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https://www.readbyqxmd.com/read/29449575/actionable-perturbations-of-damage-responses-by-tcl1-atm-and-epigenetic-lesions-form-the-basis-of-t-pll
#1
A Schrader, G Crispatzu, S Oberbeck, P Mayer, S Pützer, J von Jan, E Vasyutina, K Warner, N Weit, N Pflug, T Braun, E I Andersson, B Yadav, A Riabinska, B Maurer, M S Ventura Ferreira, F Beier, J Altmüller, M Lanasa, C D Herling, T Haferlach, S Stilgenbauer, G Hopfinger, M Peifer, T H Brümmendorf, P Nürnberg, K S J Elenitoba-Johnson, S Zha, M Hallek, R Moriggl, H C Reinhardt, M-H Stern, S Mustjoki, S Newrzela, P Frommolt, M Herling
T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. Here we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identify novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor/cytokine signaling, and histone modulation...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29436965/gene-to-gene-network-analysis-of-the-mediation-of-plant-innate-immunity-by-the-eliciting-plant-response-like-1-epl1-elicitor-of-trichoderma-formosa
#2
Chi-Hua Cheng, Bing-Nan Shen, Qian-Wen Shang, Li-Yu Liu, Kou-Cheng Peng, Yan-Huey Chen, Fang-Fang Chen, Sin-Fen Hu, Yu-Tai Wang, Hao-Ching Wang, Hsin-Yi Wu, Chaur-Tsuen Lo, Shih-Shun Lin
A new clade, Trichoderma formosa, secretes eliciting plant response-like 1 (Epl1), a small peptide elicitor that stimulates plant immunity. Nicotiana benthamiana pretreated with Epl1 for three days developed immunity against tomato mosaic virus (ToMV) infection. The transcriptome profiles of T. formosa and N. benthamiana were obtained by deep sequencing; the transcript of Epl1 is 736 nt in length and encodes a 12 kDa peptide. Identifying critical genes in Epl1-mediated immunity was challenging due to the high similarity between the transcriptome expression profiles of Epl1-treated and ToMV-infected N...
February 13, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29434220/the-plant-specific-histone-residue-phe41-is-important-for-genome-wide-h3-1-distribution
#3
Li Lu, Xiangsong Chen, Shuiming Qian, Xuehua Zhong
The dynamic incorporation of histone variants influences chromatin structure and many biological processes. In Arabidopsis, the canonical variant H3.1 differs from H3.3 in four residues, one of which (H3.1Phe41) is unique and conserved in plants. However, its evolutionary significance remains unclear. Here, we show that Phe41 first appeared in H3.1 in ferns and became stable during land plant evolution. Unlike H3.1, which is specifically enriched in silent regions, H3.1F41Y variants gain ectopic accumulation at actively transcribed regions...
February 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29432128/n-terminal-sumoylation-of-centromeric-histone-h3-variant-cse4-regulates-its-proteolysis-to-prevent-mislocalization-to-non-centromeric-chromatin
#4
Kentaro Ohkuni, Reuben Levy-Myers, Jack Warren, Wei-Chun Au, Yoshimitsu Takahashi, Richard E Baker, Munira A Basrai
Stringent regulation of cellular levels of evolutionarily conserved centromeric histone H3 variant (CENP-A in humans, CID in flies, Cse4 in yeast) prevents its mislocalization to non-centromeric chromatin. Overexpression and mislocalization of CENP-A has been observed in cancers and leads to aneuploidy in yeast, flies, and human cells. Ubiquitin-mediated proteolysis of Cse4 by E3 ligases such as Psh1 and Sumo-Targeted Ubiquitin Ligase (STUbL) Slx5 prevent mislocalization of Cse4. Previously, we identified Siz1 and Siz2 as the major E3 ligases for sumoylation of Cse4...
February 5, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29429572/mutations-in-the-baf-complex-subunit-dpf2-are-associated-with-coffin-siris-syndrome
#5
Georgia Vasileiou, Silvia Vergarajauregui, Sabine Endele, Bernt Popp, Christian Büttner, Arif B Ekici, Marion Gerard, Nuria C Bramswig, Beate Albrecht, Jill Clayton-Smith, Jenny Morton, Susan Tomkins, Karen Low, Astrid Weber, Maren Wenzel, Janine Altmüller, Yun Li, Bernd Wollnik, George Hoganson, Maria-Renée Plona, Megan T Cho, Christian T Thiel, Hermann-Josef Lüdecke, Tim M Strom, Eduardo Calpena, Andrew O M Wilkie, Dagmar Wieczorek, Felix B Engel, André Reis
Variants affecting the function of different subunits of the BAF chromatin-remodelling complex lead to various neurodevelopmental syndromes, including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental-delay disorders. Here, we report eight heterozygous de novo variants (one frameshift, two splice site, and five missense) in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2)...
