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https://www.readbyqxmd.com/read/29916387/genomic-insights-into-the-causes-of-type-2-diabetes
#1
REVIEW
Claudia Langenberg, Luca A Lotta
Genome-wide association studies have implicated around 250 genomic regions in predisposition to type 2 diabetes, with evidence for causal variants and genes emerging for several of these regions. Understanding of the underlying mechanisms, including the interplay between β-cell failure, insulin sensitivity, appetite regulation, and adipose storage has been facilitated by the integration of multidimensional data for diabetes-related intermediate phenotypes, detailed genomic annotations, functional experiments, and now multiomic molecular features...
June 16, 2018: Lancet
https://www.readbyqxmd.com/read/29872542/a-machine-learning-approach-to-predict-metabolic-pathway-dynamics-from-time-series-multiomics-data
#2
Zak Costello, Hector Garcia Martin
New synthetic biology capabilities hold the promise of dramatically improving our ability to engineer biological systems. However, a fundamental hurdle in realizing this potential is our inability to accurately predict biological behavior after modifying the corresponding genotype. Kinetic models have traditionally been used to predict pathway dynamics in bioengineered systems, but they take significant time to develop, and rely heavily on domain expertise. Here, we show that the combination of machine learning and abundant multiomics data (proteomics and metabolomics) can be used to effectively predict pathway dynamics in an automated fashion...
2018: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29784310/effects-of-fermented-milk-treatment-on-microbial-population-and-metabolomic-outcomes-in-a-three-stage-semi-continuous-culture-system
#3
Kwang Hyun Cha, Eun Ha Lee, Hyo Shin Yoon, Jae Ho Lee, Joo Yun Kim, Kyungsu Kang, Jin-Soo Park, Jong Beom Jin, GwangPyo Ko, Cheol-Ho Pan
We investigated the impact of a fermented milk product on gut microbiota and their metabolism in 3 different conditions of the colon with a systemic viewpoint. An in vitro semi-continuous anaerobic cultivation was used to assess the colon compartment-specific influence of fermented milk, followed by a multiomics approach combining 16S rDNA amplicon sequencing and nuclear magnetic resonance (NMR) spectroscopy. The microbiome profiling and metabolomic features were significantly different across three colon compartments and after fermented milk treatment...
October 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29765774/how-shall-we-treat-early-triple-negative-breast-cancer-tnbc-from-the-current-standard-to-upcoming-immuno-molecular-strategies
#4
REVIEW
Ji Hyun Park, Jin-Hee Ahn, Sung-Bae Kim
Triple-negative breast cancer (TNBC) is a long-lasting orphan disease in terms of little therapeutic progress during the past several decades and still the standard of care remains chemotherapy. Experimental discovery of molecular signatures including the 'BRCAness' highlighted the innate heterogeneity of TNBC, generating the diversity of TNBC phenotypes. As it contributes to enhancing genomic instability, it has widened the therapeutic spectrum of TNBC. In particular, unusual sensitivity to DNA damaging agents was denoted in patients with BRCA deficiency, suggesting therapeutic benefit from platinum and poly(ADP-ribose) polymerase inhibitors...
2018: ESMO Open
https://www.readbyqxmd.com/read/29762088/an-updated-taxonomy-and-a-graphical-summary-tool-for-optimal-classification-and-comprehension-of-omics-research
#5
Nina Pirih, Tanja Kunej
The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e...
May 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29748366/omics-of-blood-pressure-and-hypertension
#6
REVIEW
Donna K Arnett, Steven A Claas
Essential hypertension is a common, complex disorder affecting ≤1 billion adults globally. Blood pressure is a highly heritable trait, with ≤50% of the variation between individuals accounted for by familial relationships. Despite this strong heritability, determining the genetic architecture of hypertension in humans has proved challenging. Recent technological and methodological developments have given rise to what is now known as omics-a domain of study that includes genomics, as well as epigenomics, transcriptomics, proteomics, and metabolomics...
May 11, 2018: Circulation Research
https://www.readbyqxmd.com/read/29746212/harnessing-omics-big-data-in-nine-vertebrate-species-by-genome-wide-prioritization-of-sequence-variants-with-the-highest-predicted-deleterious-effect-on-protein-function
#7
Vita Rozman, Tanja Kunej
Harnessing the genomics big data requires innovation in how we extract and interpret biologically relevant variants. Currently, there is no established catalog of prioritized missense variants associated with deleterious protein function phenotypes. We report in this study, to the best of our knowledge, the first genome-wide prioritization of sequence variants with the most deleterious effect on protein function (potentially deleterious variants [pDelVars]) in nine vertebrate species: human, cattle, horse, sheep, pig, dog, rat, mouse, and zebrafish...
May 10, 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29731456/-diagnosis-and-treatment-of-rheumatoid-arthritis-toward-the-best-practice-towards-precision-medicine-in-rheumatoid-arthritis
#8
Katsuya Suzuki, Tsutomu Takeuchi
Biologics made a big paradigm shift in the treatment for rheumatoid arthritis(RA). In the next step, current research for RA shifts from traditional approach for average patients to precision medicine using huge omics data from patients. Multiomics analysis for the specimen from patients will play an important role for the establishment of precision medicine for RA.
