DOCSLIB.ORG

(12) Patent Application Publication (10) Pub. No.: US 2012/0252869 A1 Collard Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) Patent Application Publication (10) Pub. No.: US 2012/0252869 A1 Collard Et Al US 20120252869A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0252869 A1 Collard et al. (43) Pub. Date: Oct. 4, 2012 (54) TREATMENT OF SIRTUIN (SIRT) RELATED A6IP 25/28 (2006.01) DISEASES BY INHIBITION OF NATURAL A6IP 25/6 (2006.01) ANTISENSE TRANSCRIPT TO A SIRTUN A6IP 9/00 (2006.01) (SIRT) A6IP3/00 (2006.01) A6IP3/10 (2006.01) (75) Inventors: Joseph Collard, Delray Beach, FL A6IP3/04 (2006.01) (US): Olga Khorkova Sherman, A6IP3/06 (2006.01) Tequesta, FL (US) A6IPL/I6 (2006.01) A6IP27/02 (2006.01) (73) Assignee: pro CuRNA, LLC, Miami, FL A6IP 9/109/08 3882006.O1 A6IP 7/00 (2006.01) A6IP35/02 (2006.01) (21) Appl. No.: 13/386,057 A6IP3 L/18 (2006.01) (22) PCT Filed: Jul. 23, 2010 A6IP 9/10 (2006.01) A6IP 9/00 (2006.01) (86). PCT No.: PCT/US 10/43.075 A6IP 2L/00 (2006.01) A6IPL/04 (2006.01) S371 (c)(1), A6IP 9/02 (2006.01) (2), (4) Date: Jan. 20, 2012 A6IPI/00 (2006.01) A6IP 29/00 (2006.01) Related U.S. Application Data A6IP II/00 (2006.01) A6IPI3/00 (2006.01) (63) Continuation-in-part of application No. PCT/US2009/ A6IP 700 (2006.01) 066445, filed on Dec. 2, 2009. A6IP35/00 (2006.01) (60) Provisional application No. 61/259,072, filed on Nov. CI2N 5/071 (2010.01) 6, 2009, provisional application No. 61/228,392, filed (52) U.S. Cl. ....... 514/44. A 435/375; 536/24.5; 3. on Jul. 24, 2009. (57) ABSTRACT Publication Classification The present invention relates to antisense oligonucleotides (51) Int. Cl. that modulate the expression of and/or function of a Sirtuin A6 IK3I/7088 (2006.01) (SIRT), in particular, by targeting natural antisense poly C7H 2L/04 (2006.01) nucleotides of a Sirtuin (SIRT). The invention also relates to C07K 9/00 (2006.01) the identification of these antisense oligonucleotides and their A6 IK 38/14 (2006.01) use in treating diseases and disorders associated with the A6IP 25/00 (2006.01) expression of Sirtuins (SIRT)s. Patent Application Publication Oct. 4, 2012 Sheet 1 of 10 US 2012/O252869 A1 *:::::::::::::::: :38:8;&: 8:::::::: & :::::::::::::::8: 8:8: 8:8:::::::::::::::::::::::::::::::::8:88: 8:::::: six. Patent Application Publication Oct. 4, 2012 Sheet 2 of 10 US 2012/O252869 A1 ex-xx-secrease, : . W.M.W.M.W.W ::::::::::: :::::::::::::::::$88: 8888&:::::::::::::::::::::::::::::::: :3. : & & - s : : 3. Patent Application Publication Oct. 4, 2012 Sheet 3 of 10 US 2012/O252869 A1 x: 8:8:88:38:88: 8::::::::::: Patent Application Publication Oct. 4, 2012 Sheet 4 of 10 US 2012/O252869 A1 *:::::::: 8:883:... 8 Patent Application Publication Oct. 4, 2012 Sheet 5 of 10 US 2012/O252869 A1 Patent Application Publication Oct. 4, 2012 Sheet 6 of 10 US 2012/O252869 A1 ::::::::::: s''WY'':----ass''''------''''''''''''''''''''''''''''''''''''''''MTY''''''''''------MYX'v's 8::::::::::::::::::::::::::::: : 88: 8x8:::::::::::::::: 88. : 3.3 : & Patent Application Publication Oct. 4, 2012 Sheet 7 of 10 US 2012/O252869 A1 :8::::::::::::::::::::::::::::: 8 s:& Patent Application Publication Oct. 4, 2012 Sheet 8 of 10 US 2012/O252869 A1 :::::::::::: Patent Application Publication Oct. 4, 2012 Sheet 9 of 10 US 2012/O252869 A1 8. &::::::::: & 8: Patent Application Publication Oct. 4, 2012 Sheet 10 of 10 US 2012/O252869 A1 US 2012/0252869 A1 Oct. 4, 2012 TREATMENT OF SIRTUIN (SIRT) RELATED otide, for example, nucleotides set forth in SEQID NO: 5 to DISEASES BY INHIBITION OF NATURAL 14, and any variants, alleles, homologs, mutants, derivatives, ANTISENSE TRANSCRIPT TO A SIRTUIN fragments and complementary sequences thereto. Examples (SIRT) of antisense oligonucleotides are set forth as SEQID NOS: 15 to 94. 