DOCSLIB.ORG

Wo2019/135816

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

( (51) International Patent Classification: GOPADHYAY, Soumyashree Ashok [US/US]; c/o 75 A61K 48/00 (2006.01) Francis Street, Boston, Massachusetts 021 15 (US). (21) International Application Number: (74) Agent: RUTLEDGE, Rachel D. et al.; Johnson, Marcou & PCT/US20 18/057 182 Isaacs, LLC, P. O .Box 691, Floschton, Georgia 30548 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 23 October 2018 (23. 10.2018) kind of national protection av ailable) . AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, (25) Filing Language: English CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, (26) Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (30) Priority Data: KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, 62/575,948 23 October 2017 (23. 10.2017) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 62/765,347 20 August 2018 (20.08.2018) US OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (71) Applicants: THE BROAD INSTITUTE, INC. [US/US]; SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 415 Main Street, Cambridge, Massachusetts 02142 (US). TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. THE BRIGHAM AND WOMEN'S HOSPITAL, INC. (84) Designated States (unless otherwise indicated, for every [US/US]; 75 Francis Street, Boston, Massachusetts 021 15 kind of regional protection available) . ARIPO (BW, GH, (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (72) Inventors; and UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (71) Applicants: CHOUDHARY, Amit [US/US]; c/o 75 Fran¬ TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, cis Street, Boston, Massachusetts 021 15 (US). LIM, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Donghyun [US/US]; c/o 415 Main Street, Cambridge, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, Massachusetts 02142 (US). COX, Kurt [US/US]; c/o 415 TR), OAPI (BF, BJ, CF, CG, Cl, CM, GA, GN, GQ, GW, Main Street, Cambridge, Massachusetts 02142 (US). GAN- KM, ML, MR, NE, SN, TD, TG). (54) Title: NOVEL NUCLEIC ACID MODIFIERS HDR NHEJ activator inhibitor FIG. 1 (57) Abstract: The present inventions generally relate to site-specific delivery of nucleic acid modifiers and includes novel DNA- binding proteins and effectors that can be rapidly programmed to make site-specific DNA modifications. The present inventions also provide a synthetic all-in-one genome editor (SAGE) systems comprising designer DNA sequence readers and a set of small molecules that induce double-strand breaks, enhance cellular permeability, inhibit NHEJ and activate HDR, as well as methods of using and delivering such systems. [Continued on next page] ||| ||||| ||||| ||||| |||| 11| ||| ||||| ||||| ||||| ||||| ||||| |||| limn nil nil nil Published: without international search report and to be republished upon receipt of that report (Rule 48.2(g)) with sequence listing part of description (Rule 5.2(a)) NOVEL NUCLEIC ACID MODIFIERS CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No. 62/575,948, filed October 23, 2017, and U.S. Provisional Application No. 62/765,347 filed August 20, 2018. The entire contents of the above-identified applications are hereby fully incorporated herein by reference. STATEMENT AS TO FEDERALLY FUNDED RESEARCH [0002] This invention was made with government support under contract number N66001-17- 2-4055 awarded by the Defense Advanced Research Projects Agency, Grant No. W91 1NF1610586 awarded by the Army Research Office, and Grant No. AI126239 awarded by the National Institutes of Health. The government has certain rights in the invention. REFERENCE TO AN ELECTRONIC SEQUENCE LISTING [0003] The contents of the electronic sequence listing (BROD-2770WP.ST25.txt”; Size is 4 Kilobytes and it was created on October 23, 2018) is herein incorporated by reference in its entirety. TECHNICAL FIELD [0004] The present inventions generally relate to nucleic acid modifiers with novel DNA readers and effectors that can be rapidly programmed to make site-specific DNA modifications. Among other aspects, the DNA readers provide features of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), CRISPR proteins (e.g., Cas, Cas9, Cpfl, C2cl, Casl3 and the like), CRISPR-Cas or CRISPR systems or CRISPR-Cas complexes, components thereof, peptide nucleic acid (PNA), nucleic acid molecules, vectors, involving the same and uses of all of the foregoing. BACKGROUND [0005] Of the three elements of central dogma (Proteins, RNA, and DNA), nearly all therapeutic agents target proteins. Genome and RNA editing have ushered in an era where DNA and RNA can be potential targets, expanding the scope of therapeutic targets to both the coding and non-coding regions of the genome. However, the agents used to accomplish genome editing do not display attributes of a typical therapeutic agent, and in many cases, the activity of these agents are described as genome vandalism rather than genome editing. As such, there is much room to expand the repertoire of