Variability in the Degree of Expression of Phosphorylated I B in Chronic
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A Genome-Wide Association Study of a Coronary Artery Disease Risk Variant
Journal of Human Genetics (2013) 58, 120–126 & 2013 The Japan Society of Human Genetics All rights reserved 1434-5161/13 www.nature.com/jhg ORIGINAL ARTICLE A genome-wide association study of a coronary artery diseaseriskvariant Ji-Young Lee1,16, Bok-Soo Lee2,16, Dong-Jik Shin3,16, Kyung Woo Park4,16, Young-Ah Shin1, Kwang Joong Kim1, Lyong Heo1, Ji Young Lee1, Yun Kyoung Kim1, Young Jin Kim1, Chang Bum Hong1, Sang-Hak Lee3, Dankyu Yoon5, Hyo Jung Ku2, Il-Young Oh4, Bong-Jo Kim1, Juyoung Lee1, Seon-Joo Park1, Jimin Kim1, Hye-kyung Kawk1, Jong-Eun Lee6, Hye-kyung Park1, Jae-Eun Lee1, Hye-young Nam1, Hyun-young Park7, Chol Shin8, Mitsuhiro Yokota9, Hiroyuki Asano10, Masahiro Nakatochi11, Tatsuaki Matsubara12, Hidetoshi Kitajima13, Ken Yamamoto13, Hyung-Lae Kim14, Bok-Ghee Han1, Myeong-Chan Cho15, Yangsoo Jang3,17, Hyo-Soo Kim4,17, Jeong Euy Park2,17 and Jong-Young Lee1,17 Although over 30 common genetic susceptibility loci have been identified to be independently associated with coronary artery disease (CAD) risk through genome-wide association studies (GWAS), genetic risk variants reported to date explain only a small fraction of heritability. To identify novel susceptibility variants for CAD and confirm those previously identified in European population, GWAS and a replication study were performed in the Koreans and Japanese. In the discovery stage, we genotyped 2123 cases and 3591 controls with 521 786 SNPs using the Affymetrix SNP Array 6.0 chips in Korean. In the replication, direct genotyping was performed using 3052 cases and 4976 controls from the KItaNagoya Genome study of Japan with 14 selected SNPs. -
KLF2 Induced
UvA-DARE (Digital Academic Repository) The transcription factor KLF2 in vascular biology Boon, R.A. Publication date 2008 Link to publication Citation for published version (APA): Boon, R. A. (2008). The transcription factor KLF2 in vascular biology. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:23 Sep 2021 Supplementary data: Genes induced by KLF2 Dekker et al. LocusLink Accession Gene Sequence Description Fold p-value ID number symbol change (FDR) 6654 AK022099 SOS1 cDNA FLJ12037 fis, clone HEMBB1001921. 100.00 5.9E-09 56999 AF086069 ADAMTS9 full length insert cDNA clone YZ35C05. 100.00 1.2E-09 6672 AF085934 SP100 full length insert cDNA clone YR57D07. 100.00 6.7E-13 9031 AF132602 BAZ1B Williams Syndrome critical region WS25 mRNA, partial sequence. -
Kids First Pediatric Research Program (Kids First) Poster Session at ASHG Accelerating Pediatric Genomics Research Through Collaboration October 15Th, 2019
The Gabriella Miller Kids First Pediatric Research Program (Kids First) Poster Session at ASHG Accelerating Pediatric Genomics Research through Collaboration October 15th, 2019 Background The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans- NIH Common Fund program initiated in response to the 2014 Gabriella Miller Kids First Research Act. The program’s vision is to alleviate suffering from childhood cancer and structural birth defects by fostering collaborative research to uncover the etiology of these diseases and support data sharing within the pediatric research community. This is implemented through developing the Gabriella Miller Kids First Data Resource (Kids First Data Resource) and populating this resource with whole genome sequence datasets and associated clinical and phenotypic information. Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. Purpose During this evening poster session, attendees will gain a broad understanding of the utility of the genomic data generated by Kids First, learn about the progress of Kids First X01 cohort projects, and observe demonstrations of the tools and functionalities of the recently launched Kids First Data Resource Portal. The session is an opportunity for the scientific community and public to engage with Kids First investigators, collaborators, and a growing community of researchers, patient foundations, and families. Several other NIH and external data efforts will present posters and be available to discuss collaboration opportunities as we work together to accelerate pediatric research. -
2007-05 TLE1 Synovial Sarcoma