0007 Another embodiment provides a method of modu 0001. The present application claims the priority of U.S. lating function and/or expression of a Sirtuin (SIRT) poly provisional patent application No. 61/228,392 filed Jul. 24. nucleotide in patient cells or tissues in vivo or in vitro com 2009, U.S. provisional patent application No. 61/259,072, prising contacting said cells or tissues with an antisense filed Nov. 6, 2009, PCT patent application No. PCT/ oligonucleotide 5 to 30 nucleotides in length wherein said US09166445 filed Dec. 2, 2009, PCT patent application No. oligonucleotide has at least 50% sequence identity to a PCT/US10/26119 filed Mar. 3, 2010 and U.S. provisional reverse complement of the an antisense of the Sirtuin (SIRT) patent application No. 61/330.427 filed May 3, 2010. polynucleotide; thereby modulating function and/or expres sion of the Sirtuin (SIRT) polynucleotide in patient cells or FIELD OF TILE INVENTION tissues in viva or in vitro. 0008. Another embodiment provides a method of modu 0002 Embodiments of the invention comprise oligonucle lating function and/or expression of a Sirtuin (SIRT) poly otides modulating expression and/or function of a Sirloin nucleotide in patient cells or tissues in vivo or in vitro com (SERF) and associated molecules. prising contacting said cells or tissues with an antisense oligonucleotide 5 to 30 nucleotides in length wherein said BACKGROUND oligonucleotide has at least 50% sequence identity to an anti 0003 DNA-RNA and RNA-RNA hybridization are sense oligonucleotide to a Sirtuin (SIRT) antisense poly important to many aspects of nucleic acid function including nucleotide; thereby modulating function and/or expression of DNA replication, transcription, and translation. Hybridiza the Sirtuin (SIRT) polynucleotide in patient cells or tissues in tion is also central to a variety of technologies that either vivo or in vitro. detect a particular nucleic acid or alter its expression. Anti 0009. In one embodiment, a composition comprises one or sense nucleotides, for example, disrupt gene expression by more antisense oligonucleotides which bind to sense and/or hybridizing to target RNA, thereby interfering with RNA antisense Sirtuin (SIRT) polynucleotides. splicing, transcription, translation, and replication. Antisense 0010. In another embodiment, the oligonucleotides com DNA has the added feature that DNA-RNA hybrids serve as prise one or more modified or substituted nucleotides. a substrate for digestion by ribonuclease H, an activity that is 0011. In another embodiment, the oligonucleotides com present in most cell types. Antisense molecules can be deliv prise one or more modified bonds. ered into cells, as is the case for oligodeoxynucleotides (0012. In yet another embodiment, the modified nucle (ODNs), or they can be expressed from endogenous genes as otides comprise modified bases comprising phosphorothio RNA molecules. The FDA recently approved an antisense ate, methylphosphonate, peptide nucleic acids. 2'-O-methyl, drug, VITRAVENETM (for treatment of cytomegalovirus fluoro- or carbon, methylene or other locked nucleic acid retinitis), reflecting that antisense has therapeutic utility. (LNA) molecules. Preferably, the modified nucleotides are locked nucleic acid molecules, including C-L-LNA. SUMMARY 0013. In another embodiment, the oligonucleotides are 0004. In one embodiment, the invention provides methods administered to a patient subcutaneously, intramuscularly, for inhibiting the action of a natural antisense transcript by intravenously or intraperitoneally. using antisense oligonucleotide(s) targeted to any region of 0014. In another embodiment, the oligonucleotides are the natural antisense transcript resulting in up-regulation of administered in a pharmaceutical composition. A treatment the corresponding sense gene. It is also contemplated herein regimen comprises administering the antisense compounds at that inhibition of the natural antisense transcript can be least once to patient; however, this treatment can be modified achieved by siRNA, ribozymes and small molecules, which to include multiple doses over a period of time. The treatment are considered to be within the scope of the present invention. can be combined with one or more other types of therapies. 