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https://www.readbyqxmd.com/read/29330893/mitogenomic-differences-between-the-normal-and-tumour-cells-of-colorectal-cancer-patients
#1
Katarzyna Skonieczna, Boris Malyarchuk, Arkadiusz Jawień, Andrzej Marszałek, Zbigniew Banaszkiewicz, Paweł Jarmocik, Tomasz Grzybowski
So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome...
January 12, 2018: Human Mutation
https://www.readbyqxmd.com/read/29330202/high-risk-tp53-mutations-are-associated-with-extra-nodal-extension-ene-in-oral-cavity-squamous-cell-carcinoma-oscc
#2
Vlad C Sandulache, Chieko Michikawa, Pranav Kataria, Frederico O Gleber-Netto, Diana Bell, Sanchit Trivedi, Xiayu Rao, Jing Wang, Mei Zhao, Samar A Jasser, Jeffrey N Myers, Curtis R Pickering
PURPOSE:   Development of extra-nodal extension (ENE) has been associated with poor survival in patients with oral cavity squamous cell carcinoma (OSCC). Here we sought to confirm the role of ENE as a poor prognostic factor, and identify genomic and epigenetic markers of ENE in order to develop a predictive model and improve treatment selection. EXPERIMENTAL DESIGN: An institutional cohort (University of Texas MD Anderson Cancer Center) was utilized to confirm the impact of ENE on clinical outcomes and evaluate the genomic signature of primary and ENE containing tissue...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29329538/peripheral-blood-gene-expression-signatures-which-reflect-smoking-and-aspirin-exposure-are-associated-with-cardiovascular-events
#3
James A Wingrove, Karen Fitch, Brian Rhees, Steven Rosenberg, Deepak Voora
BACKGROUND: Cardiovascular disease and its sequelae are major causes of global mortality, and better methods are needed to identify patients at risk for future cardiovascular events. Gene expression analysis can inform on the molecular underpinnings of risk factors for cardiovascular events. Smoking and aspirin have known opposing effects on platelet reactivity and MACE, however their effects on each other and on MACE are not well described. METHODS: We measured peripheral blood gene expression levels of ITGA2B, which is upregulated by aspirin and correlates with platelet reactivity on aspirin, and a 5 gene validated smoking gene expression score (sGES) where higher expression correlates with smoking status, in participants from the previously reported PREDICT trial (NCT 00500617)...
January 12, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29329366/delineating-differential-regulatory-signatures-of-the-human-transcriptome-in-the-choriodecidua-and-myometrium-at-term-labor
#4
Sylvia Lui, Cyntia Duval, Farkhondeh Farrokhnia, Sylvie Girard, Lynda K Harris, Clare L Tower, Adam Stevens, Rebecca L Jones
Background: Preterm deliveries remain the leading cause of neonatal morbidity and mortality. Current therapies target only myometrial contractions and are largely ineffective. As labor involves multiple coordinated events across maternal and fetal tissues, identifying fundamental regulatory pathways of normal term labor is vital to understanding successful parturition and consequently labor pathologies. We aimed to identify transcriptomic signatures of human normal term labor of two tissues: in the fetal-facing choriodecidua and the maternal myometrium...
January 10, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29328635/adsorption-and-molecular-fractionation-of-dissolved-organic-matter-on-iron-bearing-mineral-matrices-of-varying-crystallinity
#5
Elizabeth K Coward, Tsutomu Ohno, Alain F Plante
Iron (Fe)-bearing mineral phases contribute disproportionately to adsorption of soil organic matter (SOM), due to their elevated chemical reactivity and specific surface area (SSA). However, the spectrum of Fe solid-phase speciation present in oxidation-reduction-active soils challenges analysis of SOM-mineral interactions and may induce differential molecular fractionation of dissolved organic matter (DOM). This work used paired selective dissolution experiments and batch sorption of post-extraction residues to 1) quantify the contributions of Fe-bearing minerals of varying crystallinity to DOM sorption, and 2) characterize molecular fractionation using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS)...
January 12, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29328493/meta-analysis-of-mrna-expression-profiles-to-identify-differentially-expressed-genes-in-lung-adenocarcinoma-tissue-from-smokers-and-non-smokers
#6
Xiaona He, Cheng Zhang, Chao Shi, Quqin Lu
Compared to other types of lung cancer, lung adenocarcinoma patients with a history of smoking have a poor prognosis during the treatment of lung cancer. How lung adenocarcinoma-related genes are differentially expressed between smoker and non-smoker patients has yet to be fully elucidated. We performed a meta-analysis of four publicly available microarray datasets related to lung adenocarcinoma tissue in patients with a history of smoking using R statistical software. The top 50 differentially expressed genes (DEGs) in smoking vs...