February 5, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29423952/a-splice-site-variant-in-the-suv39h2-gene-in-greyhounds-with-nasal-parakeratosis
#6
A Bauer, J Nimmo, R Newman, M Brunner, M M Welle, V Jagannathan, T Leeb
Hereditary nasal parakeratosis (HNPK), described in the Labrador Retriever breed, is a monogenic autosomal recessive disorder that causes crusts and fissures on the nasal planum of otherwise healthy dogs. Our group previously showed that this genodermatosis may be caused by a missense variant located in the SUV39H2 gene encoding a histone 3 lysine 9 methyltransferase, a chromatin modifying enzyme with a potential role in keratinocyte differentiation. In the present study, we investigated a litter of Greyhounds in which six out of eight puppies were affected with parakeratotic lesions restricted to the nasal planum...
February 9, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29420340/phase-i-trial-of-belinostat-with-cisplatin-and-etoposide-in-advanced-solid-tumors-with-a-focus-on-neuroendocrine-and-small-cell-cancers-of-the-lung
#7
Sanjeeve Balasubramaniam, Christophe E Redon, Cody J Peer, Christine Bryla, Min-Jung Lee, Jane B Trepel, Yusuke Tomita, Arun Rajan, Giuseppe Giaccone, William M Bonner, William D Figg, Tito Fojo, Richard L Piekarz, Susan E Bates
The standard-of-care for advanced small cell lung cancer (SCLC) is chemotherapy with cisplatin+etoposide (C+E). Most patients have chemosensitive disease at the outset, but disease frequently relapses and limits survival. Efforts to improve therapeutic outcomes in SCLC and other neuroendocrine cancers have focused on epigenetic agents, including the histone deacetylase inhibitor belinostat. The primary objective was to determine the maximum tolerated dose of the combination of belinostat (B) with C+E. Belinostat was administered as a 48-h continuous intravenous infusion on days 1-2; cisplatin was administered as a 1-h intravenous infusion on day 2; and etoposide was administered as a 1-h intravenous infusion on days 2, 3, and 4...
February 7, 2018: Anti-cancer Drugs
https://www.readbyqxmd.com/read/29397781/ionizing-radiation-deregulates-the-microrna-expression-profile-in-differentiated-thyroid-cells
#8
Ricardo Cortez Cardoso Penha, Simona Pellecchia, Roberto Pacelli, Luis Felipe Ribeiro Pinto, Alfredo Fusco
BACKGROUND: Ionizing Radiation (IR) is a well-known risk factor for papillary thyroid cancer, and it has been reported to deregulate microRNA expression, which is important to thyroid carcinogenesis. Therefore, we have investigated the impact of IR on microRNA expression profile of the normal thyroid cell line (FRTL-5 CL2) and as well as its effect on radiosensitivity of thyroid cancer cell lines, especially the human anaplastic thyroid carcinoma cell line (8505c). METHODS: The global microRNA expression profile of irradiated FRTL-5 CL2 cells (5 Gy X-ray) was characterized and data were confirmed by qRT-PCR evaluating the expression of rno-miR-10b-5p, rno-miR-33-5p, rno-miR-128-1-5p, rno-miR-199a-3p, rno-miR-296-5p, rno-miR-328a-3p and rno-miR-541-5p in irradiated cells...
February 3, 2018: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29396562/cytochrome-c-oxidase-deficiency-oxidative-stress-possible-antioxidant-therapy-and-link-to-nuclear-dna-damage
#9
Liza Douiev, Bassam Abu-Libdeh, Ann Saada
In response to Ravera et al. "Fanconi anemia: from DNA repair to metabolism" commenting on our recent publication by Abu-Libdeh, Douiev et al., describing a pathogenic variant in the COX 4I1 gene simulating Fanconi anemia, we wish to add supplementary, pertinent information linking cytochrome c oxidase (COX, mitochondrial respiratory chain complex IV) dysfunction to oxidative stress and nuclear DNA damage. Elevated production of reactive oxygen species (ROS) in COX 4I1 deficient fibroblasts was detected in cells grown in glucose free medium and normalized by ascorbate or N-acetylcysteine supplementation...