0005. One embodiment provides a method of modulating 0015. In another embodiment, the oligonucleotides are function and/or expression of a Sirtuin (SIRT) polynucleotide encapsulated in a liposome or attached to a carrier molecule in patient cells or tissues in vivo or in vitro comprising con (e.g. cholesterol, TAT peptide). tacting said cells or tissues with an antisense oligonucleotide 10016. Other aspects are described infra. 5 to 30 nucleotides in length wherein said oligonucleotide has at least 50% sequence identity to a reverse complement of a BRIEF DESCRIPTION OF THE DRAWINGS polynucleotide comprising 5 to 30 consecutive nucleotides 0017 FIGS. 1 and 2 show Real time PCR results of oligo within nucleotides 1 to 1028 of SEQID NO: 5 or nucleotides nucleotides designed to SIRT antisense CV396200. The 1 to 429 of SEQID NO: 6, or nucleotides 1 to 156 of SEQID results show that the levels of the SIRT1 mRNA in HepG2 NO: 7 or nucleotides 1 to 593 of SEQID NO:8, 1 to 373 of cells are significantly increased 48 h after treatment with one SEQID NO:9, 1 to 1713 of SEQID NO: 10, 1 to 660 of SEQ of the siRNAs designed to sofas (sirtas 5, P=0.01). In the ID NO: 11, 1 to 589 of SEQID NO: 12, 1 to 428 of SEQID same samples the levels of sirtas RNA were significantly NO: 13 and 1 to 4441 of SEQID NO: 14 thereby modulating decreased after treatment with sirtas 5, but unchanged after function and/or expression of the Sirtuin (SIRT) polynucle treatment with sirtas 6 and sirtas 7, which also had no otide in patient cells or tissues in vivo or in vitro. effect on the SIRT1 mRNA levels (FIG.2).sirtas 5, sirtas 6 0006. In another embodiment, an oligonucleotide targets a and sirtas 7 correspond to SEQ ID NOs: 38, 39 and 40 natural antisense sequence of a Sirtuin (SIRT) polynucle respectively. US 2012/O252869 A1 Oct. 4, 2012 0018 FIG. 3 shows results for the oligonucleotide walk (0027 FIG. 13 is a graph of real time PCR results showing across the SIRT antisense.
Load more

Recommended publications
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
    Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A.
    [Show full text]
  • Supplementary Table 1
    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
    [Show full text]
  • Induction of Therapeutic Tissue Tolerance Foxp3 Expression Is
    Downloaded from http://www.jimmunol.org/ by guest on October 2, 2021 is online at: average * The Journal of Immunology , 13 of which you can access for free at: 2012; 189:3947-3956; Prepublished online 17 from submission to initial decision 4 weeks from acceptance to publication September 2012; doi: 10.4049/jimmunol.1200449 http://www.jimmunol.org/content/189/8/3947 Foxp3 Expression Is Required for the Induction of Therapeutic Tissue Tolerance Frederico S. Regateiro, Ye Chen, Adrian R. Kendal, Robert Hilbrands, Elizabeth Adams, Stephen P. Cobbold, Jianbo Ma, Kristian G. Andersen, Alexander G. Betz, Mindy Zhang, Shruti Madhiwalla, Bruce Roberts, Herman Waldmann, Kathleen F. Nolan and Duncan Howie J Immunol cites 35 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2012/09/17/jimmunol.120044 9.DC1 This article http://www.jimmunol.org/content/189/8/3947.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2012 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of October 2, 2021.