2018: Clinical Calcium
https://www.readbyqxmd.com/read/29727584/single-cell-multi-omics-technologies
#9
Lia Chappell, Andrew J C Russell, Thierry Voet
Single-cell multiomics technologies typically measure multiple types of molecule from the same individual cell, enabling more profound biological insight than can be inferred by analyzing each molecular layer from separate cells. These single-cell multiomics technologies can reveal cellular heterogeneity at multiple molecular layers within a population of cells and reveal how this variation is coupled or uncoupled between the captured omic layers. The data sets generated by these techniques have the potential to enable a deeper understanding of the key biological processes and mechanisms driving cellular heterogeneity and how they are linked with normal development and aging as well as disease etiology...
May 4, 2018: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/29704148/clinical-lipidomics-a-new-way-to-diagnose-human-diseases
#10
Jiapei Lv, Linlin Zhang, Furong Yan, Xiangdong Wang
Lipidomics is a measurement of a large scale of lipid species to understand roles of their carbon atoms, dual bonds, or isomerism in the lipid molecule. Clinical lipidomics was recently defined "as a new integrative biomedicine to discover the correlation and regulation between a large scale of lipid elements measured and analyzed in liquid biopsies from patients with those patient phenomes and clinical phenotypes". The first step to translate lipidomics into clinical lipidomics is to settle a number of standard operation procedures and protocols of lipidomics performance and measurement...
April 27, 2018: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/29700067/epigenomics-technologies-and-applications
#11
REVIEW
Kevin C Wang, Howard Y Chang
The advent of high-throughput epigenome mapping technologies has ushered in a new era of multiomics where powerful tools can now delineate and record different layers of genomic output. Integrating various components of the epigenome from these multiomics measurements allows the interrogation of cellular heterogeneity in addition to the discovery of molecular connectivity maps between the genome and its functional output. Mapping of chromatin accessibility dynamics and higher-order chromatin structure has enabled new levels of understanding of cell fate decisions, identity, and function in normal development, physiology, and disease...
April 27, 2018: Circulation Research
https://www.readbyqxmd.com/read/29695975/characterizing-the-key-metabolic-pathways-of-the-neonatal-mouse-heart-using-a-quantitative-combinatorial-omics-approach
#12
Maciej M Lalowski, Susann Björk, Piet Finckenberg, Rabah Soliymani, Miikka Tarkia, Giulio Calza, Daria Blokhina, Sari Tulokas, Matti Kankainen, Päivi Lakkisto, Marc Baumann, Esko Kankuri, Eero Mervaala
The heart of a newborn mouse has an exceptional capacity to regenerate from myocardial injury that is lost within the first week of its life. In order to elucidate the molecular mechanisms taking place in the mouse heart during this critical period we applied an untargeted combinatory multiomics approach using large-scale mass spectrometry-based quantitative proteomics, metabolomics and mRNA sequencing on hearts from 1-day-old and 7-day-old mice. As a result, we quantified 1.937 proteins (366 differentially expressed), 612 metabolites (263 differentially regulated) and revealed 2...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29691682/clinical-trans-omics-an-integration-of-clinical-phenomes-with-molecular-multiomics
#13
EDITORIAL
Xiangdong Wang
No abstract text is available yet for this article.
June 2018: Cell Biology and Toxicology
https://www.readbyqxmd.com/read/29690719/-precise-medicine-for-diabetic-nephropathy-based-on-multiomics
#14
S Jiang
No abstract text is available yet for this article.
April 10, 2018: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/29686467/multiomics-biomarkers-for-the-prediction-of-nonalcoholic-fatty-liver-disease-severity
#15
REVIEW
Carlos J Pirola, Silvia Sookoian
This review intends to uncover how information from large-scale genetic profiling (whole genome sequencing, and whole exome sequencing) of nonalcoholic fatty liver disease (NAFLD), as well as information from circulating transcriptomics (cell-free miRNAs) and metabolomics, contributes to the understanding of NAFLD pathogenesis. A further aim is to address the question of whether OMICs information is ready to be implemented in the clinics. The available evidence suggests that any new knowledge pertaining to molecular signatures associated with NAFLD and nonalcoholic steatohepatitis should be promptly translated into the clinical setting...
April 21, 2018: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29686404/systems-biology-in-hepatology-approaches-and-applications
#16
REVIEW
Adil Mardinoglu, Jan Boren, Ulf Smith, Mathias Uhlen, Jens Nielsen
Detailed insights into the biological functions of the liver and an understanding of its crosstalk with other human tissues and the gut microbiota can be used to develop novel strategies for the prevention and treatment of liver-associated diseases, including fatty liver disease, cirrhosis, hepatocellular carcinoma and type 2 diabetes mellitus. Biological network models, including metabolic, transcriptional regulatory, protein-protein interaction, signalling and co-expression networks, can provide a scaffold for studying the biological pathways operating in the liver in connection with disease development in a systematic manner...
June 2018: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/29663340/molecular-signatures-in-hepatocellular-carcinoma-a-step-toward-rationally-designed-cancer-therapy
#17
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
#18
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
#19
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
#20
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
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