The Two Tort Dit U Nani Minuta Omulutni

Total Page:16

File Type:pdf, Size:1020Kb

The Two Tort Dit U Nani Minuta Omulutni THETWO TORT DIT USU 20180273906A1NANI MINUTA OMULUTNI ( 19) United States (12 ) Patent Application Publication (10 ) Pub. No. : US 2018/ 0273906 A1 Ashraf (43 ) Pub . Date : Sep . 27 , 2018 ( 54 ) MICROVESICLE AND STEM CELL Publication Classification COMPOSITIONS FOR THERAPEUTIC (51 ) Int. Cl. (54 ) COMPOSATIONSAPPLICATIONS C12N 57074 (2006 .01 ) C12N 5 / 077 ( 2006 . 01) (71 ) Applicant: Muhammad Ashraf, Cincinnati , OH C12N 5 /071 (2006 . 01 ) (US ) A61K 35 / 12 ( 2006 .01 ) ( 72 ) Inventor: Muhammad Ashraf , Cincinnati, OH (52 ) U . S . CI. CPC . .. C12N 5 / 0696 ( 2013 .01 ) ; C12N 5 /0657 (US ) (2013 .01 ) ; C12N 2506 / 45 ( 2013 .01 ) ; C12N (21 ) Appl. No .: 15 / 881, 693 570661 ( 2013 .01 ) ; A61K 35 / 12 ( 2013. 01 ) ; C12N 5 / 069 ( 2013 . 01 ) ( 22 ) Filed : Jan . 26 , 2018 Related U . S . Application Data (57 ) ABSTRACT (63 ) Continuation - in -part of application No . 14 / 255, 789, Provided herein are stem cell and exosome compositions filed on Apr. 17 , 2014 , Continuation - in - part of appli having therapeutic utility to treat a variety of diseases and (63 ) Condcation on No Apr . .14 17 / 951, 20152 , 354 , filed onon Nov;. 5201 24 , 2015, 292 , Con file disorders , e . g . , cardiovascular disease , Duchenne muscular tinuation - in -part of application No . 15 / 201, 292 , filed dystrophy , and fibrotic disease . on Jul. 1 , 2016 . Specification includes a Sequence Listing . Patent Application Publication Sep . 27 , 2018 Sheet 1 of 56 US 2018 /0273906 A1 Mergest BAX : 2:5 . * 7:22 . .2 .: . W . Nanog FIG . 1 111111111111111111111111111111111111111111111111VVVVVVVVVVVVVVVV Patent Application Publication Sep . 27 , 2018 Sheet 2 of 56 US 2018 /0273906 A1 : : : ????????????????????? 8 8 DNMTinhibition% 8 . 8 8 o wwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Non treated IPS Small molecule - IPS FIG . 2 Patent Application Publication Sep . 27 , 2018 Sheet 3 of 56 US 2018 /0273906 A1 DAP JUNOY Merced . * . ? ?????? , .. .. ::: .. * . .. **** - :. : . :. :. :. .: : . + .. SEON .. .:1 +1 + : 1 . ::111 **: :1, 1 .1. 1+ .. : an ri * 7 . Vm . * XV. i . i ..: : . : . :: SasaWIS . FIG . 3A Absorbance490nm 1.11 :# + + + + IiIi - + + + . II. 1 +!1 ! !! + + ++ + 11! ? ! ? + ++ + - + .- ! * + + - IIIY ++ - -II. + + * !! II ** * + + 55545454 ! * . * , * . * , - * , * - * , * . * , - , * - * , * . * * * , Non treated IPS Small molecule -IPS FIG . 3B Patent Application Publication Sep . 27 , 2018 Sheet 4 of 56 US 2018 /0273906 A1 O nošivate DAMEDAV MergentMore .. .. ** 3 SON ::. wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww * al 1 . "Ti. FIG . 4 Patent Application Publication Sep . 27 , 2018 Sheet 5 of 56 US 2018 /0273906 A1 AT 12 FIG, SA AXIS CGATION Non treated IPS Small molecule - IPS FIG. SB Patent Application Publication Sep . 27, 2018 Sheet 6 of 56 US 2018 / 0273906 A1 ?? ?? ? ?????? ?? ? ?? ???? ????? .. .. .. :: : ??????? ??? ???? ??? :: : ??.?.??. .. .. .. :???? .. .? ? ????? . ? ???????? ?????? ? ?? ???????????? ??? ??????????? ????????? ? ?????? ? ???? ?? ??? ????? ?? . ??? . ???????? ?? ????? ?? ? ??? ????? ???? ?? ??? ????? ?? ? ????? ? ??? ?? ???? ?? ?? ??? ??? ???? ?? ?? ????? ?? ? ???? ?? ??????? ????? ?? ??? ? ?? :: : : : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : :: : : : :: : :: : : :: : : :: : : :: ??????????????????????????????????????????????????????????????????????????????? ? ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ????????????? Non treated IPS Small molecule - IPS FIG . 6 Patent Application Publication Sep . 27 , 2018 Sheet 7 of 56 US 2018 /0273906 A1 ule1 Smallmolecule-IPS * * www * * * FIG.7D FIG.7B stratitiktiassistenitori tt **** * * odoperp 111111111111 prostit * * cit. tiiiiiiiii* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * NontreatedIPS wisiiniisiin* pakan * NOWO 5000 ol 00% ww Smallmolecule-IPS ** .. **** * ... * .. ILUS ***** * posti FIG.7A WWWMW. .. ----- - - -- - -- - - -- - -- - - - - - - - .. * FIG.7C *** * *** * **ta* . SHIPajtaVOXDO Wym termostat . * ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? 60 1989 WA * NontreatedIPS Patent Application Publication Sep . 27 , 2018 Sheet 8 of 56 US 2018 /0273906 A1 Ga (. pan . ). B - actin *. Nontreated IPS Smallmolecule -IPS + Smallmolecule -IPSGPCR blocker FIG . 7E 11111 . NRY t FIGS . SA - SD Patent Application Publication Sep . 27 , 2018 Sheet 9 of 56 US 2018 /0273906 A1 )aw(ur ( VIDs (mm ) VIDD ( mm ) FIG . SE * < 0 . 05 en os CardiacFunction(%) mahamannannnnnnnnnnnnnnnn mwanaume wallet EF (1 % ) FS ( % ) FIG . 8F Heterogeneous BMSCs SJSCS 10 um FIG . 9A Patent Application Publication Sep . 27, 2018 Sheet 10 of 56 US 2018 /0273906 A1 . ' . ' . ' . ' . ' . ' . ' . ' . ' . ' . ' . w 6900 iiiiiiiiiiiiiiiiiiiiiiiiiii . 46.0% %0 CD44 * 21100 * 13 * 6700 inter 9666 CD45 Www * FIG.9B WW W * * * * * * ?: %0.00! * * CD90 * joguooodkjosi * * * * * . * * * * * * * * * * * * * * * ** * * * ** * * * ** * * * * * * * . * ** * * * : Patent Application Publication Sep . 27, 2018 Sheet 11 of 56 US 2018 /0273906 A1 sosrsx+ agedSISCS YBMSCs BBMSCS ??? ? ?? ? ? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ?? ? ? ? ?? ?? ? ? ? ?? ?? ? ? ? ?? ?? ? ? ? ?? ?? ? ? ? ?? ?? ? ? ? ? . 10 7 FIG.9C 5 days 0123 (401x ) zub /s | j80 Patent Application Publication Sep . 27 , 2018 Sheet 12 of 56 US 2018 /0273906 A1 *WWW Sint Tert Gapdh . wwwwwwwwwww Aged wwwwwwwwwwwwwwwwwww wiss Siti FIG.9F ) Gaooh to normalized( expression Relativo * Gata! Nkx2.5 Meta Gapdh * Mef2cNkx26 w * Aged * FIG.SE * Gatau (uodes o pozjeudou ) vosso do angeon * * * * * * * * * * * * ws W Rex- Gapoh Oct Nanog KIEM wwwww Oc14NanogSox2K:14Rex1 . ** * ** * * * ** * ** * * ** * * * * * * «* Aged W SJSCBMSC s wiwiwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww FIG.9D S (updeg oj pozjewou ) expression Relative Patent Application Publication Sep . 27, 2018 Sheet 13 of 56 US 2018 /0273906 A1 Agent SUSOSBMSCSSJSCS w FIG.91 wwwwwwwww firmox . ) 60( vai BMSCS 000 Wow Aged FIG.9G 0000000000000 SJSCS Aged NYUV wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww Bugal wwwwwwwwwwwwwwwwwwwwwwwwwwwwwww FIG.9H VOM ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????voj gubew Patent Application Publication Sep . 27, 2018 Sheet 14 of 56 US 2018 /0273906 A1 * * * .. ON FIG . 10A OXAT Neg conto 01 * * * * * * ** * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * W * * * * WWW * * 0 % * 85 % * 90 . 