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https://www.readbyqxmd.com/read/27801551/sample-preparation-method-considerations-for-integrated-transcriptomic-and-proteomic-analysis-of-tumors
#1
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
#2
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
#3
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
#4
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
#5
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...
August 4, 2016: Archives of Toxicology
https://www.readbyqxmd.com/read/27465131/pvtfdb-a-phaseolus-vulgaris-transcription-factors-database-for-expediting-functional-genomics-in-legumes
#6
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
#7
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
#8
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
#9
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...
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
#10
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
#11
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
https://www.readbyqxmd.com/read/26948350/molecular-classification-of-gliomas
#12
Kenta Masui, Paul S Mischel, Guido Reifenberger
The identification of distinct genetic and epigenetic profiles in different types of gliomas has revealed novel diagnostic, prognostic, and predictive molecular biomarkers for refinement of glioma classification and improved prediction of therapy response and outcome. Therefore, the new (2016) World Health Organization (WHO) classification of tumors of the central nervous system breaks with the traditional principle of diagnosis based on histologic criteria only and incorporates molecular markers. This will involve a multilayered approach combining histologic features and molecular information in an "integrated diagnosis"...
2016: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/26939758/challenges-in-large-scale-computational-mass-spectrometry-and-multiomics
#13
EDITORIAL
Oliver Kohlbacher, Olga Vitek, Susan T Weintraub
No abstract text is available yet for this article.
March 4, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/26925598/atlas-regeneration-inc
#14
Eugene Makarev, Olexandr Isayev, Anthony Atala
Atlas Regeneration is dedicated to the development of novel data-driven solutions for regenerative medicine, adapting proven technologies, and analysis strategies to take a multiomics-wide view of stem cell quality and cell fate design. Our core offering is a global comprehensive map of stem cell differentiation, Universal Signalome Atlas for Regenerative Medicine, reflecting the pathway activation states across all characterized stem cells and their differentiated products. Key applications of Universal Signalome Atlas for Regenerative Medicine will include quality assurance for engineered cell products, and directed regeneration pharmacology, where we will screen and identify compounds that can efficiently convert pluripotent cells into desired subtypes...
March 2016: Regenerative Medicine
https://www.readbyqxmd.com/read/26757801/sports-genetics-moving-forward-lessons-learned-from-medical-research
#15
REVIEW
C Mikael Mattsson, Matthew T Wheeler, Daryl Waggott, Colleen Caleshu, Euan A Ashley
Sports genetics can take advantage of lessons learned from human disease genetics. By righting past mistakes and increasing scientific rigor, we can magnify the breadth and depth of knowledge in the field. We present an outline of challenges facing sports genetics in the light of experiences from medical research. Sports performance is complex, resulting from a combination of a wide variety of different traits and attributes. Improving sports genetics will foremost require analyses based on detailed phenotyping...
March 2016: Physiological Genomics
https://www.readbyqxmd.com/read/26689812/multiomic-analysis-of-mice-epilepsy-models-suggest-that-mir-21a-expression-modulates-mrna-and-protein-levels-related-to-seizure-deterioration
#16
Xiaoxiao Hu, Xin Fu, A O Jiang, Xukui Yang, Xiaodong Fang, Guohua Gong, Chengxi Wei
Epilepsy is now recognized as the second most common neurological disease in China. To determine the genetic cause of epileptic encephalopathy, we performed a multiomics study using mouse models of controls, anticonvulsant mice treated with five drugs and epileptic mice. Based on genome-wide profiling analysis, we discovered four genes in the epileptic mouse group with differentially-expressed mRNA. After isobaric tags for relative and absolute quantification (iTRAQ) validation, only one gene, SNCA, remained, which was associated with apoptotic response of neuronal cells, and regulation of dopamine release and transport...
December 22, 2015: Genetics Research
https://www.readbyqxmd.com/read/26556047/implementation-of-a-pan-genomic-approach-to-investigate-holobiont-infecting-microbe-interaction-a-case-report-of-a-leukemic-patient-with-invasive-mucormycosis
#17
Samuel A Shelburne, Nadim J Ajami, Marcus C Chibucos, Hannah C Beird, Jeffrey Tarrand, Jessica Galloway-Peña, Nathan Albert, Roy F Chemaly, Shashank S Ghantoji, Lisa Marsh, Naveen Pemmaraju, Michael Andreeff, Elizabeth J Shpall, Jennifer A Wargo, Katayoun Rezvani, Amin Alousi, Vincent M Bruno, Phillip A Futreal, Joseph F Petrosino, Dimitrios P Kontoyiannis
Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis...
2015: PloS One
https://www.readbyqxmd.com/read/26468186/transcriptomic-approaches-to-neural-repair
#18
REVIEW
Jennifer N Dulin, Ana Antunes-Martins, Vijayendran Chandran, Michael Costigan, Jessica K Lerch, Dianna E Willis, Mark H Tuszynski
UNLABELLED: Understanding why adult CNS neurons fail to regenerate their axons following injury remains a central challenge of neuroscience research. A more complete appreciation of the biological mechanisms shaping the injured nervous system is a crucial prerequisite for the development of robust therapies to promote neural repair. Historically, the identification of regeneration associated signaling pathways has been impeded by the limitations of available genetic and molecular tools...
October 14, 2015: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/26456192/multiomics-approach-showing-genome-wide-copy-number-alterations-and-differential-gene-expression-in-different-types-of-north-indian-pediatric-brain-tumors
#19
Neetu Singh, Dinesh Kumar Sahu, Archana Mishra, Preeti Agarwal, Madhu Mati Goel, Anil Chandra, Sunil Kumar Singh, Chhitij Srivastava, Bal Krishna Ojha, Devendra Kumar Gupta, Ravi Kant
PURPOSE: Based on copy number alterations and transcriptional profiles, the posterior fossa tumors (medulloblastoma (MB), ependymoma and pilocytic astrocytoma) have been classified into various subgroups. The study design was aimed to identify and catalog genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric posterior fossa tumors and matched control tissue through Molecular Inversion Probe (MIP) Based and Human Transcriptome Array...
February 1, 2016: Gene
https://www.readbyqxmd.com/read/26453699/systems-wide-high-dimensional-data-acquisition-and-informatics-using-structural-mass-spectrometry-strategies
#20
REVIEW
Stacy D Sherrod, John A McLean
BACKGROUND: Untargeted multiomics data sets are obtained for samples in systems, synthetic, and chemical biology by integrating chromatographic separations with ion mobility-mass spectrometry (IM-MS) analysis. The data sets are interrogated using bioinformatics strategies to organize the data for identification prioritization. CONTENT: The use of big data approaches for data mining of massive data sets in systems-wide analyses is presented. Untargeted biological data across multiomics dimensions are obtained using a variety of chromatography strategies with structural MS...
January 2016: Clinical Chemistry
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