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Expression genomic integration

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https://www.readbyqxmd.com/read/28930592/choline-the-brain-and-neurodegeneration-insights-from-epigenetics
#1
Rola A Bekdash
  Neurodegenerative disorders are a major public health problem worldwide with huge socioeconomic effect. Recent evidence suggests that neurodegeneration is not only caused by genetic factors but also affected by environmental factors including nutrients. Environmental influences have been shown to cause epigenetic modifications in the brain with long-lasting effects on behavior if they occur in early life. It has been suggested that early nutritional intervention that includes choline, betaine, VitB6, VitB12 and/or folic acid could attenuate decline in cognitive functions...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28928286/hpv-integration-in-hnscc-correlates-with-survival-outcomes-immune-response-signatures-and-candidate-drivers
#2
Lada A Koneva, Yanxiao Zhang, Shama Virani, Pelle B Hall, Jonathan B McHugh, Douglas B Chepeha, Gregory Wolf, Thomas E Carey, Laura S Rozek, Maureen A Sartor
The incidence of human papillomavirus (HPV)-related oropharynx cancer has steadily increased over the past two decades, and now represents a majority of oropharyngeal cancer cases. Integration of the HPV genome into the host genome is a common event during carcinogenesis that has clinically-relevant effects if the viral early genes are transcribed. Understanding the impact of HPV integration on clinical outcomes of head and neck squamous cell carcinoma (HNSCC) is critical for implementing de-escalated treatment approaches for HPV-positive HNSCC patients...
September 19, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28927585/whole-genome-and-transcriptome-sequencing-of-prostate-cancer-identify-new-genetic-alterations-driving-disease-progression
#3
Shancheng Ren, Gong-Hong Wei, Dongbing Liu, Liguo Wang, Yong Hou, Shida Zhu, Lihua Peng, Qin Zhang, Yanbing Cheng, Hong Su, Xiuqing Zhou, Jibin Zhang, Fuqiang Li, Hancheng Zheng, Zhikun Zhao, Changjun Yin, Zengquan He, Xin Gao, Haiyen E Zhau, Chia-Yi Chu, Jason Boyang Wu, Colin Collins, Stanislav V Volik, Robert Bell, Jiaoti Huang, Kui Wu, Danfeng Xu, Dingwei Ye, Yongwei Yu, Lianhui Zhu, Meng Qiao, Hang-Mao Lee, Yuehong Yang, Yasheng Zhu, Xiaolei Shi, Rui Chen, Yang Wang, Weidong Xu, Yanqiong Cheng, Chuanliang Xu, Xu Gao, Tie Zhou, Bo Yang, Jianguo Hou, Li Liu, Zhensheng Zhang, Yao Zhu, Chao Qin, Pengfei Shao, Jun Pang, Leland W K Chung, Jianfeng Xu, Chin-Lee Wu, Weide Zhong, Xun Xu, Yingrui Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Jun Wang, Haojie Huang, Yinghao Sun
BACKGROUND: Global disparities in prostate cancer (PCa) incidence highlight the urgent need to identify genomic abnormalities in prostate tumors in different ethnic populations including Asian men. OBJECTIVE: To systematically explore the genomic complexity and define disease-driven genetic alterations in PCa. DESIGN, SETTING, AND PARTICIPANTS: The study sequenced whole-genome and transcriptome of tumor-benign paired tissues from 65 treatment-naive Chinese PCa patients...
September 15, 2017: European Urology
https://www.readbyqxmd.com/read/28927378/genome-wide-imaging-association-study-implicates-functional-activity-and-glial-homeostasis-of-the-caudate-in-smoking-addiction
#4
David C Qian, David L Molfese, Jennifer L Jin, Alexander J Titus, Yixuan He, Yafang Li, Maxime Vaissié, Humsini Viswanath, Philip R Baldwin, Ralf Krahe, Ramiro Salas, Christopher I Amos
BACKGROUND: Nearly 6 million deaths and over a half trillion dollars in healthcare costs worldwide are attributed to tobacco smoking each year. Extensive research efforts have been pursued to elucidate the molecular underpinnings of smoking addiction and facilitate cessation. In this study, we genotyped and obtained both resting state and task-based functional magnetic resonance imaging from 64 non-smokers and 42 smokers. Smokers were imaged after having smoked normally ("sated") and after having not smoked for at least 12 h ("abstinent")...