5 % * www * * * * * * * * * * * * * * * * 147777777777777777777777444 17171717171717171717171724244714 * FIG . 10B Patent Application Publication Sep . 27 , 2018 Sheet 15 of 56 US 2018 /0273906 A1 Cardiac sordblasts . * WA BUZWV . * www . + + - + + . - . - . * . * . * . * . wwww . * . * . * . * . FIG . 10C 01 0 CX 1024 * Windle sowy" 0 - 60701 W * * 2 . 5 A14 NO20 FIG . 10D Patent Application Publication Sep . 27 , 2018 Sheet 16 of 56 US 2018 /0273906 A1 . * . * . * . * . NO. * . * . * . * . * . * . * . * . * . * . * . * . * . * www * * * * * * * * * * * . w wwwwwwwwwwwwwwwwwwwww4444444444444 Posteriou Otak* * * * * * * * * * * * * * * * * * * * * * * * * * ** * * * * * * * * * * * * * * * * * * * * * * ** * * Vias ** * ** * * ** * * * * ** * ** * ** * * * * * * * * FIG . 11A Eles Eles . CTGF Actin N 0037 M Caca) * 003Boeta poyo MIOVE90( www. ( www Eles de la 03 FIG . 11B FIG . 11C Nom eles bles ?? ? ?? ? ? ? ? ? ? ?? ? ? ? ?? ? ?? ? ? ? ? ? ?? ? ? ? ?? ?? ?? ? ?? ?? ?? ? Merged with DANI CIGA Merced with DARI FIG . 110 Patent Application Publication Sep . 27 , 2018 Sheet 17 of 56 US 2018 /0273906 A1 transton region 3 UIR ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? ???? WWW mo MORNA mmmm COGUVAUA MAGAC ACGACGAW 6 MR 195 873 .5 % agCUAUGGUCUUGCAGCUGCUC * * miert FIG . 12A OXSCS QU $ C $ * wwwwwwwwwwwwwww 109 1990 - 1991 wwwwwwwwwwwwwwwwwwwwwww BE ACH *995 *64vopage wwww* * em 199 en 1991 LLLFIG . 12B FIG . 12C Patent Application Publication Sep . 27, 2018 Sheet 18 of 56 US 2018 /0273906 A1 . Luciferaseactivity(14) xemtie MR 19% Peluamimi VIR FIG . 12D - Cumhem m hentiLenti -miR - -195 195 inhibitorinhibito Lenti scramble FIG . 13A Patent Application Publication Sep . 27 , 2018 Sheet 19 of 56 US 2018 /0273906 A1 * OMSCs * ** MOMSCs Adevou 9- wwwww * OMSCS WOMSCX FIG . 13B XOMSCS * * * ** SOMSCS * * * .:. wwwwwww Sows Wwwwwwwwwwwwwwwww . wwwmmmmmmmmmmm MOUSE MOUSC FIG . 13C Patent Application Publication Sep . 27, 2018 Sheet 20 of 56 US 2018 /0273906 A1 SCIOMSCS anu -195OMSCS YYYYYYYYYYYYYY WWWWWWWWWWWWwwwhere the two other two wwwwwwwwwwwwwwwwwwwwwwww :LE 00000000000000000 * TUNELcells stagjezov .. .. .. .. .. .. scramble anti-miR - 195 FIG . 13D Patent Application Publication Sep . 27, 2018 Sheet 21 of 56 US 2018 /0273906 A1 SIOMSC $ 19OMSC : TERE SIRI FOXO1 FOXO1 AKT 8023 Cleavad Caspase 3 40B FIG . 13E * * * * * * * * * * * * * * * * * * * * * * * * iren SOMSCS COLX)Bello * * * -19SONSCS Culonyformation(9 * **** standartinis in.. ???? ?? ???? ???? days SOOMSC - CONSC FIG
Recommended publications
  • 1 Early Patterning and Specification of Cardiac Progenitors In
    Early Patterning and Specification of Cardiac Progenitors in Gastrulating Mesoderm W. Patrick Devine1,2,3,4, Joshua D. Wythe1,2, Matthew George1,2,5 , Kazuko Koshiba- Takeuchi1,2, Benoit G. Bruneau1,2,4,5 1. Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158 USA 2. Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA 3. Department of Pathology, University of California, San Francisco, CA 94143 USA 4. Cardiovascular Research Institute, University of California, San Francisco, CA 94158 USA 5. Developmental and Stem Cell Biology Program, University of San Francisco, CA 94143, USA 6. Department of Pediatrics, University of California, San Francisco, CA 94143 USA Competing interests statement: The authors declare no competing interests. 