Dietary Erythrodiol Modifies Hepatic Transcriptome in Mice in a Sex And
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Accurate Annotation of Human Protein-Coding Small Open Reading Frames
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Chem Manuscript Author Biol. Author Manuscript Author manuscript; available in PMC 2020 June 09. Published in final edited form as: Nat Chem Biol. 2020 April ; 16(4): 458–468. doi:10.1038/s41589-019-0425-0. Accurate annotation of human protein-coding small open reading frames Thomas F. Martinez1,*, Qian Chu1, Cynthia Donaldson1, Dan Tan1, Maxim N. Shokhirev2, Alan Saghatelian1,* 1Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA 2Razavi Newman Integrative Genomics Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California 92037, USA Abstract Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-Seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-Seq into an improved workflow that overcomes obstacles with previous methods to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes. Annotation of open reading frames (ORFs) from genome sequencing was initially carried out by locating in-frame start (AUG) and stop codons1–3. -
Dissecting the Genetic Relationship Between Cardiovascular Risk Factors and Alzheimer's Disease
UC San Diego UC San Diego Previously Published Works Title Dissecting the genetic relationship between cardiovascular risk factors and Alzheimer's disease. Permalink https://escholarship.org/uc/item/7137q6g1 Journal Acta neuropathologica, 137(2) ISSN 0001-6322 Authors Broce, Iris J Tan, Chin Hong Fan, Chun Chieh et al. Publication Date 2019-02-01 DOI 10.1007/s00401-018-1928-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Acta Neuropathologica https://doi.org/10.1007/s00401-018-1928-6 ORIGINAL PAPER Dissecting the genetic relationship between cardiovascular risk factors and Alzheimer’s disease Iris J. Broce1 · Chin Hong Tan1,2 · Chun Chieh Fan3 · Iris Jansen4 · Jeanne E. Savage4 · Aree Witoelar5 · Natalie Wen6 · Christopher P. Hess1 · William P. Dillon1 · Christine M. Glastonbury1 · Maria Glymour7 · Jennifer S. Yokoyama8 · Fanny M. Elahi8 · Gil D. Rabinovici8 · Bruce L. Miller8 · Elizabeth C. Mormino9 · Reisa A. Sperling10,11 · David A. Bennett12 · Linda K. McEvoy13 · James B. Brewer13,14,15 · Howard H. Feldman14 · Bradley T. Hyman10 · Margaret Pericak‑Vance16 · Jonathan L. Haines17,18 · Lindsay A. Farrer19,20,21,22,23 · Richard Mayeux24,25,26 · Gerard D. Schellenberg27 · Kristine Yafe7,8,28 · Leo P. Sugrue1 · Anders M. Dale3,13,14 · Danielle Posthuma4 · Ole A. Andreassen5 · Celeste M. Karch6 · Rahul S. Desikan1 Received: 22 September 2018 / Revised: 28 October 2018 / Accepted: 28 October 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Cardiovascular (CV)- and lifestyle-associated risk factors (RFs) are increasingly recognized as important for Alzheimer’s disease (AD) pathogenesis. Beyond the ε4 allele of apolipoprotein E (APOE), comparatively little is known about whether CV-associated genes also increase risk for AD. -
Funktionelle in Vitro Und in Vivo Charakterisierung Des Putativen Tumorsuppressorgens SFRP1 Im Humanen Mammakarzinom
Funktionelle in vitro und in vivo Charakterisierung des putativen Tumorsuppressorgens SFRP1 im humanen Mammakarzinom Von der Fakult¨at fur¨ Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades einer Doktorin der Naturwissenschaften genehmigte Dissertation vorgelegt von Diplom-Biologin Laura Huth (geb. Franken) aus Julich¨ Berichter: Universit¨atsprofessor Dr. rer. nat. Edgar Dahl Universit¨atsprofessor Dr. rer. nat. Ralph Panstruga Tag der mundlichen¨ Prufung:¨ 6. August 2014 Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verfugbar.¨ Zusammenfassung Krebserkrankungen stellen weltweit eine der h¨aufigsten Todesursachen dar. Aus diesem Grund ist die Aufkl¨arung der zugrunde liegenden Mechanismen und Ur- sachen ein essentielles Ziel der molekularen Onkologie. Die Tumorforschung der letzten Jahre hat gezeigt, dass die Entstehung solider Karzinome ein Mehrstufen- Prozess ist, bei dem neben Onkogenen auch Tumorsuppresorgene eine entschei- dende Rolle spielen. Viele der heute bekannten Gene des WNT-Signalweges wur- den bereits als Onkogene oder Tumorsuppressorgene charakterisiert. Eine Dere- gulation des WNT-Signalweges wird daher mit der Entstehung und Progression vieler humaner Tumorentit¨aten wie beispielsweise auch dem Mammakarzinom, der weltweit h¨aufigsten Krebserkrankung der Frau, assoziiert. SFRP1, ein nega- tiver Regulator der WNT-Signalkaskade, wird in Brusttumoren haupts¨achlich durch den epigenetischen Mechanismus der Promotorhypermethylierung -
Changes of Liver Transcriptome Profiles Following Oxidative Stress in Streptozotocin-Induced Diabetes in Mice
