(12) United States Patent (10) Patent No.: US 9,677,067 B2 Toro Et Al

Total Page:16

File Type:pdf, Size:1020Kb

(12) United States Patent (10) Patent No.: US 9,677,067 B2 Toro Et Al USOO9677067B2 (12) United States Patent (10) Patent No.: US 9,677,067 B2 Toro et al. (45) Date of Patent: Jun. 13, 2017 (54) COMPOSITIONS AND METHODS FOR (58) Field of Classification Search SYNTHETIC GENE ASSEMBLY None See application file for complete search history. (71) Applicant: TWIST BIOSCIENCE CORPORATION, San Francisco, CA (US) (56) References Cited (72) Inventors: Esteban Toro, Fremont, CA (US); U.S. PATENT DOCUMENTS Sebastian Treusch, San Francisco, CA 3,549,368 A 12/1970 Robert et al. (US): Siyuan Chen, San Mateo, CA 3,920,714 A 11, 1975 Streck (US); Cheng-Hsien Wu, Burlingame, 4,123,661 A 10, 1978 Wolf et al. 4.415,732 A 11/1983 Caruthers et al. CA (US) 4,613,398 A 9/1986 Chiong et al. (73) Assignee: TWIST BIOSCIENCE 4,726,877 A 2/1988 Fryd et al. CORPORATION, San Francisco, CA (Continued) (US) FOREIGN PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this EP OO90789 A1 10, 1983 patent is extended or adjusted under 35 EP O126621 B1 8, 1990 U.S.C. 154(b) by 0 days. (Continued) (21) Appl. No.: 15/154.879 OTHER PUBLICATIONS (22) Filed: May 13, 2016 Abudayyeh et al., C2c2 is a single-component programmable RNA guided RNA-targeting CRISPR effector. Science, available on line, (65) Prior Publication Data Jun. 13, 2016, at: http://zlab.mit.edu/assets/reprints Abudayyeh US 2016/0264958 A1 Sep. 15, 2016 OO Science 2016.pdf, 17 pages. (Continued) Related U.S. Application Data (63) Continuation of application No. Primary Examiner — Kaijiang Zhang PCT/US2016/016636, filed on Feb. 4, 2016. (74) Attorney, Agent, or Firm — Wilson Sonsini Goodrich (60) Provisional application No. 62/112,022, filed on Feb. & Rosati 4, 2015. (51) Int. Cl. (57) ABSTRACT CI2N IS/10 (2006.01) Methods and compositions are provided for assembly of CI2N 5/66 (2006.01) large nucleic acids where the assembled large nucleic acids CI2P 19/34 (2006.01) lack internal sequence modifications made during the assem (52) U.S. Cl. bly process. CPC ..... CI2N 15/1031 (2013.01); CI2N 15/1027 (2013.01); C12N 15/66 (2013.01); C12P 19/34 (2013.01) 25 Claims, 12 Drawing Sheets -: 88s. 3 : 53 s.33333333&&EE& US 9,677,067 B2 Page 2 (56) References Cited 6,251,588 6, 2001 Shannon et al. 6,251,595 6, 2001 Gordon et al. U.S. PATENT DOCUMENTS 6,251,685 6, 2001 Dorsel et al. 6,258.454 T/2001 Lefkowitz et al. 4,808,511 2, 1989 Holmes 6,262.490 T/2001 Hsu et al. 4,837.401 6, 1989 Hirose et al. 6,284.465 9, 2001 Wolber 4,863,557 9, 1989 Kokaku et al. 6,287,776 9, 2001 Hefti 4,981,797 1, 1991 Jessee et al. 6,297,017 10, 2001 Schmidt et al. 4,988,617 1, 1991 Landegren et al. 6,300,137 10, 2001 Earhart et al. 5,102,797 4, 1992 Tucker et al. 6,306,599 10, 2001 Perbost 5,137,814 