1 Abstract Mammalian heart development requires precise allocation of cardiac progenitors. The existence of a multipotent progenitor for all anatomic and cellular components of the heart has been predicted but its identity and contribution to the two cardiac progenitor "fields" has remained undefined. Here we show, using clonal genetic fate mapping, that Mesp1+ cells in gastrulating mesoderm are rapidly specified into committed cardiac precursors fated for distinct anatomic regions of the heart. We identify Smarcd3 as a marker of early specified cardiac precursors and identify within these precursors a compartment boundary at the future junction of the left and right ventricles that arises prior to morphogenesis. Our studies define the timing and hierarchy of cardiac progenitor specification and demonstrate that the cellular and anatomical fate of mesoderm-derived cardiac cells is specified very early. These findings will be important to understand the basis of congenital heart defects and to derive cardiac regeneration strategies.
    [Show full text]
  • Supplemental Table 1. Complete Gene Lists and GO Terms from Figure 3C
    Supplemental Table 1. Complete gene lists and GO terms from Figure 3C. Path 1 Genes: RP11-34P13.15, RP4-758J18.10, VWA1, CHD5, AZIN2, FOXO6, RP11-403I13.8, ARHGAP30, RGS4, LRRN2, RASSF5, SERTAD4, GJC2, RHOU, REEP1, FOXI3, SH3RF3, COL4A4, ZDHHC23, FGFR3, PPP2R2C, CTD-2031P19.4, RNF182, GRM4, PRR15, DGKI, CHMP4C, CALB1, SPAG1, KLF4, ENG, RET, GDF10, ADAMTS14, SPOCK2, MBL1P, ADAM8, LRP4-AS1, CARNS1, DGAT2, CRYAB, AP000783.1, OPCML, PLEKHG6, GDF3, EMP1, RASSF9, FAM101A, STON2, GREM1, ACTC1, CORO2B, FURIN, WFIKKN1, BAIAP3, TMC5, HS3ST4, ZFHX3, NLRP1, RASD1, CACNG4, EMILIN2, L3MBTL4, KLHL14, HMSD, RP11-849I19.1, SALL3, GADD45B, KANK3, CTC- 526N19.1, ZNF888, MMP9, BMP7, PIK3IP1, MCHR1, SYTL5, CAMK2N1, PINK1, ID3, PTPRU, MANEAL, MCOLN3, LRRC8C, NTNG1, KCNC4, RP11, 430C7.5, C1orf95, ID2-AS1, ID2, GDF7, KCNG3, RGPD8, PSD4, CCDC74B, BMPR2, KAT2B, LINC00693, ZNF654, FILIP1L, SH3TC1, CPEB2, NPFFR2, TRPC3, RP11-752L20.3, FAM198B, TLL1, CDH9, PDZD2, CHSY3, GALNT10, FOXQ1, ATXN1, ID4, COL11A2, CNR1, GTF2IP4, FZD1, PAX5, RP11-35N6.1, UNC5B, NKX1-2, FAM196A, EBF3, PRRG4, LRP4, SYT7, PLBD1, GRASP, ALX1, HIP1R, LPAR6, SLITRK6, C16orf89, RP11-491F9.1, MMP2, B3GNT9, NXPH3, TNRC6C-AS1, LDLRAD4, NOL4, SMAD7, HCN2, PDE4A, KANK2, SAMD1, EXOC3L2, IL11, EMILIN3, KCNB1, DOK5, EEF1A2, A4GALT, ADGRG2, ELF4, ABCD1 Term Count % PValue Genes regulation of pathway-restricted GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, SMAD protein phosphorylation 9 6.34 1.31E-08 ENG pathway-restricted SMAD protein GDF3, SMAD7, GDF7, BMPR2, GDF10, GREM1, BMP7, LDLRAD4, phosphorylation
    [Show full text]
  • Genome-Wide Transcriptome and Binding Sites Analyses Identify
