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https://www.readbyqxmd.com/read/28206814/biomarkers-in-tumor-microenvironment-upregulation-of-fibroblast-activation-protein-%C3%AE-correlates-with-gastric-cancer-progression-and-poor-prognosis
#1
Mengmou Hu, Chengjia Qian, Ziwei Hu, Bojian Fei, Haibo Zhou
Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recent evidence points to importance of cross talk between cancer cells and the surrounding stroma on gastric cancer progression. Tumor microenvironment biomarkers thus represent a new opportunity for diagnostics innovation. Reactive stromal fibroblasts selectively express the fibroblast activation protein alpha (FAP-α), a homodimeric integral membrane gelatinase that belongs to the serine protease family. We report here that FAP-α expression is significantly elevated in gastric cancer samples by more than fivefold (p < 0...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28165029/quantitative-global-proteome-and-lysine-succinylome-analyses-provide-insights-into-metabolic-regulation-and-lymph-node-metastasis-in-gastric-cancer
#2
Yongxi Song, Jun Wang, Zhongyi Cheng, Peng Gao, Jingxu Sun, Xiaowan Chen, Chen Chen, Yunlong Wang, Zhenning Wang
With the rapid development of high-throughput quantitative proteomic and transcriptomic approaches, the molecular mechanisms of cancers have been comprehensively explored. However, cancer is a multi-dimensional disease with sophisticated regulations, and few studies focus on the crosstalk among multiomics. In order to explore the molecular mechanisms of gastric cancer (GC), particularly in the process of lymph node metastasis (LNM), we investigated dynamic profiling changes as well as crosstalk between long non-coding RNAs (lncRNAs), the proteome, and the lysine succinylome...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28152499/contributions-of-polyunsaturated-fatty-acids-pufa-on-cerebral-neurobiology-an-integrated-omics-approach-with-epigenomic-focus
#3
Nabarun Chakraborty, Seid Muhie, Raina Kumar, Aarti Gautam, Seshamalini Srinivasan, Bintu Sowe, George Dimitrov, Stacy-Ann Miller, Marti Jett, Rasha Hammamieh
The epigenetic landscape is vulnerable to diets. Here, we investigated the influence of different polyunsaturated fatty acids (PUFA) dietary supplements on rodents' nervous system development and functions and potential consequences to neurodegenerative disorders. Our previous nutrigenomics study showed significant impact of high n-3 PUFA-enriched diet (ERD) on synaptogenesis and various neuromodulators. The present study introduced a second equicaloric diet with n-6 PUFA balanced by n-3 PUFA (BLD). The typical lab diet with high n-6 PUFA was the baseline...
January 5, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28126735/integrated-analysis-of-multiomic-data-reveals-the-role-of-the-antioxidant-network-in-the-quality-of-sea-buckthorn-berry
#4
Caiyun He, Guoyun Zhang, Jianguo Zhang, Yanfei Zeng, Juanjuan Liu
Berries of sea buckthorn, known as the "king of vitamin C," are abundant in antioxidants, have attractive colors, and are an excellent material with which to study the relationships between berry color, antioxidants, and berry quality. No study has yet determined the molecular basis of the relationship between sea buckhorn berries and their color and antioxidant levels. By using RNA-seq, liquid chromatography-MS/MS, and liquid chromatography/GC-MS technology and selecting red (darkest colored) and yellow (lightest colored) sea buckthorn berries at different development stages, this study showed that the red and yellow berry resulted from a higher ratio of lycopene to β-carotene and of β-carotene to lycopene content, respectively...
January 26, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28118095/multiomics-approach-to-novel-therapeutic-targets-for-cancer-and-aging-related-diseases-role-of-sld7-in-yeast-aging-network
#5
Irem E Dayan, Kazim Yalcin Arga, Kutlu O Ulgen
Genome instability has long been implicated as a salient causal factor in aging and age-related diseases such as cancer and neurodegeneration. However, the molecular mechanisms associated with genome instability remain unclear. Recent studies suggest growth signaling in the organism Saccharomyces cerevisiae and in higher eukaryotes might affect oxidative stress and aging/age-related diseases by activating DNA replication stress that causes DNA damage. In this broader integrative biology and clinical context, MDM two binding protein (MTBP) is a binding protein that has a role in activation of the tumor suppressor protein p53...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28104774/microrna-biomarkers-and-platelet-reactivity-the-clot-thickens
#6
REVIEW
Nicholas Sunderland, Philipp Skroblin, Temo Barwari, Rachael P Huntley, Ruifang Lu, Abhishek Joshi, Ruth C Lovering, Manuel Mayr
Over the last few years, several groups have evaluated the potential of microRNAs (miRNAs) as biomarkers for cardiometabolic disease. In this review, we discuss the emerging literature on the role of miRNAs and other small noncoding RNAs in platelets and in the circulation, and the potential use of miRNAs as biomarkers for platelet activation. Platelets are a major source of miRNAs, YRNAs, and circular RNAs. By harnessing multiomics approaches, we may gain valuable insights into their potential function. Because not all miRNAs are detectable in the circulation, we also created a gene ontology annotation for circulating miRNAs using the gene ontology term extracellular space as part of blood plasma...