    [Show full text]
  • Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared Amongst Δγ T, Innate Lymphoid, and Th Cells
    Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 δγ is online at: average * The Journal of Immunology , 10 of which you can access for free at: 2016; 197:1460-1470; Prepublished online 6 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600643 http://www.jimmunol.org/content/197/4/1460 Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst T, Innate Lymphoid, and Th Cells You Jeong Lee, Gabriel J. Starrett, Seungeun Thera Lee, Rendong Yang, Christine M. Henzler, Stephen C. Jameson and Kristin A. Hogquist J Immunol cites 41 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2016/07/06/jimmunol.160064 3.DCSupplemental This article http://www.jimmunol.org/content/197/4/1460.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology 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. This information is current as of September 26, 2021. The Journal of Immunology Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst gd T, Innate Lymphoid, and Th Cells You Jeong Lee,* Gabriel J.
    [Show full text]
  • Comparative Analysis of Chicken Chromosome 28 Provides New Clues to the Evolutionary Fragility of Gene-Rich Vertebrate Regions
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions Laurie Gordon,1,2,5 Shan Yang,1,5 Mary Tran-Gyamfi,1,2 Dan Baggott,1 Mari Christensen,1,2 Aaron Hamilton,1 Richard Crooijmans,3 Martien Groenen,3 Susan Lucas,2 Ivan Ovcharenko,2,4 and Lisa Stubbs1,6 1Genome Biology Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA; 2Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 3Wageningen University, Wageningen 6709 PG, The Netherlands; 4Computations Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However, some of the most gene-rich segments are missing from chicken genome draft assemblies, limiting the analysis of a substantial number of genes and preventing a closer look at regions that are especially prone to syntenic rearrangements. To facilitate the functional and evolutionary analysis of one especially gene-rich, rearrangement-prone genomic region, we analyzed sequence from BAC clones spanning chicken microchromosome GGA28; as a complement we also analyzed a gene-sparse, stable region from GGA11. In these two regions we documented the conservation and lineage-specific gain and loss of protein-coding genes and precisely mapped the locations of 31 major human-chicken syntenic breakpoints. Altogether, we identified 72 lineage-specific genes, many of which are found at or near syntenic breaks, implicating evolutionary breakpoint regions as major sites of genetic innovation and change.
    [Show full text]
  • 0Nducing *Nd Suppressing Phe *5Pern*Pive 5Engphening Of
    nducing nd suppressing he ern)ive enghening of eomeres mech)nism in cncer ce0s Dissertation submitted by Delia Braun 2018 Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Dipl.-Chem. Delia Maria Braun born in Offenburg, Germany Oral examination: 24.07.2018 nducing nd suppressing he ern)ive enghening of eomeres mech)nism in cncer ce0s Referees: Prof. Dr. Karsten Rippe Prof. Dr. Brian Luke This work was performed from September 2012 to January 2018 under the supervision of Prof. Dr. Karsten Rippe in the Division Chromatin Networks at the DKFZ and the Bioquant Center in Heidelberg, Germany. Declaration I hereby declare that I have written the submitted dissertation “Inducing and suppressing the alternative lengthening of telomeres mechanism in cancer cells” myself and in this process, have used no other sources or materials than those explicitly indicated. I hereby declare that I have not applied to be examined at any other institution, nor have I used the dissertation in this or any other form at any other institution as an examination paper, nor submitted it to any other faculty as a dissertation. ______________________________ ______________________________ (Place, Date) Delia Braun Für Philipp und Lina Tbe of conens Lis of pubicions .................................................. V Summ)r? ............................................................... V! Zusmmenfssung ................................................
