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https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#1
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28231309/improving-molecular-diagnosis-of-aniridia-and-wagr-syndrome-using-customized-targeted-array-based-cgh
#2
Fiona Blanco-Kelly, María Palomares, Elena Vallespín, Cristina Villaverde, Rubén Martín-Arenas, Camilo Vélez-Monsalve, Isabel Lorda-Sánchez, Julián Nevado, María José Trujillo-Tiebas, Pablo Lapunzina, Carmen Ayuso, Marta Corton
Chromosomal deletions at 11p13 are a frequent cause of congenital Aniridia, a rare pan-ocular genetic disease, and of WAGR syndrome, accounting up to 30% of cases. First-tier genetic testing for newborn with aniridia, to detect 11p13 rearrangements, includes Multiplex Ligation-dependent Probe Amplification (MLPA) and karyotyping. However, neither of these approaches allow obtaining a complete picture of the high complexity of chromosomal deletions and breakpoints in aniridia. Here, we report the development and validation of a customized targeted array-based comparative genomic hybridization, so called WAGR-array, for comprehensive high-resolution analysis of CNV in the WAGR locus...
2017: PloS One
https://www.readbyqxmd.com/read/28231297/cytoplasmic-deadenylase-ccr4-is-required-for-translational-repression-of-lrg1-mrna-in-the-stationary-phase
#3
Duong Long Duy, Yasuyuki Suda, Kenji Irie
Ccr4 is a major cytoplasmic deadenylase involved in mRNA poly(A) tail shortening in Saccharomyces cerevisiae. We have previously shown that Ccr4 negatively regulates expression of LRG1 mRNA encoding a GTPase-activating protein for the small GTPase Rho1, a component of cell wall integrity pathway, and deletion of LRG1 suppresses the temperature-sensitive growth defect of the ccr4Δ mutant. We have also shown that the slow growth of the ccr4Δ mutant is suppressed by deletion of another gene, PBP1, encoding a poly(A)-binding protein (Pab1)-binding protein 1; however, the underlying mechanism still remains unknown...
2017: PloS One
https://www.readbyqxmd.com/read/28231271/applying-antibody-sensitive-hypervariable-region-1-deleted-hepatitis-c-virus-to-the-study-of-escape-pathways-of-neutralizing-human-monoclonal-antibody-ar5a
#4
Rodrigo Velázquez-Moctezuma, Mansun Law, Jens Bukh, Jannick Prentoe
Hepatitis C virus (HCV) is a major cause of end-stage liver diseases. With 3-4 million new HCV infections yearly, a vaccine is urgently needed. A better understanding of virus escape from neutralizing antibodies and their corresponding epitopes are important for this effort. However, for viral isolates with high antibody resistance, or antibodies with moderate potency, it remains challenging to induce escape mutations in vitro. Here, as proof-of-concept, we used antibody-sensitive HVR1-deleted (ΔHVR1) viruses to generate escape mutants for a human monoclonal antibody, AR5A, targeting a rare cross-genotype conserved epitope...
February 23, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28231264/precision-engineering-for-prrsv-resistance-in-pigs-macrophages-from-genome-edited-pigs-lacking-cd163-srcr5-domain-are-fully-resistant-to-both-prrsv-genotypes-while-maintaining-biological-function
#5
Christine Burkard, Simon G Lillico, Elizabeth Reid, Ben Jackson, Alan J Mileham, Tahar Ait-Ali, C Bruce A Whitelaw, Alan L Archibald
Porcine Reproductive and Respiratory Syndrome (PRRS) is a panzootic infectious disease of pigs, causing major economic losses to the world-wide pig industry. PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 has been described as a fusion receptor for PRRSV, whereby the scavenger receptor cysteine-rich domain 5 (SRCR5) region was shown to be an interaction site for the virus in vitro...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28231254/rapid-generation-of-drug-resistance-alleles-at-endogenous-loci-using-crispr-cas9-indel-mutagenesis
#6
Jonathan J Ipsaro, Chen Shen, Eri Arai, Yali Xu, Justin B Kinney, Leemor Joshua-Tor, Christopher R Vakoc, Junwei Shi
Genetic alterations conferring resistance to the effects of chemical inhibitors are valuable tools for validating on-target effects in cells. Unfortunately, for many therapeutic targets such alleles are not available. To address this issue, we evaluated whether CRISPR-Cas9-mediated insertion/deletion (indel) mutagenesis can produce drug-resistance alleles at endogenous loci. This method takes advantage of the heterogeneous in-frame alleles produced following Cas9-mediated DNA cleavage, which we show can generate rare alleles that confer resistance to the growth-arrest caused by chemical inhibitors...
