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Translational genomics

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https://www.readbyqxmd.com/read/28806273/the-changing-landscape-of-gene-editing-in-hematopoietic-stem-cells-a-step-towards-cas9-clinical-translation
#1
Daniel P Dever, Matthew H Porteus
PURPOSE OF REVIEW: Since the discovery two decades ago that programmable endonucleases can be engineered to modify human cells at single nucleotide resolution, the concept of genome editing was born. Now these technologies are being applied to therapeutically relevant cell types, including hematopoietic stem cells (HSC), which possess the power to repopulate an entire blood and immune system. The purpose of this review is to discuss the changing landscape of genome editing in hematopoietic stem cells (GE-HSC) from the discovery stage to the preclinical stage, with the imminent goal of clinical translation for the treatment of serious genetic diseases of the blood and immune system...
August 12, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28806172/mobilization-of-line-1-retrotransposons-is-restricted-by-tex19-1-in-mouse-embryonic-stem-cells
#2
Marie MacLennan, Marta García-Cañadas, Judith Reichmann, Elena Khazina, Gabriele Wagner, Christopher J Playfoot, Carmen Salvador-Palomeque, Abigail R Mann, Paula Peressini, Laura Sanchez, Karen Dobie, David Read, Chao-Chun Hung, Ragnhild Eskeland, Richard R Meehan, Oliver Weichenrieder, Jose Luis García-Pérez, Ian R Adams
Mobilization of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution, but these mutagenic events can also cause genetic disorders. In humans, retrotransposon mobilization is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilize in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilization...
August 14, 2017: ELife
https://www.readbyqxmd.com/read/28803755/communicating-complex-genomic-information-a-counselling-approach-derived-from-research-experience-with-autism-spectrum-disorder
#3
Ny Hoang, Cheryl Cytrynbaum, Stephen W Scherer
Individuals with Autism Spectrum Disorder (ASD) share characteristics (impairments in socialization and communication, and repetitive interests and behaviour), but differ in their developmental course, pattern of symptoms, and cognitive and language abilities. The development of standardized phenotyping has revealed ASD to clinically be vastly heterogeneous, ranging from milder presentations to more severe forms associated with profound intellectual disability. Some 100 genes have now been implicated in the etiology of ASD, and advances in genome-wide testing continue to yield new data at an unprecedented rate...
July 29, 2017: Patient Education and Counseling
https://www.readbyqxmd.com/read/28802644/rapid-characterization-of-the-cho-platform-cell-line-and-identification-of-pseudo-attp-sites-for-phic31-integrase
#4
Narges Damavandi, Mozhgan Raigani, Atefeh Joudaki, Fatemeh Davami, Sirous Zeinali
The Chinese Hamster Ovary (CHO) cell lines, applicable to post-translational modifications, are preferred systems for biopharmaceutical protein production. In this study, by using the Jump-In™ TI™ technology which employs PhiC31 and R4 bacteriophage recombinases, a platform CHO-K1 cell line containing a R4-attP site was generated. Here, a combination of Quantitative Fluorescent-Polymerase Chain Reaction (QF-PCR) and semi-random, two-step PCR (ST-PCR), was performed to feature the platform cell clones. Our results show that QF-PCR and ST-PCR, can be utilized for efficient and accelerated cell line characterization...
August 9, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28799494/contribution-of-large-animals-to-translational-research-on-prenatal-programming-of-obesity-and-associated-diseases
#5
Gonzalez-Bulnes, Chavatte-Palmer
BACKGROUND: The awareness of factors causing obesity and associated disorders has grown up in the last years from genome to a more complicated concept (developmental programming) in which prenatal and early-postnatal conditions markedly modify the phenotype and homeostasis of the individuals and determine juvenile growth, life-time fitness/obesity and disease risks. Experimentation in human beings is impeded by ethical issues plus inherent high variability and confounding factors (genetics, lifestyle and socioeconomic heterogeneity) and preclinical studies in adequate translational animal models are therefore decisive...