    [Show full text]
  • An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice
    bioRxiv preprint doi: https://doi.org/10.1101/378711; this version posted August 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title: 2 An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice 3 Short Title: 4 Genomic response to selection for longer limbs 5 One-sentence summary: 6 Genome sequencing of mice selected for longer limbs reveals that rapid selection response is 7 due to both discrete loci and polygenic adaptation 8 Authors: 9 João P. L. Castro 1,*, Michelle N. Yancoskie 1,*, Marta Marchini 2, Stefanie Belohlavy 3, Marek 10 Kučka 1, William H. Beluch 1, Ronald Naumann 4, Isabella Skuplik 2, John Cobb 2, Nick H. 11 Barton 3, Campbell Rolian2,†, Yingguang Frank Chan 1,† 12 Affiliations: 13 1. Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany 14 2. University of Calgary, Calgary AB, Canada 15 3. IST Austria, Klosterneuburg, Austria 16 4. Max Planck Institute for Cell Biology and Genetics, Dresden, Germany 17 Corresponding author: 18 Campbell Rolian 19 Yingguang Frank Chan 20 * indicates equal contribution 21 † indicates equal contribution 22 Abstract: 23 Evolutionary studies are often limited by missing data that are critical to understanding the 24 history of selection. Selection experiments, which reproduce rapid evolution under controlled 25 conditions, are excellent tools to study how genomes evolve under strong selection. Here we 1 bioRxiv preprint doi: https://doi.org/10.1101/378711; this version posted August 19, 2018.
    [Show full text]
  • PDZD7-MYO7A Complex Identified in Enriched Stereocilia Membranes
    RESEARCH ARTICLE PDZD7-MYO7A complex identified in enriched stereocilia membranes Clive P Morgan1†, Jocelyn F Krey1†, M’hamed Grati2, Bo Zhao3, Shannon Fallen1, Abhiraami Kannan-Sundhari2, Xue Zhong Liu2, Dongseok Choi4,5, Ulrich Mu¨ ller3, Peter G Barr-Gillespie1* 1Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, United States; 2Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, United States; 3Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States; 4OHSU-PSU School of Public Health, Oregon Health and Science University, Portland, United States; 5Graduate School of Dentistry, Kyung Hee University, Seoul, Korea Abstract While more than 70 genes have been linked to deafness, most of which are expressed in mechanosensory hair cells of the inner ear, a challenge has been to link these genes into molecular pathways. One example is Myo7a (myosin VIIA), in which deafness mutations affect the development and function of the mechanically sensitive stereocilia of hair cells. We describe here a procedure for the isolation of low-abundance protein complexes from stereocilia membrane fractions. Using this procedure, combined with identification and quantitation of proteins with mass spectrometry, we demonstrate that MYO7A forms a complex with PDZD7, a paralog of USH1C and DFNB31. MYO7A and PDZD7 interact in tissue-culture cells, and co-localize to the ankle-link region of stereocilia in wild-type but not Myo7a mutant mice. Our data thus describe a new paradigm for *For correspondence: gillespp@ the interrogation of low-abundance protein complexes in hair cell stereocilia and establish an ohsu.edu unanticipated link between MYO7A and PDZD7.
    [Show full text]
  • Table S-1 Mpkccd Transcriptome
    Table S1. mpkCCD Cell Transcriptomes. Correlati on Ori. Ratio Coefficie Gene Symbol Gene Title GeneID Clone 11 Clone Clone 2 (11/2) nt Copg coatomer protein complex, subunit gamma 54161 1.99 1.81 2.48 0.80 -0.49 ns Atp6v0d1 ATPase, H+ transporting, lysosomal V0 subunit D1 11972 3.37 2.87 3.00 1.12 0.74 ns Golga7 golgi autoantigen, golgin subfamily a, 7 57437 3.03 3.40 3.58 0.84 -0.34 ns Psph phosphoserine phosphatase 100678 0.38 0.66 0.64 0.59 -0.61 ns Trappc4 trafficking protein particle complex 4 60409 1.17 1.12 1.08 1.08 0.64 ns Dpm2 dolichol-phosphate (beta-D) mannosyltransferase 2 13481 0.74 0.87 0.81 0.91 -0.31 ns Psmb5 proteasome (prosome, macropain) subunit, beta type 5 19173 2.92 3.00 2.92 0.99 0.32 ns Dhrs1 dehydrogenase/reductase (SDR family) member 1 52585 0.74 0.68 0.88 0.83 -0.18 ns Ppm1a protein phosphatase 1A, magnesium dependent, alpha isoform 19042 2.43 2.60 2.96 0.82 -0.53 ns Psenen presenilin enhancer 2 homolog (C. elegans) 66340 2.52 2.88 3.80 0.66 -0.77 ns Anapc1 anaphase promoting complex subunit 1 17222 1.16 1.33 1.61 0.72 -0.33 ns Mrpl43 mitochondrial ribosomal protein L43 94067 2.15 2.15 1.84 1.16 0.91 * Nmt1 N-myristoyltransferase 1 18107 3.21 2.71 3.36 0.95 0.31 ns Atg5 autophagy-related 5 (yeast) 11793 0.70 0.73 0.66 1.05 -0.23 ns Mtif2 mitochondrial translational initiation factor 2 76784 1.16 1.29 1.19 0.97 -0.36 ns Psap prosaposin 19156 8.07 7.25 8.37 0.96 0.02 ns Ube2g1 ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, C.
