provides a higher resolution of cellular differences and a better understanding of the underlying genetic and epigenetic mechanisms of an individual cell in the context of its survival and adaptation to microenvironment. However, it is more challenging to perform single-cell sequencing and downstream data analysis, owing to the minimal amount of starting materials, sample loss, and contamination...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29536202/multiomics-tools-for-the-diagnosis-and-treatment-of-rare-neurological-disease
#5
REVIEW
L M Crowther, M Poms, Barbara Plecko
Conventional workup of rare neurological disease is frequently hampered by diagnostic delay or lack of diagnosis. While biomarkers have been established for many neurometabolic disorders, improved methods are required for diagnosis of previously unidentified or underreported causes of rare neurological disease. This would result in a higher diagnostic yield and increased patient numbers required for interventional studies. Recent studies using next-generation sequencing and metabolomics have led to identification of novel disease-causing genes and biomarkers...
March 13, 2018: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29515689/the-crucial-role-of-multiomic-approach-in-cancer-research-and-clinically-relevant-outcomes
#6
REVIEW
Miaolong Lu, Xianquan Zhan
Cancer with heavily economic and social burden is the hot point in the field of medical research. Some remarkable achievements have been made; however, the exact mechanisms of tumor initiation and development remain unclear. Cancer is a complex, whole-body disease that involves multiple abnormalities in the levels of DNA, RNA, protein, metabolite and medical imaging. Biological omics including genomics, transcriptomics, proteomics, metabolomics and radiomics aims to systematically understand carcinogenesis in different biological levels, which is driving the shift of cancer research paradigm from single parameter model to multi-parameter systematical model...
March 2018: EPMA Journal
https://www.readbyqxmd.com/read/29507758/a-personalized-multiomics-approach-identifies-genes-involved-in-cardiac-hypertrophy-and-heart-failure
#7
Marc Santolini, Milagros C Romay, Clara L Yukhtman, Christoph D Rau, Shuxun Ren, Jeffrey J Saucerman, Jessica J Wang, James N Weiss, Yibin Wang, Aldons J Lusis, Alain Karma
A traditional approach to investigate the genetic basis of complex diseases is to identify genes with a global change in expression between diseased and healthy individuals. However, population heterogeneity may undermine the effort to uncover genes with significant but individual contribution to the spectrum of disease phenotypes within a population. Here we investigate individual changes of gene expression when inducing hypertrophy and heart failure in 100 + strains of genetically distinct mice from the Hybrid Mouse Diversity Panel (HMDP)...
2018: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29507209/linking-imaging-to-omics-utilizing-image-guided-tissue-extraction
#8
Jonathan A Disselhorst, Marcel A Krueger, S M Minhaz Ud-Dean, Ilja Bezrukov, Mohamed A Jarboui, Christoph Trautwein, Andreas Traube, Christian Spindler, Jonathan M Cotton, Dieter Leibfritz, Bernd J Pichler
Phenotypic heterogeneity is commonly observed in diseased tissue, specifically in tumors. Multimodal imaging technologies can reveal tissue heterogeneity noninvasively in vivo, enabling imaging-based profiling of receptors, metabolism, morphology, or function on a macroscopic scale. In contrast, in vitro multiomics, immunohistochemistry, or histology techniques accurately characterize these heterogeneities in the cellular and subcellular scales in a more comprehensive but ex vivo manner. The complementary in vivo and ex vivo information would provide an enormous potential to better characterize a disease...
March 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29488968/infectious-helminth-ova-in-wastewater-and-sludge-a-review-on-public-health-issues-and-current-quantification-practices
#9
P Gyawali
Raw and partially treated wastewater has been widely used to maintain the global water demand. Presence of viable helminth ova and larvae in the wastewater raised significant public health concern especially when used for agriculture and aquaculture. Depending on the prevalence of helminth infections in communities, up to 1.0 × 103 ova/larvae can be presented per litre of wastewater and 4 gm (dry weight) of sludge. Multi-barrier approaches including pathogen reduction, risk assessment, and exposure reduction have been suggested by health regulators to minimise the potential health risk...
February 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/29487189/integrated-in-vivo-multiomics-analysis-identifies-p21-activated-kinase-signaling-as-a-driver-of-colitis
#10
Jesse Lyons, Douglas K Brubaker, Phaedra C Ghazi, Katherine R Baldwin, Amanda Edwards, Myriam Boukhali, Samantha Dale Strasser, Lucia Suarez-Lopez, Yi-Jang Lin, Vijay Yajnik, Joseph L Kissil, Wilhelm Haas, Douglas A Lauffenburger, Kevin M Haigis
Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo...
February 27, 2018: Science Signaling
https://www.readbyqxmd.com/read/29470681/a-large-scale-multiomics-analysis-of-wheat-stem-solidness-and-the-wheat-stem-sawfly-feeding-response-and-syntenic-associations-in-barley-brachypodium-and-rice
#11
Sezgi Biyiklioglu, Burcu Alptekin, B Ani Akpinar, Andrea C Varella, Megan L Hofland, David K Weaver, Brian Bothner, Hikmet Budak
The wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae), is an important pest of wheat and other cereals, threatening the quality and quantity of grain production. WSS larvae feed and develop inside the stem where they are protected from the external environment; therefore, pest management strategies primarily rely on host plant resistance. A major locus on the long arm of wheat chromosome 3B underlies most of the variation in stem solidness; however, the impact of stem solidness on WSS feeding has not been completely characterized...
February 22, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29448284/-the-keyrole-of-multiomics-in-the-predictive-preventive-and-personalised-medical-approach-towards-glaucoma-management
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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