TLE1 Immunostains in the Diagnosis of Synovial Sarcoma May 2007 by Rodney T. Miller, M.D., Director of Immunohistochemistry The diagnosis of synovial sarcoma can be a chal- lenging task, particularly on small biopsy specimens, as the morphologic features of this tumor can be mimicked by a variety of other neoplasms. This month we call attention to a paper published in the February 2007 edition of the American Journal of Surgical Pathology describing the utility of immu- nostains for TLE1 in the diagnosis of this tumor. TLE immunostains are now available at ProPath. Synovial sarcoma occurs in three morphologic varie- ties: monophasic, biphasic, and poorly differentiated. It has been known for some time that synovial sar- coma is associated with a specific chromosomal H&E (left) and TLE1 immunostain (right) on a monophasic translocation, t(X;18), that results in the fusion of the synovial sarcoma. Note the numerous strongly positive nuclei SYT gene on chromosome 18 to either the SSX1 or on the TLE1 immunostain, a typical feature of this tumor. SSX2 gene on the X chromosome, resulting in the production of a SYT-SSX fusion protein. Identifica- In their study, the authors performed TLE1 immu- tion of this translocation in the appropriate setting is nostains on multiple tissue microarrays using two dif- regarded by many to be diagnostic of synovial sar- ferent antibodies (monoclonal and polyclonal), both coma. However, the methodologies used for this performing in a similar fashion. A total of 693 adult purpose (cytogenetics, fluorescent in situ hybridiza- soft tissue tumors were examined, including 94 cases tion, and reverse-transcriptase polymerase chain re- of synovial sarcoma that had documentation of the t action) are not readily available in many diagnostic (X;18) translocation. -
Structural Basis for the Regulatory Interactions of Proapoptotic Par-4
Cell Death and Differentiation (2017) 24, 1540–1547 Official journal of the Cell Death Differentiation Association OPEN www.nature.com/cdd Structural basis for the regulatory interactions of proapoptotic Par-4 Udaya K Tiruttani Subhramanyam1,2, Jan Kubicek2,3, Ulf B Eidhoff2 and Joerg Labahn*,1,2 Par-4 is a unique proapoptotic protein with the ability to induce apoptosis selectively in cancer cells. The X-ray crystal structure of the C-terminal domain of Par-4 (Par-4CC), which regulates its apoptotic function, was obtained by MAD phasing. Par-4 homodimerizes by forming a parallel coiled-coil structure. The N-terminal half of Par-4CC contains the homodimerization subdomain. This structure includes a nuclear export signal (Par-4NES) sequence, which is masked upon dimerization indicating a potential mechanism for nuclear localization. The heteromeric-interaction models specifically showed that charge interaction is an important factor in the stability of heteromers of the C-terminal leucine zipper subdomain of Par-4 (Par-4LZ). These heteromer models also displayed NES masking capacity and therefore the ability to influence intracellular localization. Cell Death and Differentiation (2017) 24, 1540–1547; doi:10.1038/cdd.2017.76; published online 16 June 2017 Par-4 is a 332 amino-acid proapoptotic protein with tumor mainly shown to mediates the interaction with partner proteins suppressor activity. Par-4 had been predicted to be largely such as PKCζ,15 WT1,16 Akt1,13 apoptosis antagonizing disordered.1 Its downregulation or non-functional state -
Chromatin-Associated Degradation Is Defined by UBXN-3/FAF1 To
ARTICLE Received 27 Jul 2015 | Accepted 5 Jan 2016 | Published 4 Feb 2016 DOI: 10.1038/ncomms10612 OPEN Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression Andre´ Franz1, Paul A. Pirson1, Domenic Pilger1,2, Swagata Halder2, Divya Achuthankutty2, Hamid Kashkar3, Kristijan Ramadan2 & Thorsten Hoppe1 The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin- associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. 1 Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany. 2 Department of Oncology, University of Oxford, Cancer Research UK/Medical Research Council Oxford, Institute for Radiation Oncology, Old Road Campus Research Building, OX3 7DQ Oxford, UK. -
NLRP2 and FAF1 Deficiency Blocks Early Embryogenesis in the Mouse
REPRODUCTIONRESEARCH NLRP2 and FAF1 deficiency blocks early embryogenesis in the mouse Hui Peng1,*, Haijun Liu2,*, Fang Liu1, Yuyun Gao1, Jing Chen1, Jianchao Huo1, Jinglin Han1, Tianfang Xiao1 and Wenchang Zhang1 1College of Animal Science, Fujian Agriculture and Forestry University, Fujian, Fuzhou, People’s Republic of China and 2Tianjin Institute of Animal Science and Veterinary Medicine, Tianjin, People’s Republic of China Correspondence should be addressed to W Zhang; Email: [email protected] *(H Peng and H Liu contributed equally to this work) Abstract Nlrp2 is a maternal effect gene specifically expressed by mouse ovaries; deletion of this gene from zygotes is known to result in early embryonic arrest. In the present study, we identified FAF1 protein as a specific binding partner of the NLRP2 protein in both mouse oocytes and preimplantation embryos. In addition to early embryos, both Faf1 mRNA and protein were detected in multiple tissues. NLRP2 and FAF1 proteins were co-localized to both the cytoplasm and nucleus during the development of oocytes and preimplantation embryos. Co-immunoprecipitation assays were used to confirm the specific interaction between NLRP2 and FAF1 proteins. Knockdown of the Nlrp2 or Faf1 gene in zygotes interfered with the formation of a NLRP2–FAF1 complex and led to developmental arrest during early embryogenesis. We therefore conclude that NLRP2 interacts with FAF1 under normal physiological conditions and that this interaction is probably essential for the successful development of cleavage-stage mouse embryos. Our data therefore indicated a potential role for NLRP2 in regulating early embryo development in the mouse. Reproduction (2017) 154 245–251 Introduction (Peng et al. -