January 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/28092275/mechanistic-insights-from-combining-genomics-with-metabolomics
#7
Fotios Drenos
PURPOSE OF REVIEW: Metabolomics directly measure substrates and products of biological processes and pathways. Based on instrumentation and throughput advances, the use of metabolomics has only recently become feasible at the population level. This has led to an intense interest in using the new information in combination with genomics, and other omics technologies, to give biological context to the rapidly accumulating associations between genes and diseases or their risk factors. RECENT FINDINGS: The use of metabolomics-genomic associations for the metabolic characterization of genes of interest has confirmed known pathways and permitted the identification of new ones...
January 13, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28089370/single-cell-multiomics-multiple-measurements-from-single-cells
#8
REVIEW
Iain C Macaulay, Chris P Ponting, Thierry Voet
Single-cell sequencing provides information that is not confounded by genotypic or phenotypic heterogeneity of bulk samples. Sequencing of one molecular type (RNA, methylated DNA or open chromatin) in a single cell, furthermore, provides insights into the cell's phenotype and links to its genotype. Nevertheless, only by taking measurements of these phenotypes and genotypes from the same single cells can such inferences be made unambiguously. In this review, we survey the first experimental approaches that assay, in parallel, multiple molecular types from the same single cell, before considering the challenges and opportunities afforded by these and future technologies...
January 12, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28067231/multiomics-reveal-non-alcoholic-fatty-liver-disease-in-rats-following-chronic-exposure-to-an-ultra-low-dose-of-roundup-herbicide
#9
Robin Mesnage, George Renney, Gilles-Eric Séralini, Malcolm Ward, Michael N Antoniou
The impairment of liver function by low environmentally relevant doses of glyphosate-based herbicides (GBH) is still a debatable and unresolved matter. Previously we have shown that rats administered for 2 years with 0.1 ppb (50 ng/L glyphosate equivalent dilution; 4 ng/kg body weight/day daily intake) of a Roundup GBH formulation showed signs of enhanced liver injury as indicated by anatomorphological, blood/urine biochemical changes and transcriptome profiling. Here we present a multiomic study combining metabolome and proteome liver analyses to obtain further insight into the Roundup-induced pathology...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27801551/sample-preparation-method-considerations-for-integrated-transcriptomic-and-proteomic-analysis-of-tumors
#10
Anupama Rajan Bhat, Manoj Kumar Gupta, Priya Krithivasan, Kunal Dhas, Jayalakshmi Nair, Ram Bhupal Reddy, H V Sudheendra, Sandip Chavan, Harsha Vardhan, Sujatha Darsi, Lavanya Balakrishnan, Shanmukh Katragadda, Vikram Kekatpure, Amritha Suresh, Pramila Tata, Binay Panda, Moni A Kuriakose, Ravi Sirdeshmukh
Sample processing protocols that enable compatible recovery of differentially expressed (DE) transcripts and proteins are necessary for integration of the multiomics data applied in the analysis of tumors. In this pilot study, we compared two different isolation methods for extracting RNA and protein from laryngo-pharyngeal tumor tissues and the corresponding adjacent normal sections. In Method 1, RNA and protein were isolated from a single tissue section sequentially and in Method 2, the extraction was carried out using two different sections and two independent and parallel protocols for RNA and protein...
November 1, 2016: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/27726639/genetics-of-sickle-cell-associated-cardiovascular-disease-an-expert-review-with-lessons-learned-in-africa
#11
Amy Geard, Gift D Pule, David Chelo, Valentina Josiane Ngo Bitoungui, Ambroise Wonkam
Sickle cell disease (SCD) vastly impacts the African continent and is associated with cardiovascular diseases. Stroke, kidney disease, and pulmonary hypertension are considered as proxies of severity in SCD with several genomic loci implicated in their heritability. The present expert review examined the current data on epidemiology and genetic risk factors of stroke, pulmonary hypertension, and kidney disease associated with SCD, as indexed in PubMed(®) and Google Scholar(®). Studies collectively show that stroke and kidney disease each affect ∼10% of SCD patients, with pulmonary hypertension displaying a higher prevalence of 30% among adults with SCD...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27689071/embracing-integrative-multiomics-approaches
#12
REVIEW
Daniel M Rotroff, Alison A Motsinger-Reif
As "-omics" data technology advances and becomes more readily accessible to address complex biological questions, increasing amount of cross "-omics" dataset is inspiring the use and development of integrative bioinformatics analysis. In the current review, we discuss multiple options for integrating data across "-omes" for a range of study designs. We discuss established methods for such analysis and point the reader to in-depth discussions for the various topics. Additionally, we discuss challenges and new directions in the area...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27559923/sygnaling-a-red-light-for-glioblastoma
#13
Aaron N Brooks, William F Mueller, Lars M Steinmetz
A new multiomic network inference pipeline, SYGNAL, integrates patient data with mechanistically accurate transcriptional regulatory networks to predict drug combinations with synergistic anti-proliferative effects on glioblastoma multiforme.