August 11, 2017: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/28798901/translational-dysregulation-in-cancer-molecular-insights-and-potential-clinical-applications-in-biomarker-development
#6
REVIEW
Christos Vaklavas, Scott W Blume, William E Grizzle
Although transcript levels have been traditionally used as a surrogate measure of gene expression, it is increasingly recognized that the latter is extensively and dynamically modulated at the level of translation (messenger RNA to protein). Over the recent years, significant progress has been made in dissecting the complex posttranscriptional mechanisms that regulate gene expression. This advancement in knowledge came hand in hand with the progress made in the methodologies to study translation both at gene-specific as well as global genomic level...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28798696/phylogenetic-and-molecular-evolutionary-analysis-of-mitophagy-receptors-under-hypoxic-conditions
#7
Xiaomei Wu, Fei-Hua Wu, Qianrong Wu, Shu Zhang, Suping Chen, Matthew Sima
As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy) under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28798664/interplay-of-energetics-and-er-stress-exacerbates-alzheimer-s-amyloid-%C3%AE-a%C3%AE-toxicity-in-yeast
#8
Xin Chen, Markus M M Bisschops, Nisha R Agarwal, Boyang Ji, Kumaravel P Shanmugavel, Dina Petranovic
Alzheimer's disease (AD) is a progressive neurodegeneration. Oligomers of amyloid-β peptides (Aβ) are thought to play a pivotal role in AD pathogenesis, yet the mechanisms involved remain unclear. Two major isoforms of Aβ associated with AD are Aβ40 and Aβ42, the latter being more toxic and prone to form oligomers. Here, we took a systems biology approach to study two humanized yeast AD models which expressed either Aβ40 or Aβ42 in bioreactor cultures. Strict control of oxygen availability and culture pH, strongly affected chronological lifespan and reduced variations during cell growth...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28798321/crispr-cas9-mediated-deletion-of-foxn1-in-nod-scid-il2rg-mice-results-in-severe-immunodeficiency
#9
Xinru Wei, Yunxin Lai, Baiheng Li, Le Qin, Youdi Xu, Simiao Lin, Suna Wang, Qiting Wu, Qiubin Liang, Guohua Huang, Qiuhua Deng, Pentao Liu, Donghai Wu, Liangxue Lai, Yao Yao, Peng Li
Immunodeficient mice engrafted with either normal or cancerous human cells are widely used in basic and translational research. In particular, NOD/SCID/IL2rg(-/-) mice can support the growth of various types of human cancer cells. However, the hairs of these mice interfere with the observation and imaging of engrafted tissues. Therefore, novel hairless strains exhibiting comparable immunodeficiency would be beneficial. Recently, the CRISPR/Cas9 system has been used for efficient multiplexed genome editing. In the present study, we generated a novel strain of nude NOD/SCID/IL2rg(-/-) (NSIN) mice by knocking out Foxn1 from NOD/SCID/IL2rg(-/-) (NSI) mice using the CRISPR/Cas9 system...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797229/odg-omics-database-generator-a-tool-for-generating-querying-and-analyzing-multi-omics-comparative-databases-to-facilitate-biological-understanding
#10
Joseph Guhlin, Kevin A T Silverstein, Peng Zhou, Peter Tiffin, Nevin D Young
BACKGROUND: Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28795090/consensus-datasets-of-mouse-mirna-mrna-interactions-from-multiple-online-resources
#11
Bi Zhao, Bin Xue
MiRNAs regulate gene expression by forming base pairing with mRNAs to inhibit the translation of those mRNAs. In many mammalian genomes each, about 2000 miRNAs were found to regulate roughly 60% of all the genes in that genome. Many experimental validations and computational predictions have been done on miRNA:mRNA interactions. Nonetheless, the interactions from different sources are not always consistent. In this study, we integrated multiple online resources, including mirTarBase, TarBase, miRanda, miRDB, PITA, and TargetScan, and developed eleven large-scale datasets containing miRNA:mRNA interactions that are consistent among a specific subgroup of above-mentioned online resources...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28793798/dual-aav-gene-therapy-for-duchenne-muscular-dystrophy-with-a-7-kb-mini-dystrophin-gene-in-the-canine-model
#12
Kasun Kodippili, Chady Hakim, Xiufang Pan, Hsiao T Yang, Yongping YUe, Yadong Zhang, Jin-Hong Shin, Nora N Yang, Dongsheng Duan
Dual adeno-associated virus (AAV) technology was developed in 2000 to double the packaging capacity of the AAV vector. The proof-of-principle has been demonstrated in various mouse models. Yet, pivotal evidence is lacking in large animal models of human diseases. Here we report expression of a 7-kb canine ∆H2-R15 mini-dystrophin gene using a pair of dual AAV vectors in the canine model of Duchenne muscular dystrophy (DMD). The ∆H2-R15 minigene is by far the most potent synthetic dystrophin gene engineered for DMD gene therapy...
August 10, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/28793797/the-many-faces-of-long-noncoding-rnas-in-cancer
#13
Xue Wu, Oana Tudoran, George Calin, Mircea Ivan
SIGNIFICANCE: The emerging connections between an increasing number of long noncoding RNAs (lncRNAs) and oncogenic hallmarks provide a new twist to tumor complexity. Recent Advances: In the present review, we highlight specific lncRNAs that have been studied in relationship to tumorigenesis, either as participants to the neoplastic process or as markers of pathway activity or drug response. These transcripts are typically deregulated by oncogenic or tumor-suppressing signals, or respond to microenvironmental conditions such as hypoxia...