8, 1992 Rashtchian et al. 6,309,822 10, 2001 Fodor et al. 5,143,854 9, 1992 Pirrung et al. 6,309,828 10, 2001 Schleifer et al. 5,242,794 9, 1993 Whiteley et al. 6,319,674 11/2001 Fulcrand et al. 5,242.974 9, 1993 Holmes 6,323,043 11/2001 Caren et al. 5,288,514 2, 1994 Ellman 6,329,210 12, 2001 Schleifer 5,299.491 4, 1994 Kawada 6,346,423 2, 2002 Schembri 5,384.261 1, 1995 Winkler et al. 6,365,355 4, 2002 McCutchen-Maloney 5,387,541 2, 1995 Hodge et al. 6,372.483 4, 2002 Schleifer et al. 5,395,753 3, 1995 Prakash 6,375,903 4, 2002 Cerrina et al. 5.431,720 7, 1995 Nagai et al. 6,376,285 4, 2002 Joyner et al. 5,445,934 8, 1995 Fodor et al. 6,384.210 5/2002 Blanchard 5.449,754 9, 1995 Nishioka 6,387,636 5/2002 Perbost et al. 5,459,039 10, 1995 Modrich et al. 6,399,394 6, 2002 Dahm et al. 5,474,796 12, 1995 Brennan 6,399,516 6, 2002 Ayon 5,476,930 12, 1995 Letsinger et al. 6,403,314 6, 2002 Lange et al. 5.487,993 1, 1996 Herrnstadt et al. 6,406,849 6, 2002 Dorsel et al. 5,494,810 2, 1996 Barany et al. 6,406,851 6, 2002 Bass 5,501,893 3, 1996 Laermer et al. 6,419,883 T/2002 Blanchard 5,508,169 4, 1996 Deugau et al. 6.428,957 8, 2002 Delenstarr 5,510,270 4, 1996 Fodor et al. 6,440,669 8, 2002 Bass et al. 5,514,789 5, 1996 Kempe 6,444,268 9, 2002 Lefkowitz et al. 5,527,681 6, 1996 Holmes 6,446,642 9, 2002 Caren et al. 5,530,516 6, 1996 Sheets 6,446,682 9, 2002 Viken 5,556,750 9, 1996 Modrich et al. 6,451,998 9, 2002 Perbost 5,586.211 12, 1996 Dumitrou et al. 6,458.526 10, 2002 Schembri et al. 5,641,658 6, 1997 Adams et al. 6,458,583 10, 2002 Bruhn et al. 5,677, 195 10, 1997 Winkler et al. 6,461,812 10, 2002 Barth et al. 5,679,522 10, 1997 Modrich et al. 6,461,816 10, 2002 Wolber et al. 5,700,637 12, 1997 Southern 6,469,156 10, 2002 Schafer et al. 5,700,642 12, 1997 Monforte et al. 6,518,056 2, 2003 Schembri et al. 5,702,894 12, 1997 Modrich et al. 6,521,427 2, 2003 Evans 5,707,806 1, 1998 Shuber 6,521,453 2, 2003 Crameri et al. 5,712,124 1, 1998 Walker 6,558,908 5/2003 Wolber et al. 5,739,386 4, 1998 Holmes 6,566,495 5/2003 Fodor et al. 5,750,672 5, 1998 Kempe 6,582,908 6, 2003 Fodor et al. 5,780,613 7, 1998 Letsinger et al. 6,582,938 6, 2003 Su et al. 5,830,655 11, 1998 Monforte et al. 6,586.211 T/2003 Staehler et al. 5,834,252 11, 1998 Stemmer et al. 6,587,579 T/2003 Bass 5,843,767 12, 1998 Beattie 6,589,739 T/2003 Fisher 5,858,754 1, 1999 Modrich et al. 6,599,693 T/2003 Webb 5,861,482 1, 1999 Modrich et al. 6,602,472 8, 2003 Zimmermann et al. 5,869,245 2, 1999 Yeung 6,610,978 8, 2003 Yin et al. 5,877,280 3, 1999 Wetmur 6,613,513 9, 2003 Parce et al. 5,882,496 3, 1999 Northrup et al. 6,613,523 9, 2003 Fischer 5,922,539 7, 1999 Modrich et al. 6,613,560 9, 2003 Tso et al. 5,922,593 7, 1999 Livingston 6,613,893 9, 2003 Webb 5,928,907 7, 1999 Woudenberg et al. 6,621,076 9, 2003 van de Goor et al. 6,008,031 