    www.nature.com/scientificreports OPEN Genome-Wide Transcriptome and Binding Sites Analyses Identify Early FOX Expressions Received:​06​October​2015 Accepted:​14​July​2016 for Enhancing Cardiomyogenesis Published:​09​August​2016 Efficiency of hESC Cultures Hock Chuan Yeo1,2, Sherwin Ting1, Romulo Martin Brena3, Geoffrey Koh1, Allen Chen1, Siew Qi Toh2, Yu Ming Lim1, Steve Kah Weng Oh1 & Dong-Yup Lee1,2,4 The differentiation efficiency of human embryonic stem cells (hESCs) into heart muscle cells (cardiomyocytes) is highly sensitive to culture conditions. To elucidate the regulatory mechanisms involved, we investigated hESCs grown on three distinct culture platforms: feeder-free Matrigel, mouse embryonic fibroblast feeders, and Matrigel replated on feeders. At the outset, we profiled and quantified their differentiation efficiency, transcriptome, transcription factor binding sites and DNA- methylation. Subsequent genome-wide analyses allowed us to reconstruct the relevant interactome, thereby forming the regulatory basis for implicating the contrasting differentiation efficiency of the culture conditions. We hypothesized that the parental expressions of FOXC1, FOXD1 and FOXQ1 transcription factors (TFs) are correlative with eventual cardiomyogenic outcome. Through WNT induction of the FOX TFs, we observed the co-activation of WNT3 and EOMES which are potent inducers of mesoderm differentiation. The result strengthened our hypothesis on the regulatory role of the FOX TFs in enhancing mesoderm differentiation capacity of hESCs. Importantly, the final proportions of cells expressing cardiac markers were directly correlated to the strength of FOX inductions within 72 hours after initiation of differentiation across different cell lines and protocols. Thus, we affirmed the relationship between early FOX TF expressions and cardiomyogenesis efficiency.
    [Show full text]
  • Grimme, Acadia.Pdf
    MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Bachelors of Science in Biological Sciences with Distinction Spring 2018 © 2018 Acadia Grimme All Rights Reserved MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme Approved: __________________________________________________________ Matthew E. R. Butchbach, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Deni S. Galileo, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Carlton R. Cooper, Ph.D. Committee member from the Department of Biological Sciences Approved: __________________________________________________________ Gary H. Laverty, Ph.D. Committee member from the Board of Senior Thesis Readers Approved: __________________________________________________________ Michael Chajes, Ph.D. Chair of the University Committee on Student and Faculty Honors ACKNOWLEDGMENTS I would like to acknowledge my thesis director Dr. Butchbach for his wonderful guidance and patience as I worked through my project. He has been an excellent research mentor over the last two years and I am forever thankful that he welcomed me into his lab. His dedication to his work inspires me as an aspiring research scientist. His lessons will carry on with me as I pursue future research in graduate school and beyond. I would like to thank both current and former members of the Motor Neuron Disease Laboratory: Sambee Kanda, Kyle Hinkle, and Andrew Connell. Sambee and Andrew patiently taught me many of the techniques I utilized in my project, and without them it would not be what it is today.