genome editors. [0006] There is an urgent need to develop countermeasures that will rectify any accidental or malevolent genomic alterations in an organism or population. Currently, such genomic alterations can be corrected using CRISPR-nucleases. Following induction of double-strand breaks by the nuclease, most cells adopt Non-Homologous End Joining (NHEJ) repair pathway over Homology Directed Repair (HDR), resulting in random insertions and deletions (indels). The in vivo applications face additional challenges. This state-of-art of genomic remediation method is unsuitable for countermeasures for multiples reasons. First, HDR pathways are poorly activated in most cells and nearly always out-competed by non-homologous end joining (NHEJ) resulting in imprecise, error-prone, and uncontrolled genetic alterations. Second, efficient cellular delivery of CRISPR-nucleases requires the development of paradigm shifting delivery technologies that are currently unavailable. Third, owing to delivery issues, multiplex genomic remediation on a scale to match the genomic diversity present in a population is not feasible. Fourth, CRISPR-based systems are sensitive to proteases/nucleases, limiting their use in multiple countermeasure scenarios (e.g., ecosystem setting). Fifth, the slow kinetics of CRISPR-system will be problematic from a countermeasure perspective, where often fast genomic remediation is desired. Sixth, the components of the CRISPR-system (i.e., a large protein and RNA) potentially will be difficult and expensive to mass-produce. [0007] CRISPR-Cas9 from S. pyogenes was evolved for rapid and efficient destruction of phage DNA but lacks the functionalities needed for precision genome edits. Following a double-strand break in a knock-in experiment, an exogenously supplied single-stranded oligo donor (ssODN) is integrated at the break site. This integration can be facilitated if the ssODN is readily available at the break site. Further, local inhibition of the NHEJ pathway and/or local activation of HDR at the strand-break site can also tip the balance in favor of DNA recombination. Several small- molecule inhibitors of NHEJ pathway and HDR activators have been reported. However, the mutagenicity and toxicity of genome-wide NHEJ inhibition or HDR activation severely limit the utility of such molecules. There is also a need to improve homology-directed repair (HDR) efficiency. Increased efficiency of repair is highly desirable in disease models and therapies. [0008] Precise genome targeting technologies are needed to enable systematic reverse engineering of causal genetic variations by allowing selective perturbation of individual genetic elements, as well as to advance synthetic biology, biotechnological, and medical applications. There remains a need for new genome engineering technologies. [0009] Citation or identification of any document in this application is not an admission that such document is available as prior art to the present invention. SUMMARY [0010] The present disclosure provides a synthetic all-in-one genome editor (SAGE) comprising designer DNA sequence readers and a set of small molecules that induce double- strand breaks and enhance DNA repair by homology directed repair (HDR). [0011] In one aspect, the disclosure relates to an engineered, non-naturally occurring nucleic acid modifying system, comprising: (a) an engineered, non-naturally occurring CRISPR/Cas protein; (b) a guide nucleic acid, wherein the guide nucleic acid directs sequence specific binding of the CRISPR/Cas protein to a target nucleic acid; and (c) one or more effector components, wherein the one or more effector components facilitate DNA repair by homology directed repair (HDR). [0012] In certain embodiments, the one or more effector components comprise one or more single-stranded oligo donors (ssODNs). In certain embodiments, the one or more effector components comprise one or more NHEJ inhibitors. In certain embodiments, the one or more effector components comprise one or more HDR activators. In certain embodiments, the one or more effector components comprise a single-stranded oligo donor (ssODN), one or more NHEJ inhibitors, and one or more HDR activators. [0013] The CRISPR/Cas protein can be selected from the group consisting of an engineered Cas9, Cpfl, Casl2b, Casl2c, Casl3a, Casl3b, Casl3c, and Casl3d protein. In certain embodiments, the CRISPR/Cas protein is an engineered Cas9 protein. The CRISPR/Cas protein can comprise one or more engineered cysteine amino acids. In a preferred embodiment, the CRISPR/Cas protein is an SpCas9 protein comprising C80S and C574S mutations and one or more mutations selected from the group consisting of M1C, S204C, D435C, E532C, Q674C, Q826C, S867C, E945C, S1025C, E1026C, N1054C, E1068C, S 1116C, K 1153C, E1207C. In certain embodiments, the CRISPR/Cas protein comprises a sortase recognition sequence Leu- Pro-Xxx-Thr-Gly.
Recommended publications
  • C-1027, a Radiomimetic Enediyne Anticancer Drug, Preferentially Targets Hypoxic Cells