2017: PloS One
https://www.readbyqxmd.com/read/28230862/inactivation-of-lsd1-triggers-senescence-in-trophoblast-stem-cells-by-induction-of-sirt4
#7
Josefina Castex, Dominica Willmann, Toufike Kanouni, Laura Arrigoni, Yan Li, Marcel Friedrich, Michael Schleicher, Simon Wöhrle, Mark Pearson, Norbert Kraut, Michaël Méret, Thomas Manke, Eric Metzger, Roland Schüle, Thomas Günther
Coordination of energy metabolism is essential for homeostasis of stem cells, whereas an imbalance in energy homeostasis causes disease and accelerated aging. Here we show that deletion or enzymatic inactivation of lysine-specific demethylase 1 (Lsd1) triggers senescence in trophoblast stem cells (TSCs). Genome-wide transcriptional profiling of TSCs following Lsd1 inhibition shows gene set enrichment of aging and metabolic pathways. Consistently, global metabolomic and phenotypic analyses disclose an unbalanced redox status, decreased glutamine anaplerosis and mitochondrial function...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230630/update-on-the-22q11-2-deletion-syndrome-and-its-relevance-to-schizophrenia
#8
Lily Van, Erik Boot, Anne S Bassett
PURPOSE OF REVIEW: Schizophrenia occurs in ∼25% of individuals with 22q11.2 deletion syndrome (22q11.2DS), the strongest known molecular genetic risk factor for schizophrenia. This review highlights recent literature in 22q11.2DS as it pertains to psychosis and schizophrenia. RECENT FINDINGS: Advances in noninvasive prenatal testing allow for early detection of 22q11.2DS in utero, whereas premature birth has been shown to be a significant risk factor for development of psychotic illness in 22q11...
February 21, 2017: Current Opinion in Psychiatry
https://www.readbyqxmd.com/read/28230321/disruption-of-genes-involved-in-corvet-complex-leads-to-enhanced-secretion-of-heterologous-carboxylesterase-only-in-protease-deficient-pichia-pastoris
#9
Lukas Marsalek, Clemens Gruber, Friedrich Altmann, Markus Aleschko, Diethard Mattanovich, Brigitte Gasser, Verena Puxbaum
The methylotrophic yeast Pichia pastoris (Komagataella spp.) is a popular microbial host for the production of recombinant proteins. Previous studies have shown that mis-sorting to the vacuole can be a bottleneck during production of recombinant secretory proteins in yeast, however, no information was available for P. pastoris. In this work we have therefore generated vps (vacuolar protein sorting) mutant strains disrupted in genes involved in the CORVET tethering complex at the early stages of endosomal sorting...
February 23, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28230282/ablation-of-cyclophilin-d-results-in-an-activation-of-fak-akt-and-erk-pathways-in-the-mouse-heart
#10
Jelena Klawitter, Tamas Seres, Alexander Pennington, Jonathan-Thomas Beatty, Jost Klawitter, Uwe Christians
Cyclophilin D (CypD) is a mitochondrial chaperone that regulates the mitochondrial permeability transition pore. Metabolically, deletion of Ppif (the gene encoding CypD) in mice is associated with elevated levels of mitochondrial matrix Ca(2+) that leads to increased glucose as relative to fatty acid oxidation. Here, we characterized the adaptive mechanisms involved in the regulation of glucose metabolism including the regulation of Akt and ERK kinases that we evaluated by Western blot analysis of Ppif-/-in comparison to wild type (WT) mouse hearts...