12, 1999 Modrich et al. 6,630,581 10, 2003 Dellinger et al. 6,015,674 1, 2000 Woudenberg et al. 6,632,641 10, 2003 Brennan et al. 6,027,898 2, 2000 Gjerde et al. 6,635,226 10, 2003 Tso et al. 6,028, 189 2, 2000 Blanchard 6,649,348 11/2003 Bass et al. 6,028, 198 2, 2000 Liu et al. 6,660,338 12, 2003 Hargreaves 6,040,138 3, 2000 Lockhart et al. 6,664,112 12, 2003 Mulligan et al. 6,077,674 6, 2000 Schleifer et al. 6,670,127 12, 2003 Evans 6,103,474 8, 2000 Dellinger et al. 6,670.461 12, 2003 Wengel et al. 6,107,038 8, 2000 Choudhary et al. 6,673,552 1, 2004 Frey 6,110,682 8, 2000 Dellinger et al. 6,682,702 1, 2004 Barth et al. 6,114,115 9, 2000 Wagner, Jr. 6,689,319 2, 2004 Fisher et al. 6,132,997 10, 2000 Shannon 6,702.256 3, 2004 Killeen et al. 6,136,568 10, 2000 Hiatt et al. 6,706,875 3, 2004 Goldberg et al. 6,171,797 1, 2001 Perbost 6,709,852 3, 2004 Bloom et al. 6,180,351 1, 2001 Cattell 6,709,854 3, 2004 Donahue et al. 6,201,112 3, 2001 Ach 6,713,262 3, 2004 Gillibolian et al. 6,218,118 4, 2001 Sampson et al. 6,716,629 4, 2004 Hess et al. 6,221,653 4, 2001 Caren et al. 6,716,634 4, 2004 Myerson 6,222,030 4, 2001 Dellinger et al. 6,723,509 4, 2004 Ach 6,232,072 5, 2001 Fisher 6,743,585 6, 2004 Dellinger et al. 6,235,483 5, 2001 Wolber et al. 6,753,145 6, 2004 Holcomb et al. 6,242.266 6, 2001 Schleifer et al. 6,770,748 8, 2004 Imanishi et al. US 9,677,067 B2 Page 3 (56) References Cited 7,128,876 B2 10, 2006 Yin et al. 7,129,075 B2 10, 2006 Gerard et al. U.S. PATENT DOCUMENTS 7,135,565 B2 11/2006 Dellinger et al. 7,138,062 B2 11/2006 Yin et al. 6,770,892 B2 8, 2004 Corson et al. 7,141,368 B2 11/2006 Fisher et al. 6,773,676 B2 8, 2004 Schembri 7,141,807 B2 11/2006 Joyce et al.
Recommended publications
  • Anti-TERF2 / Trf2 Antibody (ARG59099)
    Product datasheet [email protected] ARG59099 Package: 50 μg anti-TERF2 / Trf2 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes TERF2 / Trf2 Tested Reactivity Hu, Rat Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name TERF2 / Trf2 Antigen Species Human Immunogen Recombinant protein corresponding to A81-K287 of Human TERF2 / Trf2. Conjugation Un-conjugated Alternate Names Telomeric DNA-binding protein; TRF2; TTAGGG repeat-binding factor 2; TRBF2; Telomeric repeat- binding factor 2 Application Instructions Application table Application Dilution IHC-P 0.5 - 1 µg/ml WB 0.1 - 0.5 µg/ml Application Note IHC-P: Antigen Retrieval: By heat mediation. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 60 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer 0.9% NaCl, 0.2% Na2HPO4, 0.05% Sodium azide and 5% BSA. Preservative 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 TERF2 Gene Full Name telomeric repeat binding factor 2 Background This gene encodes a telomere specific protein, TERF2, which is a component of the telomere nucleoprotein complex.