    [Show full text]
  • Transcription Factors ETS2 and MESP1 Transdifferentiate Human Dermal fibroblasts Into Cardiac Progenitors
    Transcription factors ETS2 and MESP1 transdifferentiate human dermal fibroblasts into cardiac progenitors Jose Francisco Islasa,b,1, Yu Liuc,1, Kuo-Chan Wenga,b,1, Matthew J. Robertsonb, Shuxing Zhangc, Allan Prejusab, John Hargerc, Dariya Tikhomirovab,c, Mani Choprac, Dinakar Iyerd,MarkMercolae,RobertG.Oshimae, James T. Willersonb, Vladimir N. Potamanb,2, and Robert J. Schwartzb,c,2,3 aGraduate School of Biomedical Sciences, Institute of Bioscience and Technology, Texas A&M Health Science Center, Houston, TX 77030; bStem Cell Engineering Laboratory, Texas Heart Institute at St. Luke’s Episcopal Hospital, Houston, TX 77030; dDepartment of Medicine, Baylor College of Medicine, Houston, TX 77030; cDepartment of Biology and Biochemistry, University of Houston, Houston, TX 77204; and eSanford-Burnham Medical Research Institute, La Jolla, CA 92037 Edited* by Eric N. Olson, University of Texas Southwestern Medical Center, Dallas, TX, and approved June 25, 2012 (received for review December 12, 2011) Unique insights for the reprograming of cell lineages have come Results from embryonic development in the ascidian Ciona, which is depen- ETS2 Is a Critical Cardiopoiesis Factor. We compared the expression dent upon the transcription factors Ci-ets1/2 and Ci-mesp to gener- profiles of mammalian cardiomyogenic genes in wild-type E14 −/− ate cardiac progenitors. We tested the idea that mammalian v-ets and Ets2 mouse ES cells. T-brachyury, a core T-box factor erythroblastosis virus E26 oncogene homolog 2 (ETS2) and meso- required for initiating the appearance of cardiac mesoderm was derm posterior (MESP) homolog may be used to convert human not affected by the loss of Ets2 (Fig.
    [Show full text]
  • A Thesis Entitled Snps and Indels Analysis in Human Genome Using
    A Thesis entitled SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data by Sharmistha Chakrabortty Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Master of Science Degree in Biomedical Sciences: Bioinformatics, Proteomics and Genomics ________________________________________ Dr. Alexei Fedorov, Committee Chair ________________________________________ Dr. Robert Blumenthal, Committee Member ________________________________________ Dr. Sadik Khuder, Committee Member ________________________________________ Dr. Amanda Bryant-Friedrich, Dean College of Graduate Studies The University of Toledo August 2017 Copyright 2017, Sharmistha Chakrabortty This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of SNPs and Indels Analysis in Human Genome using Computer Simulation and Sequencing Data by Sharmistha Chakrabortty Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Master of Science Degree in Biomedical Sciences: Bioinformatics, Proteomics and Genomics The University of Toledo August 2017 Genetic variations are the heritable changes in DNA caused by mutation and can be present in both coding and non-coding region of the DNA. They provide great resources for the evolution of an organism in response to environmental and biological changes. Analysis of these variants (such as Single Nucleotide Polymorphism (SNPs), Indels, and other structural variants like Copy Number Variations (CNV)) thus, have a wide range of potential applications. These include identification of causative variants and the genes for genetic diseases, personalized genomics, population and evolutionary genetics, and forensic biology. This study represents two such applications of human variant analysis (particularly the analysis of SNPs and Indels).
    [Show full text]
  • Transcription Factors ETS2 and MESP1 Transdifferentiate Human Dermal fibroblasts Into Cardiac Progenitors
    Transcription factors ETS2 and MESP1 transdifferentiate human dermal fibroblasts into cardiac progenitors Jose Francisco Islasa,b,1, Yu Liuc,1, Kuo-Chan Wenga,b,1, Matthew J. Robertsonb, Shuxing Zhangc, Allan Prejusab, John Hargerc, Dariya Tikhomirovab,c, Mani Choprac, Dinakar Iyerd, Mark Mercolae,RobertG.Oshimae, James T. Willersonb, Vladimir N. Potamanb,2, and Robert J. Schwartzb,c,2,3 aGraduate School of Biomedical Sciences, Institute of Bioscience and Technology, Texas A&M Health Science Center, Houston, TX 77030; bStem Cell Engineering Laboratory, Texas Heart Institute at St. Luke’s Episcopal Hospital, Houston, TX 77030; dDepartment of Medicine, Baylor College of Medicine, Houston, TX 77030; cDepartment of Biology and Biochemistry, University of Houston, Houston, TX 77204; and eSanford-Burnham Medical Research Institute, La Jolla, CA 92037 Edited* by Eric N. Olson, University of Texas Southwestern Medical Center, Dallas, TX, and approved June 25, 2012 (received for review December 12, 2011) Unique insights for the reprograming of cell lineages have come Results from embryonic development in the ascidian Ciona, which is depen- ETS2 Is a Critical Cardiopoiesis Factor. We compared the expression dent upon the transcription factors Ci-ets1/2 and Ci-mesp to gener- profiles of mammalian cardiomyogenic genes in wild-type E14 −/− ate cardiac progenitors. We tested the idea that mammalian v-ets and Ets2 mouse ES cells. T-brachyury, a core T-box factor erythroblastosis virus E26 oncogene homolog 2 (ETS2) and meso- required for initiating the appearance of cardiac mesoderm was derm posterior (MESP) homolog may be used to convert human not affected by the loss of Ets2 (Fig.
