DOCSLIB.ORG

Trisomy 21-Associated Defects in Human Primitive Hematopoiesis Revealed Through Induced Pluripotent Stem Cells

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Trisomy 21-Associated Defects in Human Primitive Hematopoiesis Revealed Through Induced Pluripotent Stem Cells Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells Stella T. Choua,1, Marta Byrska-Bishopb, Joanna M. Toberc, Yu Yaoa, Daniel VanDorna, Joanna B. Opalinskaa, Jason A. Millsd, John Kim Choie, Nancy A. Speckc, Paul Gadued,e, Ross C. Hardisonb, Richard L. Nemirofff, Deborah L. Frenchd,e, and Mitchell J. Weissa,1 aDivision of Hematology, eDepartment of Pathology and Laboratory Medicine, and dCenter for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104; bDepartment of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802; and cAbramson Family Cancer Institute and Department of Cell and Developmental Biology, and fDepartment of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 Edited* by Stuart H. Orkin, Children’s Hospital and the Dana Farber Cancer Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, and approved September 14, 2012 (received for review July 5, 2012) Patients with Down syndrome (trisomy 21, T21) have hematologic hematopoiesis is unknown and difficult to examine in human tissues abnormalities throughout life. Newborns frequently exhibit ab- at such early stages of embryogenesis. Moreover, murine models for normal blood counts and a clonal preleukemia. Human T21 fetal DS only partially recapitulate the hematopoietic abnormalities ob- livers contain expanded erythro-megakaryocytic precursors with served in humans (14–16). As an alternative approach, we examined enhanced proliferative capacity. The impact of T21 on the earliest the effects of T21 on embryonic hematopoiesis by studying human stages of embryonic hematopoiesis is unknown and nearly impos- induced pluripotent stem cells (iPSCs) with germ-line T21. sible to examine in human subjects. We modeled T21 yolk sac iPSCs generated by reprogramming somatic cells resemble ES hematopoiesis using human induced pluripotent stem cells (iPSCs). cells in their ability to self-renew in culture and generate nu- Blood progenitor populations generated from T21 iPSCs were merous mature cell types (17). In vitro differentiation of ES/iPSCs present at normal frequency and proliferated normally. However, recapitulates the ontogeny of hematopoiesis (18, 19). Human their developmental potential was altered with enhanced eryth- ES/iPSCs can be differentiated into erythroid cells expressing MEDICAL SCIENCES mainly ε-orγ/β-globins, likely reflecting primitive and definitive ropoiesis and reduced myelopoiesis, but normal megakaryocyte hematopoietic lineages, respectively (20–24). However, the cul- production. These abnormalities overlap with those of T21 fetal ture conditions and mechanisms that specify these distinct de- livers, but also reflect important differences. Our studies show that fi fi velopmental outcomes are not well de ned or understood. We T21 confers distinct developmental stage- and species-speci chema- analyzed iPSC lines from seven individuals (four T21, three eu- topoietic defects. More generally, we illustrate how iPSCs can pro- ploid) using an in vitro differentiation protocol optimized for vide insight into early stages of normal and pathological human primitive hematopoiesis (20). Our results further define the scope development. of T21 abnormalities during early human embryogenesis and illustrate that the associated hematopoietic defects are species- own syndrome (DS, trisomy 21, T21) affects many tissues, in- and developmental stage-specific. More generally, our findings Dcluding blood (1). Many DS neonates exhibit erythrocytosis, illustrate the power of iPSCs for studying the consequences of thrombocytopenia, and leukocytosis (2, 3). Approximately 10% genetic disorders on human ontogeny, particularly the earliest of DS newborns exhibit a clonal preleukemia, termed transient stages that are least accessible via primary tissue samples. myeloproliferative disease (TMD), which progresses to acute megakaryoblastic leukemia (AMKL) in ∼30% of cases. Both TMD Results and AMKL are accompanied by somatic mutations in the GATA1 Generation of iPSCs. iPSCs were derived from four T21 and three gene, causing production of an amino-truncated form of the tran- euploid control subjects (Table S1) by reprogramming somatic scription factor GATA-1 (reviewed in refs. 4 and 5). Importantly, tissues using four retroviruses, encoding OCT4, SOX2, KLF4,or somatic GATA1 mutations do not predispose to leukemia without MYC individually (17), or by a single polycistronic lentivirus en- T21 (6), and the most common DS blood abnormalities occur coding all four genes regulated by a doxycycline-inducible pro- without GATA1 mutations. Thus, T21 influences blood formation moter (25). Consistent experimental results were obtained using independently, particularly during embryogenesis (7, 8). These iPSC clones derived from different cell types and reprogramming derangements likely predispose to TMD/AMKL and could also vectors. All clones used in this