    [Show full text]
  • Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways
    biomolecules Article Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways Aayushi Srivastava 1,2,3,4 , Abhishek Kumar 1,5,6 , Sara Giangiobbe 1, Elena Bonora 7, Kari Hemminki 1, Asta Försti 1,2,3 and Obul Reddy Bandapalli 1,2,3,* 1 Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; [email protected] (A.S.); [email protected] (A.K.); [email protected] (S.G.); [email protected] (K.H.); [email protected] (A.F.) 2 Hopp Children’s Cancer Center (KiTZ), D-69120 Heidelberg, Germany 3 Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany 4 Medical Faculty, Heidelberg University, D-69120 Heidelberg, Germany 5 Institute of Bioinformatics, International Technology Park, Bangalore 560066, India 6 Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India 7 S.Orsola-Malphigi Hospital, Unit of Medical Genetics, 40138 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +49-6221-42-1709 Received: 29 August 2019; Accepted: 10 October 2019; Published: 13 October 2019 Abstract: Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family.
    [Show full text]
  • SUPPLEMENTARY APPENDIX a Homozygous Missense Variant in UBE2T Is Associated with a Mild Fanconi Anemia Phenotype
    SUPPLEMENTARY APPENDIX A homozygous missense variant in UBE2T is associated with a mild Fanconi anemia phenotype Laura Schultz-Rogers, 1* Francis P. Lach, 2* Kimberly A. Rickman, 2 Alejandro Ferrer, 1 Abhishek A. Mangaonkar, 3 Tanya L. Schwab, 4 Christo - pher T. Schmitz, 4 Karl J. Clark, 4 Nikita R. Dsouza, 5 Michael T. Zimmermann, 5,6 Mark Litzow, 3 Nicole Jacobi, 7 Eric W. Klee, 1,8 Agata Smogorzewska 2# and Mrinal M. Patnaik 3# 1Center for Individualized Medicine, Mayo Clinic, Rochester, MN; 2Laboratory of Genome Maintenance, The Rockefeller University, New York, NY; 3De - partment of Hematology, Mayo Clinic, Rochester, MN; 4Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN; 5Bioinformatics Re - search and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI; 6Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI; 7Department of Hematology Oncology, Hennepin County Medical Center, Min - neapolis, MN and 8Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA *LS-R and FPL contributed equally as co-first authors. #EWK, AS and MMP contributed equally as co-senior authors. Correspondence: MRINAL PATNAIK - [email protected] AGATA SMOGORZEWSKA - [email protected] doi:10.3324/haematol.2020.259275 Supplemental Information Homozygous missense variant in UBE2T is associated with mild Fanconi anemia phenotype Laura Schultz-Rogers1*, Francis P. Lach2*, Kimberly A. Rickman2, Alejandro Ferrer1,
    [Show full text]
  • Differential Expression Profile Analysis of DNA Damage Repair Genes in CD133+/CD133‑ Colorectal Cancer Cells
    ONCOLOGY LETTERS 14: 2359-2368, 2017 Differential expression profile analysis of DNA damage repair genes in CD133+/CD133‑ colorectal cancer cells YUHONG LU1*, XIN ZHOU2*, QINGLIANG ZENG2, DAISHUN LIU3 and CHANGWU YUE3 1College of Basic Medicine, Zunyi Medical University, Zunyi; 2Deparment of Gastroenterological Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi;3 Zunyi Key Laboratory of Genetic Diagnosis and Targeted Drug Therapy, The First People's Hospital of Zunyi, Zunyi, Guizhou 563003, P.R. China Received July 20, 2015; Accepted January 6, 2017 DOI: 10.3892/ol.2017.6415 Abstract. The present study examined differential expression cells. By contrast, 6 genes were downregulated and none levels of DNA damage repair genes in COLO 205 colorectal were upregulated in the CD133+ cells compared with the cancer cells, with the aim of identifying novel biomarkers for COLO 205 cells. These findings suggest that CD133+ cells the molecular diagnosis and treatment of colorectal cancer. may possess the same DNA repair capacity as COLO 205 COLO 205-derived cell spheres were cultured in serum-free cells. Heterogeneity in the expression profile of DNA damage medium supplemented with cell factors, and CD133+/CD133- repair genes was observed in COLO 205 cells, and COLO cells were subsequently sorted using an indirect CD133 205-derived CD133- cells and CD133+ cells may therefore microbead kit. In vitro differentiation and tumorigenicity assays provide a reference for molecular diagnosis, therapeutic target in BABA/c nude mice were performed to determine whether selection and determination of the treatment and prognosis for the CD133+ cells also possessed stem cell characteristics, in colorectal cancer.