    [Show full text]
  • Early Patterning and Specification of Cardiac Progenitors in Gastrulating
    RESEARCH ARTICLE elifesciences.org Early patterning and specification of cardiac progenitors in gastrulating mesoderm W Patrick Devine1,2,3,5*, Joshua D Wythe1,2, Matthew George1,2,4, Kazuko Koshiba-Takeuchi1,2, Benoit G Bruneau1,2,3,4* 1Gladstone Institute of Cardiovascular Disease, San Francisco, United States; 2Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, United States; 3Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States; 4Developmental and Stem Cell Biology Program, University of San Francisco, San Francisco, United States; 5Department of Pathology, University of California, San Francisco, San Francisco, United States Abstract Mammalian heart development requires precise allocation of cardiac progenitors. The existence of a multipotent progenitor for all anatomic and cellular components of the heart has been predicted but its identity and contribution to the two cardiac progenitor ‘fields’ has remained undefined. Here we show, using clonal genetic fate mapping, that Mesp1+ cells in gastrulating mesoderm are rapidly specified into committed cardiac precursors fated for distinct anatomic regions of the heart. We identify Smarcd3 as a marker of early specified cardiac precursors and identify within these precursors a compartment boundary at the future junction of the left and right ventricles that arises prior to morphogenesis. Our studies define the timing and hierarchy of cardiac progenitor specification and demonstrate that the cellular and anatomical fate of *For correspondence: patrick. mesoderm-derived cardiac cells is specified very early. These findings will be important to [email protected] understand the basis of congenital heart defects and to derive cardiac regeneration strategies. (WPD); bbruneau@gladstone.
    [Show full text]
  • Transcriptome Profiling Reveals the Complexity of Pirfenidone Effects in IPF
    ERJ Express. Published on August 30, 2018 as doi: 10.1183/13993003.00564-2018 Early View Original article Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska, Anna Gungl, Jochen Wilhelm, Leigh M. Marsh, Helene Thekkekara Puthenparampil, Katharina Sinn, Miroslava Didiasova, Walter Klepetko, Djuro Kosanovic, Ralph T. Schermuly, Lukasz Wujak, Benjamin Weiss, Liliana Schaefer, Marc Schneider, Michael Kreuter, Andrea Olschewski, Werner Seeger, Horst Olschewski, Malgorzata Wygrecka Please cite this article as: Kwapiszewska G, Gungl A, Wilhelm J, et al. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF. Eur Respir J 2018; in press (https://doi.org/10.1183/13993003.00564-2018). This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Copyright ©ERS 2018 Copyright 2018 by the European Respiratory Society. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska1,2, Anna Gungl2, Jochen Wilhelm3†, Leigh M. Marsh1, Helene Thekkekara Puthenparampil1, Katharina Sinn4, Miroslava Didiasova5, Walter Klepetko4, Djuro Kosanovic3, Ralph T. Schermuly3†, Lukasz Wujak5, Benjamin Weiss6, Liliana Schaefer7, Marc Schneider8†, Michael Kreuter8†, Andrea Olschewski1,
    [Show full text]
  • Inhibitor of DNA Binding in Heart Development and Cardiovascular Diseases Wenyu Hu1, Yanguo Xin1,2, Jian Hu1, Yingxian Sun1 and Yinan Zhao3*
    Hu et al. Cell Communication and Signaling (2019) 17:51 https://doi.org/10.1186/s12964-019-0365-z REVIEW Open Access Inhibitor of DNA binding in heart development and cardiovascular diseases Wenyu Hu1, Yanguo Xin1,2, Jian Hu1, Yingxian Sun1 and Yinan Zhao3* Abstract Id proteins, inhibitors of DNA binding, are transcription regulators containing a highly conserved helix-loop-helix domain. During multiple stages of normal cardiogenesis, Id proteins play major roles in early development and participate in the differentiation and proliferation of cardiac progenitor cells and mature cardiomyocytes. The fact that a depletion of Ids can cause a variety of defects in cardiac structure and conduction function is further evidence of their involvement in heart development. Multiple signalling pathways and growth factors are involved in the regulation of Ids in a cell- and tissue- specific manner to affect heart development. Recent studies have demonstrated that Ids are related to multiple aspects of cardiovascular diseases, including congenital structural, coronary heart disease, and arrhythmia. Although a growing body of research has elucidated the important role of Ids, no comprehensive review has previously compiled these scattered findings. Here, we introduce and summarize the roles of Id proteins in heart development, with the hope that this overview of key findings might shed light on the molecular basis of consequential cardiovascular diseases. Furthermore, we described the future prospective researches needed to enable advancement in the maintainance of the proliferative capacity of cardiomyocytes. Additionally, research focusing on increasing embryonic stem cell culture adaptability will help to improve the future therapeutic application of cardiac regeneration.