    C-1027, a Radiomimetic Enediyne Anticancer Drug, Preferentially Targets Hypoxic Cells

    Research Article C-1027, A Radiomimetic Enediyne Anticancer Drug, Preferentially Targets Hypoxic Cells Terry A. Beerman,1 Loretta S. Gawron,1 Seulkih Shin,1 Ben Shen,2 and Mary M. McHugh1 1Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York;and 2Division of Pharmaceutical Sciences, University of Wisconsin National Cooperative Drug Discovery Group, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin Abstract identified primarily from studies with neocarzinostatin (NCS), a The hypoxic nature of cells within solid tumors limits the holo-form drug, consisting of an apoprotein carrier and an active efficacy of anticancer therapies such as ionizing radiation and chromophore, and was assumed to be representative of all agents conventional radiomimetics because their mechanisms re- in this class (11). The NCS chromophore contains a bicyclic quire oxygen to induce lethal DNA breaks. For example, the enediyne that damages DNA via a Myers-Saito cycloaromatization conventional radiomimetic enediyne neocarzinostatin is 4- reaction, resulting in a 2,6-indacene diradical structure capable of fold less cytotoxic to cells maintained in low oxygen (hypoxic) hydrogen abstractions from deoxyribose (12, 13). Subsequent to compared with normoxic conditions. By contrast, the ene- generation of a sugar radical, reaction with oxygen quickly and diyne C-1027 was nearly 3-fold more cytotoxic to hypoxic than efficiently leads to formation of hydroxyl radicals that induce to normoxic cells. Like other radiomimetics, C-1027 induced DSBs/SSBs at a 1:5 ratio. The more recently discovered holo-form DNA breaks to a lesser extent in cell-free, or cellular hypoxic, enediyne C-1027 (Fig.
  • A Rare Missense Mutation in GJB3 (Cx31g45e) Is Associated with a Unique Cellular Phenotype Resulting in Necrotic Cell Death Easton, J

    A Rare Missense Mutation in GJB3 (Cx31g45e) Is Associated with a Unique Cellular Phenotype Resulting in Necrotic Cell Death Easton, J

    University of Dundee A rare missense mutation in GJB3 (Cx31G45E) is associated with a unique cellular phenotype resulting in necrotic cell death Easton, J. A.; Alboulshi, A. K.; Kamps, M. A. F.; Brouns, G. H.; Broers, M. R.; Coull, B. J.; Oji, V.; van Geel, M.; van Steensel, M. A. M.; Martin, P. E. Published in: Experimental Dermatology DOI: 10.1111/exd.13542 Publication date: 2018 Document Version Peer reviewed version Link to publication in Discovery Research Portal Citation for published version (APA): Easton, J. A., Alboulshi, A. K., Kamps, M. A. F., Brouns, G. H., Broers, M. R., Coull, B. J., ... Martin, P. E. (2018). A rare missense mutation in GJB3 (Cx31G45E) is associated with a unique cellular phenotype resulting in necrotic cell death. Experimental Dermatology. https://doi.org/10.1111/exd.13542 General rights Copyright and moral rights for the publications made accessible in Discovery Research Portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from Discovery Research Portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain. • You may freely distribute the URL identifying the publication in the public portal. Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
  • Supplemental Figure 1. Vimentin