    [Show full text]
  • Anti-TERF2 / Trf2 Antibody (ARG59098)
    Product datasheet [email protected] ARG59098 Package: 100 μl anti-TERF2 / Trf2 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes TERF2 / Trf2 Tested Reactivity Hu, Ms Tested Application WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name TERF2 / Trf2 Antigen Species Human Immunogen Recombinant protein of Human TERF2 / Trf2. Conjugation Un-conjugated Alternate Names Telomeric DNA-binding protein; TRF2; TTAGGG repeat-binding factor 2; TRBF2; Telomeric repeat- binding factor 2 Application Instructions Application table Application Dilution WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Jurkat Calculated Mw 60 kDa Observed Size 70kDa Properties Form Liquid Purification Affinity purified. Buffer PBS (pH 7.3), 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol 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. 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. Note For laboratory research only, not for drug, diagnostic or other use. www.arigobio.com 1/2 Bioinformation Gene Symbol TERF2 Gene Full Name telomeric repeat binding factor 2 Background This gene encodes a telomere specific protein, TERF2, which is a component of the telomere nucleoprotein complex. This protein is present at telomeres in metaphase of the cell cycle, is a second negative regulator of telomere length and plays a key role in the protective activity of telomeres.
    [Show full text]
  • A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family
    Rockefeller University Digital Commons @ RU Student Theses and Dissertations 2018 A High-Throughput Approach to Uncover Novel Roles of APOBEC2, a Functional Orphan of the AID/APOBEC Family Linda Molla Follow this and additional works at: https://digitalcommons.rockefeller.edu/ student_theses_and_dissertations Part of the Life Sciences Commons A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy by Linda Molla June 2018 © Copyright by Linda Molla 2018 A HIGH-THROUGHPUT APPROACH TO UNCOVER NOVEL ROLES OF APOBEC2, A FUNCTIONAL ORPHAN OF THE AID/APOBEC FAMILY Linda Molla, Ph.D. The Rockefeller University 2018 APOBEC2 is a member of the AID/APOBEC cytidine deaminase family of proteins. Unlike most of AID/APOBEC, however, APOBEC2’s function remains elusive. Previous research has implicated APOBEC2 in diverse organisms and cellular processes such as muscle biology (in Mus musculus), regeneration (in Danio rerio), and development (in Xenopus laevis). APOBEC2 has also been implicated in cancer. However the enzymatic activity, substrate or physiological target(s) of APOBEC2 are unknown. For this thesis, I have combined Next Generation Sequencing (NGS) techniques with state-of-the-art molecular biology to determine the physiological targets of APOBEC2. Using a cell culture muscle differentiation system, and RNA sequencing (RNA-Seq) by polyA capture, I demonstrated that unlike the AID/APOBEC family member APOBEC1, APOBEC2 is not an RNA editor. Using the same system combined with enhanced Reduced Representation Bisulfite Sequencing (eRRBS) analyses I showed that, unlike the AID/APOBEC family member AID, APOBEC2 does not act as a 5-methyl-C deaminase.