    [Show full text]
  • Identification of EOMES-Expressing Spermatogonial Stem Cells and Their Regulation by PLZF
    RESEARCH ARTICLE Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF Manju Sharma, Anuj Srivastava, Heather E Fairfield, David Bergstrom, William F Flynn, Robert E Braun* The Jackson Laboratory, Bar Harbor, United States Abstract Long-term maintenance of spermatogenesis in mammals is supported by GDNF, an essential growth factor required for spermatogonial stem cell (SSC) self-renewal. Exploiting a transgenic GDNF overexpression model, which expands and normalizes the pool of +/+ lu/lu undifferentiated spermatogonia between Plzf and Plzf mice, we used RNAseq to identify a rare subpopulation of cells that express EOMES, a T-box transcription factor. Lineage tracing and busulfan challenge show that these are SSCs that contribute to steady state spermatogenesis as well as regeneration following chemical injury. EOMES+ SSCs have a lower proliferation index in lu/lu wild-type than in Plzf mice, suggesting that PLZF regulates their proliferative activity and that lu/lu EOMES+ SSCs are lost through proliferative exhaustion in Plzf mice. Single cell RNA +/+ lu/lu sequencing of EOMES+ cells from Plzf and Plzf mice support the conclusion that SSCs are hierarchical yet heterogeneous. DOI: https://doi.org/10.7554/eLife.43352.001 Introduction Fertility in males is supported by a robust stem cell system that allows for continuous sperm produc- tion throughout the reproductive life of the individual. In humans this lasts for decades and in a *For correspondence: mouse can last for nearly its entire lifetime. However, despite more than a half century of research, [email protected] and intensive investigation by many labs over the last decade, the identity of the germline stem cell Competing interests: The continues to be elusive and controversial.
    [Show full text]
  • MESP1 Loss‑Of‑Function Mutation Contributes to Double Outlet Right Ventricle
    MOLECULAR MEDICINE REPORTS 16: 2747-2754, 2017 MESP1 loss‑of‑function mutation contributes to double outlet right ventricle MIN ZHANG1*, FU-XING LI2*, XING-YUAN LIU2, RI-TAI HUANG3, SONG XUE3, XIAO-XIAO YANG4, YAN-JIE LI4, HUA LIU4, HONG-YU SHI4, XIN PAN4, XING-BIAO QIU4 and YI-QING YANG4-6 1Department of Pediatrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072; 2Department of Pediatrics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065; 3Department of Cardiovascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127; 4Department of Cardiology; 5Cardiovascular Research Laboratory; 6Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China Received May 15, 2016; Accepted March 30, 2017 DOI: 10.3892/mmr.2017.6875 Abstract. Congenital heart disease (CHD) is the most absent in the 400 reference chromosomes and the altered common form of birth defect in humans, and remains a amino acid was completely conserved evolutionarily across leading non-infectious cause of infant mortality worldwide. An species. Functional assays indicated that the mutant MESP1 increasing number of studies have demonstrated that genetic protein had no transcriptional activity when compared with defects serve a pivotal role in the pathogenesis of CHD, and its wild‑type counterpart. The present study firstly provided mutations in >60 genes have been causally associated with experimental evidence supporting the concept that a MESP1 CHD. CHD is a heterogeneous disease and the genetic basis loss-of-function mutation may contribute to the development of CHD in the majority of patients remains poorly under- of DORV in humans, which presents a significant insight into stood.
    [Show full text]