August 10, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28792639/circadian-rhythms-vary-over-the-growing-season-and-correlate-with-fitness-components
#14
Matthew J Rubin, Marcus T Brock, Amanda M Davis, Zachary M German, Mary Knapp, Stephen M Welch, Stacey L Harmer, Julin N Maloof, Seth J Davis, Cynthia Weinig
Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle length (referred to as clock period) via mutation reduce both survival and fecundity...
August 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28791707/preface-cholinergic-mechanisms
#15
Marco A M Prado, Pascale Marchot, Israel Silman
This special issue is a companion to the meeting 'XVth International Symposium on Cholinergic Mechanisms', and is edited by Israel Silman, Marco Prado and Pascale Marchot. In the review articles, renowned researchers in the field capture key mechanisms of cholinergic neurotransmission, from genomic amplification of cholinesterase genes, splicing and post-translational modifications; features of the neuromuscular junction, implications of cholinergic circuitry that are relevant to addiction, anxiety and mood, to preclinical models, protein biomarkers, and clinical findings that are relevant to pathology, for example, developmental neurotoxicity...
August 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28782606/epigenetics-in-ovarian-cancer
#16
REVIEW
Yanina Natanzon, Ellen L Goode, Julie M Cunningham
Ovarian cancer is a disease with a poor prognosis and little progress has been made to improve treatment. It is now recognized that there are several histotypes of ovarian cancer, each with distinct epidemiologic and genomic characteristics. Cancer therapy is moving beyond classical chemotherapy to include epigenetic approaches. Epigenetics is the dynamic regulation of gene expression by DNA methylation and histone post translational modification in response to environmental cues. Improvement in technology to study DNA methylation has enabled a more agnostic approach and, with larger samples sets, has begun to unravel how epigenetics contributes to the etiology, response to chemotherapy and prognosis in of ovarian cancer...
August 3, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28781970/hypoxic-modulation-of-hla-g-expression-through-the-metabolic-sensor-hif-1-in-human-cancer-cells
#17
REVIEW
Marica Garziera, Lucia Scarabel, Giuseppe Toffoli
The human leukocyte antigen-G (HLA-G) is considered an immune checkpoint molecule involved in tumor immune evasion. Hypoxia and the metabolic sensor hypoxia-inducible factor 1 (HIF-1) are hallmarks of metastasization, angiogenesis, and intense tumor metabolic activity. The purpose of this review was to examine original in vitro studies carried out in human cancer cell lines, which reported data about HLA-G expression and HIF-1 mediated-HLA-G expression in response to hypoxia. The impact of HLA-G genomic variability on the hypoxia responsive elements (HREs) specific for HIF-1 binding was also discussed...
2017: Journal of Immunology Research
https://www.readbyqxmd.com/read/28781152/speech-and-language-translating-the-genome
#18
REVIEW
Pelagia Deriziotis, Simon E Fisher
Investigation of the biological basis of human speech and language is being transformed by developments in molecular technologies, including high-throughput genotyping and next-generation sequencing of whole genomes. These advances are shedding new light on the genetic architecture underlying language-related disorders (speech apraxia, specific language impairment, developmental dyslexia) as well as that contributing to variation in relevant skills in the general population. We discuss how state-of-the-art methods are uncovering a range of genetic mechanisms, from rare mutations of large effect to common polymorphisms that increase risk in a subtle way, while converging on neurogenetic pathways that are shared between distinct disorders...
August 3, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28779964/the-c-elegans-set-2-set1-histone-h3-lys4-h3k4-methyltransferase-preserves-genome-stability-in-the-germline
#19
M Herbette, M G Mercier, F Michal, D Cluet, C Burny, G Yvert, V J Robert, F Palladino
Maintaining the integrity of genetic information across generations is essential for both cell survival and reproduction, and requires the timely repair of DNA damage. Histone-modifying enzymes play a central role in the DNA repair process through the deposition and removal of post-translational modifications on the histone tails. Specific histone modification act in the DNA repair process through the recruitment of proteins and complexes with specific enzymatic activities, or by altering the chromatin state at the site of DNA lesions...
July 29, 2017: DNA Repair
https://www.readbyqxmd.com/read/28774272/identification-of-candidate-protective-variants-for-common-diseases-and-evaluation-of-their-protective-potential
#20
Joe M Butler, Neil Hall, Niro Narendran, Yit C Yang, Luminita Paraoan
BACKGROUND: Human polymorphisms with derived alleles that are protective against disease may provide powerful translational opportunities. Here we report a method to identify such candidate polymorphisms and apply it to common non-synonymous SNPs (nsSNPs) associated with common diseases. Our study also sought to establish which of the identified protective nsSNPs show evidence of positive selection, taking this as indirect evidence that the protective variant has a beneficial effect on phenotype...
August 3, 2017: BMC Genomics
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