Changes of liver transcriptome profiles following oxidative stress in streptozotocin-induced diabetes in mice Shuren Guo1, Xiaohuan Mao2, Yunmeng Yan1, Yan Zhang1 and Liang Ming1 1 Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China 2 Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou Uni- versity, Zhengzhou, Henan, People's Republic of China ABSTRACT Background. Oxidative-stress (OS) was causal in the development of cell dysfunction and insulin resistance. Streptozotocin (STZ) was an alkylation agent that increased reactive oxygen species (ROS) levels. Here we aimed to explore the oxidative-stress and related RNAs in the liver of STZ-induced diabetic mice. Methods. RNA-sequencing was performed using liver tissues from STZ induced diabetic mice and controls. Pathway and Gene Ontology (GO) analyses were utilized to annotate the target genes. The differentially expressed RNAs involved in the peroxisome pathway were validated by qRT-PCR. The glucose metabolite and OS markers were measured in the normal control (NC) and STZ-induced diabetic mellitus (DM) group. Results. The levels of serum Fasting insulin, HbA1c, Malondialdehyde (MDA) and 8-iso-prostaglandin F2α (8-iso-PGF2α) were significant higher in DM groups than NC group, while SOD activity decreased significantly in DM groups. We found 416 lncRNAs and 910 mRNAs were differentially expressed in the STZ-induced diabetic mice compared to the control group. OS associated RNAs were differentially expressed in the liver of STZ-induced diabetic mice. Conclusion. This study confirmed that the OS was increased in the STZ-induced DM mice as evidenced by the increase of lipid peroxidation product MDA and 8-iso-PGF2α, Submitted 11 November 2019 identified aberrantly expressed lncRNAs and mRNAs in STZ-induced diabetic mice. -
Proquest Dissertations
Modeling Uncertainty in Data Integration for Improving Protein Function Assignment Brenton E. Louie A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2008 Program Authorized to Offer Degree: Medical Education and Biomedical Informatics UMI Number: 3318214 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. ® UMI UMI Microform 3318214 Copyright 2008 by ProQuest LLC. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 E. Eisenhower Parkway PO Box 1346 Ann Arbor, Ml 48106-1346 University of Washington Graduate School This is to certify that I have examined this copy of a doctoral dissertation by Brenton E. Louie and have found that it is complete and satisfactory in all respects, and that any and all revisions required by the final examining committee have been made. Chair of the Supervisory Committee: Peter Tar^zv-Hornocfey- h Reading Committee: &/&L f OMA^J "("fcf^^cM Peter Tarczy-Hornoch Dan Suciu V In presenting this dissertation in partial fulfillment of the requirements for the doctoral degree at the University of Washington, I agree that the Library shall make its copies freely available for inspection. -
Two Locus Inheritance of Non-Syndromic Midline Craniosynostosis Via Rare SMAD6 and 4 Common BMP2 Alleles 5 6 Andrew T
1 2 3 Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and 4 common BMP2 alleles 5 6 Andrew T. Timberlake1-3, Jungmin Choi1,2, Samir Zaidi1,2, Qiongshi Lu4, Carol Nelson- 7 Williams1,2, Eric D. Brooks3, Kaya Bilguvar1,5, Irina Tikhonova5, Shrikant Mane1,5, Jenny F. 8 Yang3, Rajendra Sawh-Martinez3, Sarah Persing3, Elizabeth G. Zellner3, Erin Loring1,2,5, Carolyn 9 Chuang3, Amy Galm6, Peter W. Hashim3, Derek M. Steinbacher3, Michael L. DiLuna7, Charles 10 C. Duncan7, Kevin A. Pelphrey8, Hongyu Zhao4, John A. Persing3, Richard P. Lifton1,2,5,9 11 12 1Department of Genetics, Yale University School of Medicine, New Haven, CT, USA 13 2Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA 14 3Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, CT, USA 15 4Department of Biostatistics, Yale University School of Medicine, New Haven, CT, USA 16 5Yale Center for Genome Analysis, New Haven, CT, USA 17 6Craniosynostosis and Positional Plagiocephaly Support, New York, NY, USA 18 7Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA 19 8Child Study Center, Yale University School of Medicine, New Haven, CT, USA 20 9The Rockefeller University, New York, NY, USA 21 22 ABSTRACT 23 Premature fusion of the cranial sutures (craniosynostosis), affecting 1 in 2,000 24 newborns, is treated surgically in infancy to prevent adverse neurologic outcomes. To 25 identify mutations contributing to common non-syndromic midline (sagittal and metopic) 26 craniosynostosis, we performed exome sequencing of 132 parent-offspring trios and 59 27 additional probands. -
CD56+ T-Cells in Relation to Cytomegalovirus in Healthy Subjects and Kidney Transplant Patients