    Supplemental Figure 1. Vimentin

    Double mutant specific genes Transcript gene_assignment Gene Symbol RefSeq FDR Fold- FDR Fold- FDR Fold- ID (single vs. Change (double Change (double Change wt) (single vs. wt) (double vs. single) (double vs. wt) vs. wt) vs. single) 10485013 BC085239 // 1110051M20Rik // RIKEN cDNA 1110051M20 gene // 2 E1 // 228356 /// NM 1110051M20Ri BC085239 0.164013 -1.38517 0.0345128 -2.24228 0.154535 -1.61877 k 10358717 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 /// BC 1700025G04Rik NM_197990 0.142593 -1.37878 0.0212926 -3.13385 0.093068 -2.27291 10358713 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 1700025G04Rik NM_197990 0.0655213 -1.71563 0.0222468 -2.32498 0.166843 -1.35517 10481312 NM_027283 // 1700026L06Rik // RIKEN cDNA 1700026L06 gene // 2 A3 // 69987 /// EN 1700026L06Rik NM_027283 0.0503754 -1.46385 0.0140999 -2.19537 0.0825609 -1.49972 10351465 BC150846 // 1700084C01Rik // RIKEN cDNA 1700084C01 gene // 1 H3 // 78465 /// NM_ 1700084C01Rik BC150846 0.107391 -1.5916 0.0385418 -2.05801 0.295457 -1.29305 10569654 AK007416 // 1810010D01Rik // RIKEN cDNA 1810010D01 gene // 7 F5 // 381935 /// XR 1810010D01Rik AK007416 0.145576 1.69432 0.0476957 2.51662 0.288571 1.48533 10508883 NM_001083916 // 1810019J16Rik // RIKEN cDNA 1810019J16 gene // 4 D2.3 // 69073 / 1810019J16Rik NM_001083916 0.0533206 1.57139 0.0145433 2.56417 0.0836674 1.63179 10585282 ENSMUST00000050829 // 2010007H06Rik // RIKEN cDNA 2010007H06 gene // --- // 6984 2010007H06Rik ENSMUST00000050829 0.129914 -1.71998 0.0434862 -2.51672
  • Viewed Under 23 (B) Or 203 (C) fi M M Male Cko Mice, and Largely Unaffected Magni Cation; Scale Bars, 500 M (B) and 50 M (C)

    Viewed Under 23 (B) Or 203 (C) fi M M Male Cko Mice, and Largely Unaffected Magni Cation; Scale Bars, 500 M (B) and 50 M (C)

    BRIEF COMMUNICATION www.jasn.org Renal Fanconi Syndrome and Hypophosphatemic Rickets in the Absence of Xenotropic and Polytropic Retroviral Receptor in the Nephron Camille Ansermet,* Matthias B. Moor,* Gabriel Centeno,* Muriel Auberson,* † † ‡ Dorothy Zhang Hu, Roland Baron, Svetlana Nikolaeva,* Barbara Haenzi,* | Natalya Katanaeva,* Ivan Gautschi,* Vladimir Katanaev,*§ Samuel Rotman, Robert Koesters,¶ †† Laurent Schild,* Sylvain Pradervand,** Olivier Bonny,* and Dmitri Firsov* BRIEF COMMUNICATION *Department of Pharmacology and Toxicology and **Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland; †Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts; ‡Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia; §School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia; |Services of Pathology and ††Nephrology, Department of Medicine, University Hospital of Lausanne, Lausanne, Switzerland; and ¶Université Pierre et Marie Curie, Paris, France ABSTRACT Tight control of extracellular and intracellular inorganic phosphate (Pi) levels is crit- leaves.4 Most recently, Legati et al. have ical to most biochemical and physiologic processes. Urinary Pi is freely filtered at the shown an association between genetic kidney glomerulus and is reabsorbed in the renal tubule by the action of the apical polymorphisms in Xpr1 and primary fa- sodium-dependent phosphate transporters, NaPi-IIa/NaPi-IIc/Pit2. However, the milial brain calcification disorder.5 How- molecular identity of the protein(s) participating in the basolateral Pi efflux remains ever, the role of XPR1 in the maintenance unknown. Evidence has suggested that xenotropic and polytropic retroviral recep- of Pi homeostasis remains unknown. Here, tor 1 (XPR1) might be involved in this process. Here, we show that conditional in- we addressed this issue in mice deficient for activation of Xpr1 in the renal tubule in mice resulted in impaired renal Pi Xpr1 in the nephron.
  • Nrf2 Modulates Host Defense During Streptococcus Pneumoniae Pneumonia in Mice