February 2, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29393482/cooperation-between-ets-variant-2-and-jumonji-domain%C3%A2-containing-2-histone-demethylases
#10
Xiaomeng Li, Gene Moon, Sook Shin, Bin Zhang, Ralf Janknecht
The E26 transformation-specific (ETS) variant 2 (ETV2) protein, also designated as ETS-related 71, is a member of the ETS transcription factor family and is essential for blood and vascular development in the embryo. The role of ETV2 in cancer has not yet been investigated. In the present study, the expression of ETV2 mRNA was identified in a variety of tumor types, including prostate carcinoma. In addition, ETV2 gene amplification was identified in several types of cancer, suggesting that ETV2 plays an oncogenic role in tumorigenesis...
January 26, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29386101/learning-and-age-related-changes-in-genome-wide-h2a-z-binding-in-the-mouse-hippocampus
#11
Gilda Stefanelli, Amber B Azam, Brandon J Walters, Mark A Brimble, Caroline P Gettens, Pascale Bouchard-Cannon, Hai-Ying M Cheng, Andrew M Davidoff, Klotilda Narkaj, Jeremy J Day, Andrew J Kennedy, Iva B Zovkic
Histone variants were recently discovered to regulate neural plasticity, with H2A.Z emerging as a memory suppressor. Using whole-genome sequencing of the mouse hippocampus, we show that basal H2A.Z occupancy is positively associated with steady-state transcription, whereas learning-induced H2A.Z removal is associated with learning-induced gene expression. AAV-mediated H2A.Z depletion enhanced fear memory and resulted in gene-specific alterations of learning-induced transcription, reinforcing the role of H2A...
January 30, 2018: Cell Reports
https://www.readbyqxmd.com/read/29384431/epigenetic-mechanisms-in-health-and-disease-bcec-2017
#12
Albert Jordan, Albert Carbonell, Raquel Fueyo, Andrea Izquierdo-Bouldstridge, Cristina Moreta
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Epigenetic Mechanisms in Health and Disease" was held in Barcelona, October 26-26, 2017. The 2017 BCEC was the fifth and last edition of a series of annual conferences organized as a joint effort of five leading Barcelona research institutes together with B-Debate. This edition was organized by Albert Jordan from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and Marcus Bushbeck from the Josep Carreras Leukaemia Research Institute (IJC)...
January 31, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29383847/growth-pattern-of-rahman-syndrome
#13
Toshiki Takenouchi, Tomoko Uehara, Kenjiro Kosaki, Seiji Mizuno
Recently, in a cohort study with "overgrowth syndrome with intellectual disability," five subjects were reported to have de novo heterozygous truncating variants in HIST1H1E, which encodes linker histone H 1.4. However, their growth pattern appeared complex that four out of five patients had a decreasing height percentile over time, and three of these patients began with above-average heights but exhibited reductions to average heights or below when they were older. Herein, we report a female patient with intellectual disability and distinctive facial features including a wide nasal bridge and prominent cheek bones...
January 31, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29383524/dna-double-strand-breaks-in-blood-lymphocytes-induced-by-two-day-99mtc-mibi-myocardial-perfusion-scintigraphy
#14
Matthias Rief, Lisa Hartmann, Dominik Geisel, Felicitas Richter, Winfried Brenner, Marc Dewey
OBJECTIVES: To investigate DNA double-strand breaks (DSBs) in blood lymphocytes induced by two-day 99mTc-MIBI myocardial perfusion scintigraphy (MPS) using y-H2AX immunofluorescence microscopy and to correlate the results with 99mTc activity in blood samples. METHODS: Eleven patients who underwent two-day MPS were included. DSB blood sampling was performed before and 5min, 1h and 24h after the first and second radiotracer injections. 99mTc activity was measured in each blood sample...
January 30, 2018: European Radiology
https://www.readbyqxmd.com/read/29379197/brd4-interacts-with-nipbl-and-brd4-is-mutated-in-a-cornelia-de-lange-like-syndrome
#15
Gabrielle Olley, Morad Ansari, Hemant Bengani, Graeme R Grimes, James Rhodes, Alex von Kriegsheim, Ana Blatnik, Fiona J Stewart, Emma Wakeling, Nicola Carroll, Alison Ross, Soo-Mi Park, Wendy A Bickmore, Madapura M Pradeepa, David R FitzPatrick
We found that the clinical phenotype associated with BRD4 haploinsufficiency overlapped with that of Cornelia de Lange syndrome (CdLS), which is most often caused by mutation of NIPBL. More typical CdLS was observed with a de novo BRD4 missense variant, which retained the ability to coimmunoprecipitate with NIPBL, but bound poorly to acetylated histones. BRD4 and NIPBL displayed correlated binding at super-enhancers and appeared to co-regulate developmental gene expression.