September 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28927305/discovery-and-application-of-immune-biomarkers-for-hematological-malignancies
#5
Dimitrios Zafeiris, Jayakumar Vadakekolathu, Sarah Wagner, Alan Graham Pockley, Graham Roy Ball, Sergio Rutella
Hematological malignancies originate and progress in primary and secondary lymphoid organs, where they establish a uniquely immune-suppressive tumour microenvironment. Although high-throughput transcriptomic and proteomic approaches are being employed to interrogate immune surveillance and escape mechanisms in patients with solid tumours, and to identify actionable targets for immunotherapy, our knowledge of the immunological landscape of hematological malignancies, as well as our understanding of the molecular circuits that underpin the establishment of immune tolerance, is not comprehensive...
September 19, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28927277/benchmark-dose-modeling-estimates-of-the-concentrations-of-inorganic-arsenic-that-induce-changes-to-the-neonatal-transcriptome-proteome-and-epigenome-in-a-pregnancy-cohort
#6
Julia Rager, Scott S Auerbach, Grace A Chappell, Elizabeth Martin, Chad Thompson, Rebecca C Fry
Prenatal inorganic arsenic (iAs) exposure influences the expression of critical genes and proteins associated with adverse outcomes in newborns, in part through epigenetic mediators. The doses at which these genomic and epigenomic changes occur have yet to be evaluated in the context of dose-response modeling. The goal of the present study was to estimate iAs doses that correspond to changes in transcriptomic, proteomic, epigenomic, and integrated multi-omic signatures in human cord blood through benchmark dose (BMD) modeling...
September 19, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28927115/wee1-inhibition-by-mk1775-as-a-single-agent-therapy-inhibits-ovarian-cancer-viability
#7
Minghui Zhang, Donye Dominguez, Siqi Chen, Jie Fan, Lei Qin, Alan Long, Xia Li, Yi Zhang, Huirong Shi, Bin Zhang
Wee1-like protein kinase (WEE1) physiologically serves a key function in maintaining the integrity of the cell genome through mediating the activation of cyclin-dependent kinase (CDK)1 and CDK2. Increased expression of WEE1 has been associated with the poor prognosis of patients with ovarian cancer. The present study aimed at examining the in vitro and in vivo antitumor activity of MK1775, a potent pharmacological inhibitor of WEE1, as a single agent against ovarian cancer cells. The cytotoxicity of MK1775 was examined in a panel of tumor cells using MTT in vitro...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28927082/identification-of-target-gene-of-venous-thromboembolism-in-patients-with-lymphoma-via-microarray-analysis
#8
Pengfei Liu, Wenhua Jiang, Huilai Zhang
Patients with lymphoma are at high risk of developing venous thromboembolism (VTE). The purpose of the present study was to identify the target gene associated with VTE for patients with lymphoma. Microarray data was downloaded from the gene expression omnibus database (GSE17078), which comprised the control group, 27 normal blood outgrowth endothelial cell (BOEC) samples, and the case group, 3 BOEC samples of venous thrombosis with protein C deficiency. Differentially expressed genes (DEGs) were identified by the Limma package of R...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926997/effects-of-cellular-methylation-on-transgene-expression-and-site-specific-integration-of-adeno-associated-virus
#9
Diptiman Chanda, Jonathan A Hensel, Jerome T Higgs, Rajat Grover, Niroop Kaza, Selvarangan Ponnazhagan
DNA methylation is a major epigenetic event that affects not only cellular gene expression but that also has the potential to influence bacterial and viral DNA in their host-dependent functions. Adeno-associated virus (AAV) genome contains a high degree of CpG sequences capable of methylation in its terminal repeat sequences, which are the sole elements retained in AAV-based vectors used in gene therapy. The present study determined the influence of methylation status of the host cell on wild type (wt) AAV integration and recombinant (r) AAV transgene expression in HeLa cells...