    Nrf2 Modulates Host Defense During Streptococcus Pneumoniae Pneumonia in Mice

    Nrf2 Modulates Host Defense during Streptococcus pneumoniae Pneumonia in Mice This information is current as John C. Gomez, Hong Dang, Jessica R. Martin and Claire of September 28, 2021. M. Doerschuk J Immunol published online 26 August 2016 http://www.jimmunol.org/content/early/2016/08/26/jimmun ol.1600043 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2016/08/26/jimmunol.160004 Material 3.DCSupplemental http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 28, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published August 26, 2016, doi:10.4049/jimmunol.1600043 The Journal of Immunology Nrf2 Modulates Host Defense during Streptococcus pneumoniae Pneumonia in Mice John C. Gomez,*,† Hong Dang,†,‡ Jessica R. Martin,*,† and Claire M. Doerschuk*,†,x Nrf2 regulates the transcriptional response to oxidative stress. These studies tested the role of Nrf2 during Streptococcus pneumoniae pneumonia and identified Nrf2-dependent genes and pathways in lung tissue and in recruited neutrophils.
  • Enediynes, Enyneallenes, Their Reactions, and Beyond

    Enediynes, Enyneallenes, Their Reactions, and Beyond

    Advanced Review Enediynes, enyne-allenes, their reactions, and beyond Elfi Kraka∗ and Dieter Cremer Enediynes undergo a Bergman cyclization reaction to form the labile 1,4-didehy- drobenzene (p-benzyne) biradical. The energetics of this reaction and the related Schreiner–Pascal reaction as well as that of the Myers–Saito and Schmittel reac- tions of enyne-allenes are discussed on the basis of a variety of quantum chemical and available experimental results. The computational investigation of enediynes has been beneficial for both experimentalists and theoreticians because it has led to new synthetic challenges and new computational methodologies. The accurate description of biradicals has been one of the results of this mutual fertilization. Other results have been the computer-assisted drug design of new antitumor antibiotics based on the biological activity of natural enediynes, the investigation of hetero- and metallo-enediynes, the use of enediynes in chemical synthesis and C materials science, or an understanding of catalyzed enediyne reactions. " 2013 John Wiley & Sons, Ltd. How to cite this article: WIREs Comput Mol Sci 2013. doi: 10.1002/wcms.1174 INTRODUCTION symmetry-allowed pericyclic reactions, (ii) aromatic- ity as a driving force for chemical reactions, and (iii) review on the enediynes is necessarily an ac- the investigation of labile intermediates with biradical count of intense and successful interdisciplinary A character. The henceforth called Bergman cyclization interactions of very different fields in chemistry provided deeper insight into the electronic structure involving among others organic chemistry, matrix of biradical intermediates, the mechanism of organic isolation spectroscopy, quantum chemistry, biochem- reactions, and orbital symmetry rules.
  • GJA4/Connexin 37 Mutations Correlate with Secondary Lymphedema Following Surgery in Breast Cancer Patients

    GJA4/Connexin 37 Mutations Correlate with Secondary Lymphedema Following Surgery in Breast Cancer Patients

    biomedicines Article GJA4/Connexin 37 Mutations Correlate with Secondary Lymphedema Following Surgery in Breast Cancer Patients Mahrooyeh Hadizadeh 1,2, Seiied Mojtaba Mohaddes Ardebili 1, Mansoor Salehi 2, Chris Young 3, Fariborz Mokarian 4, James McClellan 5, Qin Xu 6, Mohammad Kazemi 2, Elham Moazam 4, Behzad Mahaki 7 ID and Maziar Ashrafian Bonab 8,* 1 Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614766, Iran; [email protected] (M.H.); [email protected] (S.M.M.A.) 2 Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan 81746753461, Iran; [email protected] (M.S.); [email protected] (M.K.) 3 School of Allied Health Sciences, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK; [email protected] 4 Cancer Prevention Research Centre, Isfahan University of Medical Sciences, Isfahan 8184917911, Iran; [email protected] (F.M.); [email protected] (E.M.) 5 School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK; [email protected] 6 School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK; [email protected] 7 Department of Occupational Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran; [email protected] 8 Department of Biological Sciences, University of Chester, Chester CH1 4BJ, UK * Correspondence: [email protected]; Tel.: +44-(0)1244-513-056 Received: 31 December 2017; Accepted: 13 February 2018; Published: 22 February 2018 Abstract: Lymphedema is a condition resulting from mutations in various genes essential for lymphatic development and function, which leads to obstruction of the lymphatic system.
  • Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells

    Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells

    Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897
  • Oup Radres Rrz001 289..297 ++