Genome Sequences of Tropheus Moorii and Petrochromis Trewavasae, Two Eco‑Morphologically Divergent Cichlid Fshes Endemic to Lake Tanganyika C
www.nature.com/scientificreports OPEN Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco‑morphologically divergent cichlid fshes endemic to Lake Tanganyika C. Fischer1,2, S. Koblmüller1, C. Börger1, G. Michelitsch3, S. Trajanoski3, C. Schlötterer4, C. Guelly3, G. G. Thallinger2,5* & C. Sturmbauer1,5* With more than 1000 species, East African cichlid fshes represent the fastest and most species‑rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversifcation. We add high‑quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so‑called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecifc), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecifc). GO enrichment analysis of gene regions afected by variants revealed several candidates which may infuence phenotype modifcations related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families. -
Characterizing Novel Interactions of Transcriptional Repressor Proteins BCL6 & BCL6B
Characterizing Novel Interactions of Transcriptional Repressor Proteins BCL6 & BCL6B by Geoffrey Graham Lundell-Smith A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Biochemistry University of Toronto © Copyright by Geoffrey Lundell-Smith, 2017 Characterizing Novel Interactions of Transcriptional Repression Proteins BCL6 and BCL6B Geoffrey Graham Lundell-Smith Masters of Science Department of Biochemistry University of Toronto 2016 Abstract B-cell Lymphoma 6 (BCL6) and its close homolog BCL6B encode proteins that are members of the BTB-Zinc Finger family of transcription factors. BCL6 plays an important role in regulating the differentiation and proliferation of B-cells during the adaptive immune response, and is also involved in T cell development and inflammation. BCL6 acts by repressing genes involved in DNA damage response during the affinity maturation of immunoglobulins, and the mis- expression of BCL6 can lead to diffuse large B-cell lymphoma. Although BCL6B shares high sequence similarity with BCL6, the functions of BCL6B are not well-characterized. I used BioID, an in vivo proximity-dependent labeling method, to identify novel BCL6 and BCL6B protein interactors and validated a number of these interactions with co-purification experiments. I also examined the evolutionary relationship between BCL6 and BCL6B and identified conserved residues in an important interaction interface that mediates corepressor binding and gene repression. ii Acknowledgments Thank you to my supervisor, Gil Privé for his mentorship, guidance, and advice, and for giving me the opportunity to work in his lab. Thanks to my committee members, Dr. John Rubinstein and Dr. Jeff Lee for their ideas, thoughts, and feedback during my Masters. -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
Hes6 Inhibits Astrocyte Differentiation and Promotes Neurogenesis Through Different Mechanisms
The Journal of Neuroscience, October 25, 2006 • 26(43):11061–11071 • 11061 Cellular/Molecular Hes6 Inhibits Astrocyte Differentiation and Promotes Neurogenesis through Different Mechanisms Sumit Jhas, Sorana Ciura,* Stephanie Belanger-Jasmin,* Zhifeng Dong, Estelle Llamosas, Francesca M. Theriault, Kerline Joachim, Yeman Tang, Lauren Liu, Jisheng Liu, and Stefano Stifani Center for Neuronal Survival, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada H3A 2B4 The mechanisms regulating the generation of cell diversity in the mammalian cerebral cortex are beginning to be elucidated. In that regard, Hairy/Enhancer of split (Hes) 1 and 5 are basic helix-loop-helix (bHLH) factors that inhibit the differentiation of pluripotent cortical progenitors into neurons. In contrast, a related Hes family member termed Hes6 promotes neurogenesis. It is shown here that knockdown of endogenous Hes6 causes supernumerary cortical progenitors to differentiate into cells that exhibit an astrocytic morphol- ogy and express the astrocyte marker protein GFAP. Conversely, exogenous Hes6 expression in cortical progenitors inhibits astrocyte differentiation. The negative effect of Hes6 on astrocyte differentiation is independent of its ability to promote neuronal differentiation. We also show that neither its proneuronal nor its anti-gliogenic functions appear to depend on Hes6 ability to bind to DNA via the basic arm of its bHLH domain. Both of these activities require Hes6 to be localized to nuclei, but only its anti-gliogenic function depends on two short peptides, LNHLL and WRPW, that are conserved in all Hes6 proteins. These findings suggest that Hes6 is an important regulator of the neurogenic phase of cortical development by promoting the neuronal fate while suppressing astrocyte differentiation.