August 2016: Cell Systems
https://www.readbyqxmd.com/read/27492622/in-vitro-acute-and-developmental-neurotoxicity-screening-an-overview-of-cellular-platforms-and-high-throughput-technical-possibilities
#14
REVIEW
Béla Z Schmidt, Martin Lehmann, Simon Gutbier, Erastus Nembo, Sabrina Noel, Lena Smirnova, Anna Forsby, Jürgen Hescheler, Hasan X Avci, Thomas Hartung, Marcel Leist, Julianna Kobolák, András Dinnyés
Neurotoxicity and developmental neurotoxicity are important issues of chemical hazard assessment. Since the interpretation of animal data and their extrapolation to man is challenging, and the amount of substances with information gaps exceeds present animal testing capacities, there is a big demand for in vitro tests to provide initial information and to prioritize for further evaluation. During the last decade, many in vitro tests emerged. These are based on animal cells, human tumour cell lines, primary cells, immortalized cell lines, embryonic stem cells, or induced pluripotent stem cells...
January 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/27465131/pvtfdb-a-phaseolus-vulgaris-transcription-factors-database-for-expediting-functional-genomics-in-legumes
#15
Bhawna, V S Bonthala, Mnv Prasad Gajula
The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27184836/multiomic-analysis-of-the-uv-induced-dna-damage-response
#16
Stefan Boeing, Laura Williamson, Vesela Encheva, Ilaria Gori, Rebecca E Saunders, Rachael Instrell, Ozan Aygün, Marta Rodriguez-Martinez, Juston C Weems, Gavin P Kelly, Joan W Conaway, Ronald C Conaway, Aengus Stewart, Michael Howell, Ambrosius P Snijders, Jesper Q Svejstrup
In order to facilitate the identification of factors and pathways in the cellular response to UV-induced DNA damage, several descriptive proteomic screens and a functional genomics screen were performed in parallel. Numerous factors could be identified with high confidence when the screen results were superimposed and interpreted together, incorporating biological knowledge. A searchable database, bioLOGIC, which provides access to relevant information about a protein or process of interest, was established to host the results and facilitate data mining...
May 11, 2016: Cell Reports
https://www.readbyqxmd.com/read/27081328/network-based-enriched-gene-subnetwork-identification-a-game-theoretic-approach
#17
Abolfazl Razi, Fatemeh Afghah, Salendra Singh, Vinay Varadan
Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear...
2016: Biomedical Engineering and Computational Biology
https://www.readbyqxmd.com/read/27053136/cohort-profile-the-german-diabetes-study-gds
#18
Julia Szendroedi, Aaruni Saxena, Katharina S Weber, Klaus Strassburger, Christian Herder, Volker Burkart, Bettina Nowotny, Andrea Icks, Oliver Kuss, Dan Ziegler, Hadi Al-Hasani, Karsten Müssig, Michael Roden
BACKGROUND: The German Diabetes Study (GDS) is a prospective longitudinal cohort study describing the impact of subphenotypes on the course of the disease. GDS aims at identifying prognostic factors and mechanisms underlying the development of related comorbidities. STUDY DESIGN AND METHODS: The study comprises intensive phenotyping within 12 months after clinical diagnosis, at 5-year intervals for 20 years and annual telephone interviews in between. Dynamic tests, including glucagon, mixed meal, intravenous glucose tolerance and hyperinsulinemic clamp tests, serve to assess beta-cell function and tissue-specific insulin sensitivity...
April 7, 2016: Cardiovascular Diabetology
https://www.readbyqxmd.com/read/27027968/identifying-molecular-mechanisms-of-the-late-phase-asthmatic-response-by-integrating-cellular-gene-and-metabolite-levels-in-blood
#19
Amrit Singh, Casey P Shannon, Young Woong Kim, Mari L DeMarco, Gail M Gauvreau, J Mark FitzGerald, Louis-Philippe Boulet, Paul M O'Byrne, Kim-Anh Le Cao, Scott J Tebbutt
RATIONALE: Individuals with allergic asthma respond differently, but reproducibly, to allergen inhalation challenge. Some individuals develop an isolated early response (early responders) (ERs), whereas others go on to develop a late response (dual responders) (DRs). It is not understood why late responses do not develop in all sensitized individuals. OBJECTIVES: The aim of this study was to identify blood biomarkers that can discriminate ERs and DRs using cellular frequencies and gene and metabolite expression from whole blood...
March 2016: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/27022133/minireview-multiomic-candidate-biomarkers-for-clinical-manifestations-of-sickle-cell-severity-early-steps-to-precision-medicine
#20
Steven R Goodman, Betty S Pace, Kirk C Hansen, Angelo D'alessandro, Yang Xia, Ovidiu Daescu, Stephen J Glatt
In this review, we provide a description of those candidate biomarkers which have been demonstrated by multiple-omics approaches to vary in correlation with specific clinical manifestations of sickle cell severity. We believe that future clinical analyses of severity phenotype will require a multiomic analysis, or an omics stack approach, which includes integrated interactomics. It will also require the analysis of big data sets. These candidate biomarkers, whether they are individual or panels of functionally linked markers, will require future validation in large prospective and retrospective clinical studies...
April 2016: Experimental Biology and Medicine
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