    [Show full text]
  • Jnsclcase20102 1..5
    J Neurosurg Case Lessons 1(3):CASE20102, 2021 DOI: 10.3171/CASE20102 Bilateral squamosal synostosis: unusual presentation of chromosome 1p12–1p13.3 deletion. Illustrative case Sarut Chaisrisawadisuk, MD, FRCST,1,4 Nithiwat Vatanavicharn, MD,2 Verayuth Praphanphoj, MD,3 Peter J. Anderson, DSc, FRACS,4,5 and Mark H. Moore, MBChB, FRACS4 1Division of Plastic Surgery, Department of Surgery, and 2Division of Medical Genetics, Department of Paediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; 3Medical Genetics Center, Sai Mai District, Bangkok, Thailand; 4Cleft and Craniofacial South Australia, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia; and 5Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia BACKGROUND Squamosal sutures are minor sutures of the human skull. Early isolated fusion of the sutures (squamosal synostosis) is rarely found. OBSERVATIONS The authors report a case of a girl who presented with an abnormal head shape and bilateral squamosal synostosis. Genetic testing revealed a chromosome 1p12–1p13.3 deletion. She has been managed with conservative treatment of the synostosis. She has global developmental delay and multiple anomalies due to the chromosome abnormality. LESSONS Isolated squamosal suture synostosis could be an uncommon feature of chromosome 1p12–1p13.3 deletion. https://thejns.org/doi/abs/10.3171/CASE20102 KEYWORDS cranial sutures; craniosynostosis; chromosome 1p12–1p13.3 deletion The squamosal suture, one of the minor sutures of the human revealed chromosome 46,XX. She was born at 38 weeks of gestation. calvaria, sits between the temporal and parietal bones and extends Her physical examination at 1 year of age showed a widening of both from the pterion, curving around the temporal squama.1 The suture is parietal bones and an open anterior fontanelle.
    [Show full text]
  • Homozygous Missense Variant in UBE2T Is Associated with Mild Fanconi Anemia Phenotype by Laura Schultz-Rogers, Francis P
    Published Ahead of Print on July 9, 2020, as doi:10.3324/haematol.2020.259275. Copyright 2020 Ferrata Storti Foundation. Homozygous missense variant in UBE2T is associated with mild Fanconi anemia phenotype by Laura Schultz-Rogers, Francis P. Lach, Kimberly A. Rickman, Alejandro Ferrer, Abhishek A. Mangaonkar, Tanya L. Schwab, Christopher T. Schmitz, Karl J. Clark, Nikita R. Dsouza, Michael T. Zimmermann, Mark Litzow, Nicole Jacobi, Eric W. Klee, Agata Smogorzewska, and Mrinal M. Patnaik Haematologica 2020 [Epub ahead of print] Citation: Laura Schultz-Rogers, Francis P. Lach, Kimberly A. Rickman, Alejandro Ferrer, Abhishek A. Mangaonkar, Tanya L. Schwab, Christopher T. Schmitz, Karl J. Clark, Nikita R. Dsouza, Michael T. Zimmermann, Mark Litzow, Nicole Jacobi, Eric W. Klee, Agata Smogorzewska, and Mrinal M. Patnaik. Homozygous missense variant in UBE2T is associated with mild Fanconi anemia phenotype. Haematologica. 2020; 105:xxx doi:10.3324/haematol.2020259275 Publisher's Disclaimer. E-publishing ahead of print is increasingly important for the rapid dissemination of science. Haematologica is, therefore, E-publishing PDF files of an early version of manuscripts that have completed a regular peer review and have been accepted for publication. E-publishing of this PDF file has been approved by the authors. After having E-published Ahead of Print, manuscripts will then undergo technical and English editing, typesetting, proof correction and be presented for the authors' final approval; the final version of the manuscript will then appear in print on a regular issue of the journal. All legal disclaimers that apply to the journal also pertain to this production process. LETTER TO THE EDITOR Homozygous missense variant in UBE2T is associated with mild Fanconi anemia phenotype Laura Schultz-Rogers1*, Francis P.