January 8, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328363/support-vector-machine-classifier-for-prediction-of-the-metastasis-of-colorectal-cancer
#7
Jiajun Zhi, Jiwei Sun, Zhongchuan Wang, Wenjun Ding
Colorectal cancer (CRC) is one of the most common cancers and a major cause of mortality. The present study aimed to identify potential biomarkers for CRC metastasis and uncover the mechanisms underlying the etiology of the disease. The five datasets GSE68468, GSE62321, GSE22834, GSE14297 and GSE6988 were utilized in the study, all of which contained metastatic and non-metastatic CRC samples. Among them, three datasets were integrated via meta-analysis to identify the differentially expressed genes (DEGs) between the two types of samples...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29328002/dexamethasone-mediated-oncogenicity-in-vitro-and-in-an-animal-model-of-glioblastoma
#8
Markus M Luedi, Sanjay K Singh, Jennifer C Mosley, Islam S A Hassan, Masumeh Hatami, Joy Gumin, Lukas Andereggen, Erik P Sulman, Frederick F Lang, Frank Stueber, Gregory N Fuller, Rivka R Colen, Pascal O Zinn
OBJECTIVE Dexamethasone, a known regulator of mesenchymal programming in glioblastoma (GBM), is routinely used to manage edema in GBM patients. Dexamethasone also activates the expression of genes, such as CEBPB, in GBM stem cells (GSCs). However, the drug's impact on invasion, proliferation, and angiogenesis in GBM remains unclear. To determine whether dexamethasone induces invasion, proliferation, and angiogenesis in GBM, the authors investigated the drug's impact in vitro, in vivo, and in clinical information derived from The Cancer Genome Atlas (TCGA) cohort...
January 12, 2018: Journal of Neurosurgery
https://www.readbyqxmd.com/read/29324865/association-of-circadian-rhythm-genes-arntl-bmal1-and-clock-with-multiple-sclerosis
#9
Polona Lavtar, Gorazd Rudolf, Aleš Maver, Alenka Hodžić, Nada Starčević Čizmarević, Maja Živković, Saša Šega Jazbec, Zalika Klemenc Ketiš, Miljenko Kapović, Evica Dinčić, Ranko Raičević, Juraj Sepčić, Luca Lovrečić, Aleksandra Stanković, Smiljana Ristić, Borut Peterlin
Prevalence of multiple sclerosis varies with geographic latitude. We hypothesized that this fact might be partially associated with the influence of latitude on circadian rhythm and consequently that genetic variability of key circadian rhythm regulators, ARNTL and CLOCK genes, might contribute to the risk for multiple sclerosis. Our aim was to analyse selected polymorphisms of ARNTL and CLOCK, and their association with multiple sclerosis. A total of 900 Caucasian patients and 1024 healthy controls were compared for genetic signature at 8 SNPs, 4 for each of both genes...
2018: PloS One
https://www.readbyqxmd.com/read/29324850/generalization-of-the-ewens-sampling-formula-to-arbitrary-fitness-landscapes
#10
Pavel Khromov, Constantin D Malliaris, Alexandre V Morozov
In considering evolution of transcribed regions, regulatory sequences, and other genomic loci, we are often faced with a situation in which the number of allelic states greatly exceeds the size of the population. In this limit, the population eventually adopts a steady state characterized by mutation-selection-drift balance. Although new alleles continue to be explored through mutation, the statistics of the population, and in particular the probabilities of seeing specific allelic configurations in samples taken from the population, do not change with time...
2018: PloS One
https://www.readbyqxmd.com/read/29324753/microrna-signatures-of-endogenous-huntingtin-cag-repeat-expansion-in-mice
#11
Peter Langfelder, Fuying Gao, Nan Wang, David Howland, Seung Kwak, Thomas F Vogt, Jeffrey S Aaronson, Jim Rosinski, Giovanni Coppola, Steve Horvath, X William Yang
In Huntington's disease (HD) patients and in model organisms, messenger RNA transcriptome has been extensively studied; in contrast, comparatively little is known about expression and potential role of microRNAs. Using RNA-sequencing, we have quantified microRNA expression in four brain regions and liver, at three different ages, from an allelic series of HD model mice with increasing CAG length in the endogenous Huntingtin gene. Our analyses reveal CAG length-dependent microRNA expression changes in brain, with 159 microRNAs selectively altered in striatum, 102 in cerebellum, 51 in hippocampus, and 45 in cortex...
2018: PloS One
https://www.readbyqxmd.com/read/29323299/rotation-in-c-ii-emitting-gas-in-two-galaxies-at-a-redshift-of-6-8
#12
Renske Smit, Rychard J Bouwens, Stefano Carniani, Pascal A Oesch, Ivo Labbé, Garth D Illingworth, Paul van der Werf, Larry D Bradley, Valentino Gonzalez, Jacqueline A Hodge, Benne W Holwerda, Roberto Maiolino, Wei Zheng
The earliest galaxies are thought to have emerged during the first billion years of cosmic history, initiating the ionization of the neutral hydrogen that pervaded the Universe at this time. Studying this 'epoch of reionization' involves looking for the spectral signatures of ancient galaxies that are, owing to the expansion of the Universe, now very distant from Earth and therefore exhibit large redshifts. However, finding these spectral fingerprints is challenging. One spectral characteristic of ancient and distant galaxies is strong hydrogen-emission lines (known as Lyman-α lines), but the neutral intergalactic medium that was present early in the epoch of reionization scatters such Lyman-α photons...