February 23, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28230278/deletion-of-psychiatric-risk-gene-cacna1c-impairs-hippocampal-neurogenesis-in-cell-autonomous-fashion
#11
Bianca Völkening, Kai Schönig, Golo Kronenberg, Dusan Bartsch, Tillmann Weber
Ca(2+) is a universal signal transducer which fulfills essential functions in cell development and differentiation. CACNA1C, the gene encoding the alpha-1C subunit (i.e., Cav 1.2) of the voltage-dependent l-type calcium channel (LTCC), has been implicated as a risk gene in a variety of neuropsychiatric disorders. To parse the role of Cav 1.2 channels located on astrocyte-like stem cells and their descendants in the development of new granule neurons, we created Tg(GLAST-CreERT2) /Cacna1c(fl/fl) /RCE:loxP mice, a transgenic tool that allows cell-type-specific inducible deletion of Cacna1c...
February 23, 2017: Glia
https://www.readbyqxmd.com/read/28230109/pentose-sugars-inhibit-metabolism-and-increase-expression-of-an-agrd-type-cyclic-pentapeptide-in-clostridium-thermocellum
#12
Tobin J Verbeke, Richard J Giannone, Dawn M Klingeman, Nancy L Engle, Thomas Rydzak, Adam M Guss, Timothy J Tschaplinski, Steven D Brown, Robert L Hettich, James G Elkins
Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230087/nardilysin-regulates-inflammation-metaplasia-and-tumors-in-murine-stomach
#13
Yuto Kimura, Kozo Ikuta, Takeshi Kimura, Tsutomu Chiba, Hiroko Oshima, Masanobu Oshima, Eiichiro Nishi, Hiroshi Seno
Chronic inflammation contributes to a wide variety of human disorders. In the stomach, longstanding gastritis often results in structural alterations in the gastric mucosa, including metaplastic changes and gastric cancers. Therefore, it is important to elucidate factors that are involved in gastric inflammation. Nardilysin (N-arginine dibasic convertase; Nrdc) is a metalloendopeptidase of the M16 family that promotes ectodomain shedding of the precursor forms of various growth factors and cytokines by enhancing the protease activities of a disintegrin and metalloproteinase (ADAM) proteins...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230051/cellular-senescence-mediates-fibrotic-pulmonary-disease
#14
Marissa J Schafer, Thomas A White, Koji Iijima, Andrew J Haak, Giovanni Ligresti, Elizabeth J Atkinson, Ann L Oberg, Jodie Birch, Hanna Salmonowicz, Yi Zhu, Daniel L Mazula, Robert W Brooks, Heike Fuhrmann-Stroissnigg, Tamar Pirtskhalava, Y S Prakash, Tamara Tchkonia, Paul D Robbins, Marie Christine Aubry, João F Passos, James L Kirkland, Daniel J Tschumperlin, Hirohito Kita, Nathan K LeBrasseur
Idiopathic pulmonary fibrosis (IPF) is a fatal disease characterized by interstitial remodelling, leading to compromised lung function. Cellular senescence markers are detectable within IPF lung tissue and senescent cell deletion rejuvenates pulmonary health in aged mice. Whether and how senescent cells regulate IPF or if their removal may be an efficacious intervention strategy is unknown. Here we demonstrate elevated abundance of senescence biomarkers in IPF lung, with p16 expression increasing with disease severity...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28230015/screening-of-gene-mutations-associated-with-bone-metastasis-in-nonsmall-cell-lung-cancer
#15
Kun Zhang, Min Zhang, Jinlong Zhu, Wang Hong
OBJECTIVE: The objective of this study is to assess the gene mutation of advanced nonsmall cell lung cancer (NSCLC) patients with bone metastasis using next-generation sequencing (NGS), and screen for the driver genes which are associated with bone metastasis of lung cancer. MATERIALS AND METHODS: Eight clinicopathologic samples from advanced NSCLC combined with bone metastasis patients were collected. Exome sequencing was conducted within 483 tumor-associated genes using Hiseq 2000_PE75 NGS platform...