September 18, 2017: Genes
https://www.readbyqxmd.com/read/28925507/-epigallocatechin-3-gallate-and-ezh2-inhibitor-gsk343-have-similar-inhibitory-effects-and-mechanisms-of-action-on-colorectal-cancer-cells
#10
Le Ying, Feng Yan, Bryan R G Williams, Ping Xu, Xin Li, Yueling Zhao, Yiqun Hu, Yuefei Wang, Dakang Xu, Jing Dai
Epigallocatechin-3-gallate (EGCG) is a type of catechin. It exhibits excellent antioxidant effects and anti-tumor activities for cancer chemoprevention. The mechanism of anti-tumor effects of EGCG on different cancers has been studied for the past few decades, but remains controversial. To investigate the potential role that EGCG may play in the epigenetic regulation of colorectal cancer (CRC) cell line, we integrated bioinformatics analysis with experimental validation. We found that levels of the enhancer of zeste homolog 2 (EZH2) were significantly higher in CRC tissues compared to normal adjacent tissues, based on the Genomic Data Commons (GDC) data portal...
September 19, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28925362/generation-of-a-klf15-homozygous-knockout-human-embryonic-stem-cell-line-using-paired-crispr-cas9n-and-human-cardiomyocytes-derivation
#11
Claudia Noack, Luis Peter Haupt, Wolfram-Hubertus Zimmermann, Katrin Streckfuss-Bömeke, Laura Cecilia Zelarayán
Krueppel-like factor 15 (KLF15) is abundantly expressed in liver, kidney, and muscle, including myocardium. In the adult heart KLF15 is important to maintain homeostasis and to repress hypertrophic remodeling. We generated a homozygous hESC KLF15 knockout (KO) line using paired CRISPR/Cas9n. KLF15-KO cells maintained full pluripotency and differentiation potential as well as genomic integrity. We demonstrated that KLF15-KO cells can be differentiated into morphologically normal cardiomyocytes turning them into a valuable tool for studying human KLF15-mediated mechanisms resulting in human cardiac dysfunction...
August 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28923553/a-systematic-integrated-analysis-of-brain-expression-profiles-reveals-yap1-and-other-prioritized-hub-genes-as-important-upstream-regulators-in-alzheimer-s-disease
#12
Min Xu, Deng-Feng Zhang, Rongcan Luo, Yong Wu, Hejiang Zhou, Li-Li Kong, Rui Bi, Yong-Gang Yao
INTRODUCTION: Profiling the spatial-temporal expression pattern and characterizing the regulatory networks of brain tissues are vital for understanding the pathophysiology of Alzheimer's disease (AD). METHODS: We performed a systematic integrated analysis of expression profiles of AD-affected brain tissues (684 AD and 562 controls). A network-based convergent functional genomic approach was used to prioritize possible regulator genes during AD development, followed by functional characterization...
September 15, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28923077/development-and-evaluation-of-an-efficient-heterologous-gene-knock-in-reporter-system-in-lactococcus-lactis
#13
Yifei Lu, Hongxiang Yan, Jiezhong Deng, Zhigang Huang, Xurui Jin, Yanlan Yu, Qiwen Hu, Fuquan Hu, Jing Wang
BACKGROUND: Lactococcus lactis is a food grade probiotics and widely used to express heterologous proteins. Generally, target genes are knocked into the L. lactis genome through double-crossover recombination to express heterologous proteins stably. However, creating marker-less heterologous genes knocked-in clones is laborious. In this study, an efficient heterologous gene knock-in reporter system was developed in L. lactis NZ9000. RESULTS: Our knock-in reporter system consists of a temperature-sensitive plasmid pJW and a recombinant L...
September 18, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28923059/osteoglycin-promotes-meningioma-development-through-downregulation-of-nf2-and-activation-of-mtor-signaling
#14
Yu Mei, Ziming Du, Changchen Hu, Noah F Greenwald, Malak Abedalthagafi, Nathalie Y R Agar, Gavin P Dunn, Wenya Linda Bi, Sandro Santagata, Ian F Dunn
BACKGROUND: Meningiomas are the most common primary intracranial tumors in adults. While a majority of meningiomas are slow growing neoplasms that may cured by surgical resection, a subset demonstrates more aggressive behavior and insidiously recurs despite surgery and radiation, without effective alternative treatment options. Elucidation of critical mitogenic pathways in meningioma oncogenesis may offer new therapeutic strategies. We performed an integrated genomic and molecular analysis to characterize the expression and function of osteoglycin (OGN) in meningiomas and explored possible therapeutic approaches for OGN-expressing meningiomas...