January 10, 2018: Nature
https://www.readbyqxmd.com/read/29322932/identification-of-prognostic-signature-in-cancer-based-on-dna-methylation-interaction-network
#13
Wei-Lin Hu, Xiong-Hui Zhou
BACKGROUND: The identification of prognostic biomarkers for cancer patients is essential for cancer research. These days, DNA methylation has been proved to be associated with cancer prognosis. However, there are few methods which identify the prognostic markers based on DNA methylation data systematically, especially considering the interaction among DNA methylation sites. METHODS: In this paper, we first evaluated the stabilities of microRNA, mRNA, and DNA methylation data in prognosis of cancer...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322930/ontological-representation-integration-and-analysis-of-lincs-cell-line-cells-and-their-cellular-responses
#14
Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Sirarat Sarntivijai, Yu Lin, Daniel Cooper, Raymond Terryn, Vasileios Stathias, Caty Chung, Stephan Schürer, Yongqun He
BACKGROUND: Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the default ontology for LINCS cell line representation and integration. RESULTS: CLO has consistently represented all 1097 LINCS cell lines and included information extracted from the LINCS Data Portal and ChEMBL...
December 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29322919/hadamard-kernel-svm-with-applications-for-breast-cancer-outcome-predictions
#15
Hao Jiang, Wai-Ki Ching, Wai-Shun Cheung, Wenpin Hou, Hong Yin
BACKGROUND: Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signatures for outcome predictions. Kernel SVM for its discriminative power in dealing with small sample pattern recognition problems has attracted a lot attention. But how to select or construct an appropriate kernel for a specified problem still needs further investigation...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322204/evolving-notions-on-immune-response-in-colorectal-cancer-and-their-implications-for-biomarker-development
#16
REVIEW
Fabio Grizzi, Gianluca Basso, Elena Monica Borroni, Tommaso Cavalleri, Paolo Bianchi, Sanja Stifter, Maurizio Chiriva-Internati, Alberto Malesci, Luigi Laghi
INTRODUCTION: Colorectal cancer (CRC) still represents the third most commonly diagnosed type of cancer in men and women worldwide. CRC is acknowledged as a heterogeneous disease that develops through a multi-step sequence of events driven by clonal selections; this observation is sustained by the fact that histologically similar tumors may have completely different outcomes, including a varied response to therapy. METHODS: In "early" and "intermediate" stage of CRC (stages II and III, respectively) there is a compelling need for new biomarkers fit to assess the metastatic potential of their disease, selecting patients with aggressive disease that might benefit from adjuvant and targeted therapies...
January 10, 2018: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/29321915/comparative-genetics-of-invasive-populations-of-walnut-aphid-chromaphis-juglandicola-and-its-introduced-parasitoid-trioxys-pallidus-in-california
#17
Jeremy C Andersen, Nicholas J Mills
Coevolution may be an important component of the sustainability of importation biological control, but how frequently introduced natural enemies coevolve with their target pests is unclear. Here we explore whether comparative population genetics of the invasive walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, provide insights into the localized breakdown of biological control services in walnut orchards in California. We found that sampled populations of C. juglandicola exhibited higher estimates of genetic differentiation (FST) than co-occurring populations of T...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29321589/comparative-analysis-of-low-complexity-regions-in-plasmodia
#18
S R Chaudhry, N Lwin, D Phelan, A A Escalante, F U Battistuzzi
Low complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321538/sweep-dynamics-sd-plots-computational-identification-of-selective-sweeps-to-monitor-the-adaptation-of-influenza-a-viruses
#19
Thorsten R Klingen, Susanne Reimering, Jens Loers, Kyra Mooren, Frank Klawonn, Thomas Krey, Gülsah Gabriel, Alice C McHardy
Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321322/dengue-virus-selectively-annexes-endoplasmic-reticulum-associated-translation-machinery-as-a-strategy-for-co-opting-host-cell-protein-synthesis
#20
David W Reid, Rafael K Campos, Jessica R Child, Tianli Zheng, Kitti Wing Ki Chan, Shelton S Bradrick, Subhash G Vasudevan, Mariano A Garcia-Blanco, Christopher V Nicchitta
A primary question in Dengue virus (DENV) biology is the molecular strategy for recruitment of host cell protein synthesis machinery. Here we combined cell fractionation, ribosome profiling, and RNA-seq to investigate the subcellular organization of viral genome translation and replication as well as host cell translation and its response to DENV infection. We report that throughout the viral life cycle, DENV (+) and (-) strand RNAs were highly partitioned to the endoplasmic reticulum (ER), identifying the ER as the primary site of DENV translation...
January 10, 2018: Journal of Virology
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