December 2016: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28229935/mice-deficient-in-l-12-15-lipoxygenase-show-increased-vulnerability-to-3-nitropropionic-acid-neurotoxicity
#16
Yan He, Rita C Akumuo, Yuan Yang, Sandra J Hewett
Considerable evidence supports a contributory role for leukocyte-type 12/15 Lipoxygenase (L-12/15 LO) in mediating hippocampal and cortical neuronal injury in models of Alzheimer's disease and stroke. Whether L-12/15 LO contributes to neuronal injury in a model of Huntington's disease (HD) has yet to be determined. HD is characterized by marked striatal neuronal loss, which can be mimicked in humans and animals by inhibition of mitochondrial complex II using 3-Nitropropionic acid (3-NP). Herein, we compared histological and behavioral outcomes between mice that were wild-type or null for L-12/15 LO following systemic injection of 3NP...
February 13, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28229514/mutations-in-genes-encoding-polycomb-repressive-complex-2-subunits-cause-weaver-syndrome
#17
Eri Imagawa, Ken Higashimoto, Yasunari Sakai, Chikahiko Numakura, Nobuhiko Okamoto, Satoko Matsunaga, Akihide Ryo, Yoshinori Sato, Masafumi Sanefuji, Kenji Ihara, Yui Takada, Gen Nishimura, Hirotomo Saitsu, Takeshi Mizuguchi, Satoko Miyatake, Mitsuko Nakashima, Noriko Miyake, Hidenobu Soejima, Naomichi Matsumoto
Weaver syndrome is a rare congenital overgrowth disorder caused by heterozygous mutations in EZH2 (enhancer of zeste homolog 2) or EED (embryonic ectoderm development). EZH2 and EED are core components of the polycomb repressive complex 2 (PRC2), which possesses histone methyltransferase activity and catalyzes trimethylation of histone H3 at lysine 27. Here, we analyzed eight probands with clinically suspected Weaver syndrome by whole exome sequencing and identified three mutations: a 25.4-kb deletion partially involving EZH2 and CUL1 (individual 1), a missense mutation (c...
February 22, 2017: Human Mutation
https://www.readbyqxmd.com/read/28229450/endogenous-nitric-oxide-formation-in-cardiac-myocytes-does-not-control-respiration-during-%C3%AE-adrenergic-stimulation
#18
Michael Kohlhaas, Alexander G Nickel, Stefanie Bergem, Barbara Casadei, Ulrich Laufs, Christoph Maack
Endothelial nitric oxide (NO) controls cardiac oxygen (O2 ) consumption in a paracrine way by slowing respiration at the mitochondrial electron transport chain. While NO synthases (NOS) are also expressed in cardiac myocytes, it is unclear whether they control respiration in an intracrine way. Furthermore, the existence of a mitochondrial NOS is controversial. Here, by combining fluorescence imaging with electrical field stimulation, the patch-clamp method and knock-out technology, we determined the sources and consequences of intracellular NO formation during workload transitions in isolated murine and guinea pig cardiac myocytes and mitochondria...
February 22, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28229309/nusinersen-first-global-approval
#19
Sheridan M Hoy
Spinal muscular atrophy (SMA) is a rare autosomal recessive disorder characterized by muscle atrophy and weakness resulting from motor neuron degeneration in the spinal cord and brainstem. It is most commonly caused by insufficient levels of survival motor neuron (SMN) protein (which is critical for motor neuron maintenance) secondary to deletions or mutations in the SMN1 gene. Nusinersen (SPINRAZA™) is a modified antisense oligonucleotide that binds to a specific sequence in the intron, downstream of exon 7 on the pre-messenger ribonucleic acid (pre-mRNA) of the SMN2 gene...
February 22, 2017: Drugs
https://www.readbyqxmd.com/read/28229087/modeling-williams-syndrome-with-induced-pluripotent-stem-cells
#20
Thanathom Chailangkarn, Alysson R Muotri
The development of induced pluripotent stem cells (iPSCs) like never before has opened novel opportunity to study diseases in relevant cell types. In our recent study, Williams syndrome (WS), a rare genetic neurodevelopmental disorder, that is caused by hemizygous deletion of 25-28 genes on chromosome 7, is of interest because of its unique cognitive and social profiles. Little is known about haploinsufficiency effect of those deleted genes on molecular and cellular phenotypes at the neural level due to the lack of relevant human cellular model...
2017: Neurogenesis (Austin, Tex.)
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