September 18, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/28923004/regulatory-networks-underlying-mycorrhizal-development-delineated-by-genome-wide-expression-profiling-and-functional-analysis-of-the-transcription-factor-repertoire-of-the-plant-symbiotic-fungus-laccaria-bicolor
#15
Y Daguerre, E Levati, J Ruytinx, E Tisserant, E Morin, A Kohler, B Montanini, S Ottonello, A Brun, C Veneault-Fourrey, F Martin
BACKGROUND: Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28922955/comparison-of-zfns-versus-crispr-specific-nucleases-for-genome-edition-of-the-wiskott-aldrich-syndrome-locus
#16
Alejandra Gutierrez-Guerrero, Sabina Sanchez-Hernandez, Giuseppe Galvani, Javier Pinedo-Gomez, Almudena Sanchez-Gilabert, Rocio Martin-Guerra, Marien Cobo, Philip Gregory, Michael Holmes, Karim Benabdellah, Francisco Martin
Primary immunodeficiencies (PID), including Wiskott-Aldrich syndrome (WAS), are a main target for genome editing (GE) strategies using specific nucleases (SNs) since a small number of corrected hematopoietic stem cells (HSCs) could cure patients. In this work, we have designed different WAS gene-specific CRISPR/Cas9 systems and compared their efficiency and specificity with homodimeric and heterodimeric WAS-specific Zinc Finger Nucleases (ZFNs) using K562 cells as a cellular model and plasmid nucleofection or integrative-deficient Lentiviral Vectors (IDLVs) for delivery...
September 19, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/28922761/rapid-mapping-and-cloning-of-the-virescent-1-gene-in-cotton-by-bulked-segregant-analysis-next-generation-sequencing-and-virus-induced-gene-silencing-strategies
#17
Jiankun Zhu, Jiedan Chen, Fengkai Gao, Chenyu Xu, Huaitong Wu, Kun Chen, Zhanfeng Si, Hu Yan, Tianzhen Zhang
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922552/an-individualized-gene-expression-signature-for-prediction-of-lung-adenocarcinoma-metastases
#18
Lishuang Qi, Tianhao Li, Gengen Shi, Jiasheng Wang, Xin Li, Sainan Zhang, Libin Chen, Yuan Qin, Yunyan Gu, Wenyuan Zhao, Zheng Guo
Our laboratory previously reported an individual-level signature consisting of nine gene pairs, named 9-GPS. This signature was developed by training on microarray expression data and validated using three independent integrated microarray data sets, with samples of stage I non-small cell lung cancer after complete surgical resection. In this study, we first validated the cross-platform robustness of 9-GPS by demonstrating that 9-GPS could significantly stratify the overall survival of 213 stage I lung adenocarcinoma (LUAD) patients detected with RNA-sequencing platform in The Cancer Genome Atlas (log-rank p = 0...
September 18, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28922390/identifying-novel-transcription-factors-involved-in-the-inflammatory-response-by-using-binding-site-motif-scanning-in-genomic-regions-defined-by-histone-acetylation
#19
Peter S Askovich, Stephen A Ramsey, Alan H Diercks, Kathleen A Kennedy, Theo A Knijnenburg, Alan Aderem
The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of this response have been identified, the temporal complexity of gene expression changes in response to pathogen-associated molecular pattern receptor stimulation strongly suggest that additional layers of regulation remain to be uncovered. The evolved pathogen response program in mammalian innate immune cells is understood to reflect a compromise between the probability of clearing the infection and the extent of tissue damage and inflammatory sequelae it causes...
2017: PloS One
https://www.readbyqxmd.com/read/28922368/a-tree-of-life-based-on-ninety-eight-expressed-genes-conserved-across-diverse-eukaryotic-species
#20
Pawan Kumar Jayaswal, Vivek Dogra, Asheesh Shanker, Tilak Raj Sharma, Nagendra Kumar Singh
Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed...
2017: PloS One
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