January 29, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29374629/cross-phenotype-analysis-of-immunochip-data-identifies-kdm4c-as-a-relevant-locus-for-the-development-of-systemic-vasculitis
#16
Lourdes Ortiz-Fernández, Francisco David Carmona, Raquel López-Mejías, Maria Francisca González-Escribano, Paul A Lyons, Ann W Morgan, Amr H Sawalha, Kenneth G C Smith, Miguel A González-Gay, Javier Martín
OBJETIVE: Systemic vasculitides represent a heterogeneous group of rare complex diseases of the blood vessels with a poorly understood aetiology. To investigate the shared genetic component underlying their predisposition, we performed the first cross-phenotype meta-analysis of genetic data from different clinically distinct patterns of vasculitis. METHODS: Immunochip genotyping data from 2465 patients diagnosed with giant cell arteritis, Takayasu's arteritis , antineutrophil cytoplasmic antibody-associated vasculitis or IgA vasculitis as well as 4632 unaffected controls were analysed to identify common susceptibility loci for vasculitis development...
January 27, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29374152/distinct-epigenetic-programs-regulate-cardiac-myocyte-development-and-disease-in-the-human-heart-in-vivo
#17
Ralf Gilsbach, Martin Schwaderer, Sebastian Preissl, Björn A Grüning, David Kranzhöfer, Pedro Schneider, Thomas G Nührenberg, Sonia Mulero-Navarro, Dieter Weichenhan, Christian Braun, Martina Dreßen, Adam R Jacobs, Harald Lahm, Torsten Doenst, Rolf Backofen, Markus Krane, Bruce D Gelb, Lutz Hein
Epigenetic mechanisms and transcription factor networks essential for differentiation of cardiac myocytes have been uncovered. However, reshaping of the epigenome of these terminally differentiated cells during fetal development, postnatal maturation, and in disease remains unknown. Here, we investigate the dynamics of the cardiac myocyte epigenome during development and in chronic heart failure. We find that prenatal development and postnatal maturation are characterized by a cooperation of active CpG methylation and histone marks at cis-regulatory and genic regions to shape the cardiac myocyte transcriptome...
January 26, 2018: Nature Communications
https://www.readbyqxmd.com/read/29360988/chek1-coordinates-dna-damage-signaling-and-meiotic-progression-in-the-male-germline-of-mice
#18
Hironori Abe, Kris G Alavattam, Yasuko Kato, Diego H Castrillon, Qishen Pang, Paul R Andreassen, Satoshi H Namekawa
The continuity of life depends on mechanisms in the germline that ensure the integrity of the genome. The DNA damage response/checkpoint kinases ATM and ATR are essential signaling factors in the germline. However, it remains unknown how a downstream transducer, Checkpoint Kinase 1 (CHEK1 or CHK1), mediates signaling in the male germline. Here, we show that CHEK1 has distinct functions in both the mitotic and meiotic phases of the male germline in mice. In the mitotic phase, CHEK1 is required for the resumption of prospermatogonia proliferation after birth and the maintenance of spermatogonia...
January 17, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29359922/linear-and-differential-ion-mobility-separations-of-middle-down-proteoforms
#19
Alyssa Garabedian, Matthew A Baird, Jacob Porter, Kevin Jeanne Dit Fouque, Pavel Vyacheslavovich Shliaha, Ole Nørregaard Jensen, Todd D Williams, Francisco Fernandez-Lima, Alexandre A Shvartsburg
Comprehensive characterization of proteomes comprising same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass-spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS) relying on the mobility increment at high electric fields, but not previously by linear IMS based on absolute mobility...
January 23, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29358330/histone-variant-h3-3-mediated-chromatin-remodeling-is-essential-for-paternal-genome-activation-in-mouse-preimplantation-embryos
#20
Qingran Kong, Laura A Banaszynski, Fuqiang Geng, Xiaolei Zhang, Jiaming Zhang, Heng Zhang, Claire Liane O'Neill, Peidong Yan, Zhonghua Liu, Koji Shido, Gianpiero D Palermo, C David Allis, Shahin Rafii, Zev Rosenwaks, Duancheng Wen
Derepression of chromatin-mediated transcriptional repression of paternal and maternal genomes is considered the first major step that initiates zygotic gene expression after fertilization. The histone variant H3.3 is present in both male and female gametes and is thought to be important for remodeling the paternal and maternal genomes for activation during both fertilization and embryogenesis. However, the underlying mechanisms remain poorly understood. Using our H3.3B-HA-tagged mouse model, engineered to report H3...
January 22, 2018: Journal of Biological Chemistry
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