    [Show full text]
  • 4 353 Skin Oral 1 B
    A B Supplementary Figure S1: Differentially expressed piRNAs during skin and oral mucosal wound healing. (A) piRNA 0hr-1 0hr-3 0hr-2 24hr-2 24hr-1 24hr-3 5day-3 5day-1 5day-2 0hr-1 0hr-2 0hr-3 24hr-2 24hr-1 24hr-3 5day-1 5day-2 5day-3 profiles were obtained on mouse skin and oral mucosal (palate) wound healing time course (0hr, 24 hr, and 5 day). A total of 357 differentially expressed piRNA were identified during skin wound healing (Bonferroni adjusted P value <0.05). See Supplementary Table 1A for the full list. C (B) Five differentially expressed piRNA skin were identified during oral mucosal wound healing (P value <0.01, list presented in Supplementary Table 1B). Note: more 353 stringent statistical cut-off ((Bonferroni adjusted P value) yield 0 differentially expressed piRNA gene. (C) Venn diagram illustrates overlaps between differentially 4 expressedpiRNAsinskinandoral oral 1 mucosal wound healing. min max Supplementary Table S1a: Differentially expressed piRNAs in skin wound healing Mean StDev piRNA 0 hr 24 hr 5 day 0 hr 24 hr 5 day pVal adj P piR‐mmu‐15927330 5.418351 11.39746 10.799 0.34576 0.253492 0.154802 6.32E‐14 6.97E‐11 piR‐mmu‐49559417 5.301647 10.10777 9.816878 0.441719 0.222335 0.032479 3.95E‐12 4.36E‐09 piR‐mmu‐30053093 6.32531 11.26384 4.020902 0.280841 1.057847 0.178798 5.21E‐12 5.76E‐09 piR‐mmu‐29303577 5.15005 10.47662 9.52175 0.554877 0.26622 0.163283 1.53E‐11 1.69E‐08 piR‐mmu‐49254706 5.187673 10.19644 9.622374 0.520671 0.330378 0.191116 1.96E‐11 2.16E‐08 piR‐mmu‐49005170 5.415133 9.639725 9.565967 0.411507 0.281143
    [Show full text]
  • You Can Check If Genes Are Captured by the Agilent Sureselect V5 Exome
    IIHG Clinical Exome Sequencing Test Gene Coverage • Whole Exome Sequencing is a targeted capture platform which does not capture the entire exome. Regions not captured by the exome will not be analyzed. o Please note, it is important to understand the absence of a reportable variant in a given gene does not mean there are not pathogenic variants in that gene. • Data sensitivity and specificity for exome testing is variable as gene coverage is not uniform throughout the exome. • The Agilent SureSelect XT Human All Exon v5 kit captures ~98% of Refseq coding base pairs, and >94% of the captured coding bases in the exome are covered at our depth-of-coverage minimum threshold (30 reads). • All test reports include the following information: o Regions of the Symptom Candidate Gene List which were not captured by the current exome capture platform. o Regions of the Symptom Candidate Gene List which were not sequenced to a sufficient depth of coverage to make a clinical diagnosis. • You can check if genes are captured by the Agilent Agilent SureSelect v5 exome capture, and how well those genes are typically covered here. • Explanations for the headings; • Symbol: Gene symbol • Chr: Chromosome • % Captured: the minimum portion of the gene captured by the Agilent SureSelect XT Human All Exon v5 kit. This includes all transcripts for a given gene. o 100.00% = the entire gene is captured o 0.00% = none of the gene is captured • % Covered: the minimum portion of the gene that has at least 30x average coverage when sequenced on the Illumina HiSeq2000 with 100 base pair (bp) paired-end reads for eight CEPH samples.
    [Show full text]