    Oup Radres Rrz001 289..297 ++

    Journal of Radiation Research, Vol. 60, No. 3, 2019, pp. 289–297 doi: 10.1093/jrr/rrz001 Advance Access Publication: 26 February 2019 Ionizing radiation affects the composition of the proteome of extracellular vesicles released by head-and-neck cancer cells in vitro Agata Abramowicz1, Anna Wojakowska1, Lukasz Marczak2, Malgorzata Lysek-Gladysinska3, Mateusz Smolarz1, Michael D. Story4, Joanna Polanska5, Piotr Widlak1 and Monika Pietrowska1,* 1Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska–Curie Institute–Oncology Center, Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44-101 Gliwice, Poland 2Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznan, Poland 3The Jan Kochanowski University in Kielce, Institute of Biology, Department of Cell Biology and Electron Microscopy, ul. Swietokrzyska 15, 25-406 Kielce, Poland 4University of Texas Southwestern Medical Center, Department of Radiation Oncology, Division of Molecular Radiation Biology, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA 5Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland *Corresponding author. Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska–Curie Institute–Oncology Center, Gliwice Branch, ul. Wybrzeze Armii Krajowej 15, 44-101 Gliwice, Poland. Tel: +0048-32-278-9627; Fax: +0048-32-278-9840; Email: [email protected] (Received 29 August 2018; revised 7 November 2018; editorial decision 8 January 2019) ABSTRACT Exosomes and other extracellular vesicles are key players in cell-to-cell communication, and it has been proposed that they are involved in different aspects of the response to ionizing radiation, including transmitting the radiation-induced bystander effect and mediating radioresistance.
  • Anti-GJA4 / Connexin 37 Antibody (ARG58815)

    Anti-GJA4 / Connexin 37 Antibody (ARG58815)

    Product datasheet [email protected] ARG58815 Package: 50 μg anti-GJA4 / Connexin 37 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes GJA4 / Connexin 37 Tested Reactivity Hu, Ms, Rat Predict Reactivity Hm Tested Application ICC, IHC-Fr, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name GJA4 / Connexin 37 Species Human Immunogen Synthetic peptide corresponding to aa. 3-17 of Human Connexin 37 (DWGFLEKLLDQVQEH). Conjugation Un-conjugated Alternate Names Connexin-37; Gap junction alpha-4 protein; CX37; Cx37 Application Instructions Application table Application Dilution ICC 0.5 - 1 µg/ml IHC-Fr 1:200 - 1:1000 WB 0.1 - 0.5 µg/ml Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Properties Form Liquid Purification Affinity purification with immunogen. Buffer 0.9% NaCl, 0.2% Na2HPO4, 0.05% Thimerosal, 0.05% Sodium azide and 5% BSA. Preservative 0.05% Thimerosal and 0.05% Sodium azide Stabilizer 5% BSA Concentration 0.5 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/3 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol GJA4 Gene Full Name gap junction protein, alpha 4, 37kDa Background This gene encodes a member of the connexin gene family.
  • Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives

    Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives

    Journal of Heredity 2007:98(2):115–122 ª The American Genetic Association. 2007. All rights reserved. doi:10.1093/jhered/esl064 For permissions, please email: [email protected]. Advance Access publication January 5, 2007 Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives BRET A. PAYSEUR AND MICHAEL PLACE From the Laboratory of Genetics, University of Wisconsin, Madison, WI 53706. Address correspondence to the author at the address above, or e-mail: [email protected]. Abstract Identification of the genes that underlie reproductive isolation provides important insights into the process of speciation. According to the Dobzhansky–Muller model, these genes suffer disrupted interactions in hybrids due to independent di- vergence in separate populations. In hybrid populations, natural selection acts to remove the deleterious heterospecific com- binations that cause these functional disruptions. When selection is strong, this process can maintain multilocus associations, primarily between conspecific alleles, providing a signature that can be used to locate incompatibilities. We applied this logic to populations of house mice that were formed by hybridization involving two species that show partial reproductive isolation, Mus domesticus and Mus musculus. Using molecular markers likely to be informative about species ancestry, we scanned the genomes of 1) classical inbred strains and 2) recombinant inbred lines for pairs of loci that showed extreme linkage disequi- libria. By using the same set of markers, we identified a list of locus pairs that displayed similar patterns in both scans. These genomic regions may contain genes that contribute to reproductive isolation between M. domesticus and M.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.