    [Show full text]
  • Differential Mechanisms of Tolerance to Extreme Environmental
    www.nature.com/scientificreports OPEN Diferential mechanisms of tolerance to extreme environmental conditions in tardigrades Dido Carrero*, José G. Pérez-Silva , Víctor Quesada & Carlos López-Otín * Tardigrades, also known as water bears, are small aquatic animals that inhabit marine, fresh water or limno-terrestrial environments. While all tardigrades require surrounding water to grow and reproduce, species living in limno-terrestrial environments (e.g. Ramazzottius varieornatus) are able to undergo almost complete dehydration by entering an arrested state known as anhydrobiosis, which allows them to tolerate ionic radiation, extreme temperatures and intense pressure. Previous studies based on comparison of the genomes of R. varieornatus and Hypsibius dujardini - a less tolerant tardigrade - have pointed to potential mechanisms that may partially contribute to their remarkable ability to resist extreme physical conditions. In this work, we have further annotated the genomes of both tardigrades using a guided approach in search for novel mechanisms underlying the extremotolerance of R. varieornatus. We have found specifc amplifcations of several genes, including MRE11 and XPC, and numerous missense variants exclusive of R. varieornatus in CHEK1, POLK, UNG and TERT, all of them involved in important pathways for DNA repair and telomere maintenance. Taken collectively, these results point to genomic features that may contribute to the enhanced ability to resist extreme environmental conditions shown by R. varieornatus. Tardigrades are small
    [Show full text]
  • Cell Cycle Arrest Through Indirect Transcriptional Repression by P53: I Have a DREAM
    Cell Death and Differentiation (2018) 25, 114–132 Official journal of the Cell Death Differentiation Association OPEN www.nature.com/cdd Review Cell cycle arrest through indirect transcriptional repression by p53: I have a DREAM Kurt Engeland1 Activation of the p53 tumor suppressor can lead to cell cycle arrest. The key mechanism of p53-mediated arrest is transcriptional downregulation of many cell cycle genes. In recent years it has become evident that p53-dependent repression is controlled by the p53–p21–DREAM–E2F/CHR pathway (p53–DREAM pathway). DREAM is a transcriptional repressor that binds to E2F or CHR promoter sites. Gene regulation and deregulation by DREAM shares many mechanistic characteristics with the retinoblastoma pRB tumor suppressor that acts through E2F elements. However, because of its binding to E2F and CHR elements, DREAM regulates a larger set of target genes leading to regulatory functions distinct from pRB/E2F. The p53–DREAM pathway controls more than 250 mostly cell cycle-associated genes. The functional spectrum of these pathway targets spans from the G1 phase to the end of mitosis. Consequently, through downregulating the expression of gene products which are essential for progression through the cell cycle, the p53–DREAM pathway participates in the control of all checkpoints from DNA synthesis to cytokinesis including G1/S, G2/M and spindle assembly checkpoints. Therefore, defects in the p53–DREAM pathway contribute to a general loss of checkpoint control. Furthermore, deregulation of DREAM target genes promotes chromosomal instability and aneuploidy of cancer cells. Also, DREAM regulation is abrogated by the human papilloma virus HPV E7 protein linking the p53–DREAM pathway to carcinogenesis by HPV.Another feature of the pathway is that it downregulates many genes involved in DNA repair and telomere maintenance as well as Fanconi anemia.