CD56+ T-cells in Relation to Cytomegalovirus in Healthy Subjects and Kidney Transplant Patients Institute of Infection and Global Health Department of Clinical Infection, Microbiology and Immunology Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Mazen Mohammed Almehmadi December 2014 - 1 - Abstract Human T cells expressing CD56 are capable of tumour cell lysis following activation with interleukin-2 but their role in viral immunity has been less well studied. The work described in this thesis aimed to investigate CD56+ T-cells in relation to cytomegalovirus infection in healthy subjects and kidney transplant patients (KTPs). Proportions of CD56+ T cells were found to be highly significantly increased in healthy cytomegalovirus-seropositive (CMV+) compared to cytomegalovirus-seronegative (CMV-) subjects (8.38% ± 0.33 versus 3.29%± 0.33; P < 0.0001). In donor CMV-/recipient CMV- (D-/R-)- KTPs levels of CD56+ T cells were 1.9% ±0.35 versus 5.42% ±1.01 in D+/R- patients and 5.11% ±0.69 in R+ patients (P 0.0247 and < 0.0001 respectively). CD56+ T cells in both healthy CMV+ subjects and KTPs expressed markers of effector memory- RA T-cells (TEMRA) while in healthy CMV- subjects and D-/R- KTPs the phenotype was predominantly that of naïve T-cells. Other surface markers, CD8, CD4, CD58, CD57, CD94 and NKG2C were expressed by a significantly higher proportion of CD56+ T-cells in healthy CMV+ than CMV- subjects. Functional studies showed levels of pro-inflammatory cytokines IFN-γ and TNF-α, as well as granzyme B and CD107a were significantly higher in CD56+ T-cells from CMV+ than CMV- subjects following stimulation with CMV antigens. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
A Clinicopathological and Molecular Genetic Analysis of Low-Grade Glioma in Adults
A CLINICOPATHOLOGICAL AND MOLECULAR GENETIC ANALYSIS OF LOW-GRADE GLIOMA IN ADULTS Presented by ANUSHREE SINGH MSc A thesis submitted in partial fulfilment of the requirements of the University of Wolverhampton for the degree of Doctor of Philosophy Brain Tumour Research Centre Research Institute in Healthcare Sciences Faculty of Science and Engineering University of Wolverhampton November 2014 i DECLARATION This work or any part thereof has not previously been presented in any form to the University or to any other body whether for the purposes of assessment, publication or for any other purpose (unless otherwise indicated). Save for any express acknowledgments, references and/or bibliographies cited in the work, I confirm that the intellectual content of the work is the result of my own efforts and of no other person. The right of Anushree Singh to be identified as author of this work is asserted in accordance with ss.77 and 78 of the Copyright, Designs and Patents Act 1988. At this date copyright is owned by the author. Signature: Anushree Date: 30th November 2014 ii ABSTRACT The aim of the study was to identify molecular markers that can determine progression of low grade glioma. This was done using various approaches such as IDH1 and IDH2 mutation analysis, MGMT methylation analysis, copy number analysis using array comparative genomic hybridisation and identification of differentially expressed miRNAs using miRNA microarray analysis. IDH1 mutation was present at a frequency of 71% in low grade glioma and was identified as an independent marker for improved OS in a multivariate analysis, which confirms the previous findings in low grade glioma studies. -
Role of the Transcriptional Regulator SP140 in Resistance
RESEARCH ARTICLE Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons Daisy X Ji1†, Kristen C Witt1†, Dmitri I Kotov1,2, Shally R Margolis1, Alexander Louie1, Victoria Cheve´ e1, Katherine J Chen1,2, Moritz M Gaidt1, Harmandeep S Dhaliwal3, Angus Y Lee3, Stephen L Nishimura4, Dario S Zamboni5, Igor Kramnik6, Daniel A Portnoy1,7,8, K Heran Darwin9, Russell E Vance1,2,3* 1Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; 2Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States; 3Cancer Research Laboratory, University of California, Berkeley, Berkeley, United States; 4Department of Pathology, University of California, San Francisco, San Francisco, United States; 5Department of Cell Biology, Ribeira˜ o Preto Medical School, University of Sa˜ o Paulo, Sa˜ o Paulo, Brazil; 6The National Emerging Infectious Diseases Laboratory, Department of Medicine (Pulmonary Center), and Department of Microbiology, Boston University School of Medicine, Boston, United States; 7Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States; 8Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States; 9Department of Microbiology, New York University Grossman School of Medicine, New York, United States *For correspondence: [email protected] Abstract Type I interferons (IFNs) are essential for anti-viral immunity, but often impair †These authors contributed protective immune responses during bacterial infections. An important question is how type I IFNs equally to this work are strongly induced during viral infections, and yet are appropriately restrained during bacterial infections. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
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 .