    [Show full text]
  • Evidence for PTPN22 R620W Polymorphism As the Sole Common Risk Variant for Rheumatoid Arthritis in the 1P13.2 Region JOSE-EZEQUIEL MARTÍN, BEHROOZ Z
    Evidence for PTPN22 R620W Polymorphism As the Sole Common Risk Variant for Rheumatoid Arthritis in the 1p13.2 Region JOSE-EZEQUIEL MARTÍN, BEHROOZ Z. ALIZADEH, MIGUEL A. GONZÁLEZ-GAY, ALEJANDRO BALSA, DORA PASCUAL-SALCEDO, MARÍA F. GONZÁLEZ-ESCRIBANO, LUIS RODRIGUEZ-RODRIGUEZ, BENJAMÍN FERNÁNDEZ-GUTIÉRREZ, ENRIQUE RAYA, MARIEKE J.H. COENEN, PIET van RIEL, TIMOTHY R.D.J. RADSTAKE, TORE K. KVIEN, MARTE K. VIKEN, BENEDICTE A. LIE, BOBBY P.C. KOELEMAN, and JAVIER MARTÍN ABSTRACT. Objective. The PTPN22 rs2476601 genetic variant has been associated with rheumatoid arthritis (RA) and other autoimmune diseases. Some reports suggest that this single-nucleotide polymorphism (SNP) may not be the only causal variant in the region of PTPN22. Our aim was to identify new independent RA-associated common gene variants in the PTPN22 region. Methods. We analyzed Wellcome Trust Case-Control Consortium genome-wide association study data for associations in the 397.2 kb PTPN22 region and selected 9 associated SNP (with p < 5 × 10–3) for replication and dependence analysis. The replication cohorts comprised 2857 patients with RA and 2994 controls from Spain, Netherlands, and Norway. Results. We found that 6 of the 9 selected SNP were associated in the Spanish cohort. Of these, 4 were also associated in the Dutch and Norwegian cohorts, and all 6 were associated with RA in the combined analysis. Conditional analyses showed that none of these associations was independent of rs2476601. Conclusion. The SNP rs2476601 located in the PTPN22 gene is the sole common genetic variant asso- ciated with RA in the 1p13.2 region, suggesting that neighbor genes of PTPN22 do not have a major influence in RA.
    [Show full text]
  • DCLRE1B (NM 022836) Human Untagged Clone – SC112381
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for SC112381 DCLRE1B (NM_022836) Human Untagged Clone Product data: Product Type: Expression Plasmids Product Name: DCLRE1B (NM_022836) Human Untagged Clone Tag: Tag Free Symbol: DCLRE1B Synonyms: APOLLO; SNM1B; SNMIB Vector: pCMV6-XL4 E. coli Selection: Ampicillin (100 ug/mL) Cell Selection: None This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 DCLRE1B (NM_022836) Human Untagged Clone – SC112381 Fully Sequenced ORF: >OriGene ORF within SC112381 sequence for NM_022836 edited (data generated by NextGen Sequencing) ATGAATGGGGTCCTGATCCCCCATACGCCCATCGCAGTGGACTTCTGGAGCCTGCGCCGG GCTGGCACCGCACGTCTCTTCTTCTTGTCTCACATGCACTCGGACCACACCGTGGGCCTG TCTAGCACCTGGGCCCGGCCCCTCTACTGCTCCCCAATTACAGCCCACCTCTTGCATCGT TACCTACAGGTATCTAAGCAATGGATCCAAGCCCTGGAGGTTGGTGAGAGCCACGTATTA CCCCTAGATGAAATTGGACAAGAGACCATGACCGTAACCCTCCTCGATGCCAATCACTGT CCTGGTTCTGTCATGTTTCTCTTTGAAGGATATTTTGGAACCATCCTCTACACAGGTGAT TTTCGATACACACCATCCATGCTAAAGGAGCCAGCCCTGACACTGGGGAAACAGATCCAT ACTTTATACCTAGACAACACCAATTGCAATCCAGCCCTGGTTCTTCCTTCCCGACAAGAA GCTGCCCACCAGATTGTCCAGCTCATTCGAAAACACCCACAACATAACATAAAGATTGGA CTCTACAGCCTGGGAAAGGAATCACTGCTGGAGCAGCTGGCCCTGGAGTTTCAGACCTGG GTGGTATTGAGTCCTCGGCGCCTGGAGTTGGTACAGCTACTGGGCCTGGCAGATGTGTTC ACAGTGGAGGAGAAGGCTGGCCGCATCCATGCAGTAGACCATATGGAGATCTGCCATTCC
    [Show full text]