study exhibited typical morphol- contribute to the early fetal demise that occurs throughout gesta- ogy, cell-surface expression of pluripotency markers (Tra1-60, tion in approximately one-third of T21 pregnancies (1). For these Tra1-81, SSEA3, SSEA4, KIT, KDR), expression of endogenous reasons, it is of biological and medical importance to fully define the pluripotency genes (ABCG2, DNMT3B, NANOG, OCT4, REX1), effects of T21 on blood formation at all stages of human ontogeny. During mammalian development, hematopoiesis occurs in multiple waves that differ with respect to timing, origin, and the Author contributions: S.T.C., J.M.T., P.G., D.L.F., and M.J.W. designed research; S.T.C., types of blood cells produced (reviewed in refs. 9 and 10). At about J.M.T., Y.Y., D.V., J.B.O., and J.A.M. performed research; S.T.C., M.B.-B., J.M.T., Y.Y., week 3 of human gestation, “primitive” blood cells produced by D.V., J.B.O., J.A.M., J.K.C., N.A.S., P.G., R.C.H., R.L.N., D.L.F., and M.J.W. analyzed data; the embryonic yolk sac are released into circulation. By weeks 4– and S.T.C., M.B.-B., J.M.T., N.A.S., R.C.H., R.L.N., D.L.F., and M.J.W. wrote the paper. 5, “definitive” progenitors emerge from the yolk sac and begin to The authors declare no conflict of interest. seed the fetal liver. After wk 5, hematopoietic stem cells emerge *This Direct Submission article had a prearranged editor. in the aorta-gonad-mesonephros (AGM) region and colonize the Data deposition: The microarray data reported in this paper have been deposited in the fetal liver, which becomes the major site of blood production Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. until birth, when hematopoiesis shifts to bone marrow (11–13). GSE35561). T21 alters hematopoiesis during embryonic development. 1To whom correspondence may be addressed. E-mail: [email protected] or weissmi@ Human T21 fetal livers with normal GATA1 alleles contain ex- email.chop.edu. panded megakaryocyte-erythroid progenitors, the progeny of which This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. exhibit enhanced proliferation (7, 8). How T21 impacts yolk sac 1073/pnas.1211175109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1211175109 PNAS Early Edition | 1of6 Downloaded by guest on September 29, 2021 + + – silencing of viral encoded reprogramming genes, and production of (CD41 42 235 ) lineages by day 12 of differentiation (Fig. S2). three embryonic germ layers in teratomas (Fig. S1). Karyotype Colony-forming assays of flow cytometry-sorted cells from whole analysis of iPSCs (passages 11–21) showed no acquired abnormal- EBs performed on days 7–8 of differentiation showed that all + ities and confirmed T21 in the appropriate lines. Cells were pas- hematopoietic progenitors reside in the CD43 population (Fig. saged at least 20 times to avoid “memory effects” that could exert 1D). Erythroid colonies produced from iPSC progenitors ex- lineage bias to iPSC lines derived from different tissues (26, 27). press mainly ζ-andε-globin genes, indicative of primitive hema- topoiesis. In contrast, fetal liver-derived colonies express mostly Trisomy 21 iPSCs Produce Primitive Hematopoietic Progenitors at α-andγ-globin genes, reflecting definitive hematopoiesis (Fig. 1E). + + + Normal Frequency. We compared the blood-forming capacities of The CD43 41 235 progenitors were present at similar proportions T21 and euploid iPSC lines by generating embryoid bodies (EBs) within day 7–8 EB cultures generated from T21 and euploid iPSCs in defined media containing sequential combinations of cytokines (Fig. 1 C and F). Transcriptome analysis of flow cytometry-sorted + + + that support primitive streak/mesoderm formation, transition to CD43 41 235 progenitors showed remarkable similarity be- hematoendothelial progenitors, and terminal hematopoietic dif- tween T21 and euploid cells. Only 21 of 236 HSA21 genes were ferentiation (Fig. 1A), using modifications of a published protocol up-regulated ≥1.5-fold in T21 progenitors (Fig. 1G), consistent by Kennedy et al. (20). The kinetics for emergence of hemato- with complex lineage-specific patterns of gene-dosage imbalance poiesis varied slightly among different iPSC lines. We controlled in human and murine T21 tissues (30). Taken together, our for these differences by examining progenitors that were stage- results suggest that T21 and euploid iPSCs produce similar
Load more

Recommended publications
  • V45n4a03.Pdf
    Montoya JC/et al/Colombia Médica - Vol. 45 Nº4 2014 (Oct-Dec) Colombia Médica colombiamedica.univalle.edu.co Original Article Global differential expression of genes located in the Down Syndrome Critical Region in normal human brain Expresión diferencial global de genes localizados en la Región Crítica del Síndrome de Down en el cerebro humano normal Julio Cesar Montoya1,3, Dianora Fajardo2, Angela Peña2 , Adalberto Sánchez1, Martha C Domínguez1,2, José María Satizábal1, Felipe García-Vallejo1,2 1 Department of Physiological Sciences, School of Basic Sciences, Faculty of Health, Universidad del Valle. 2 Laboratory of Molecular Biology and Pathogenesis LABIOMOL. Universidad del Valle, Cali, Colombia. 3 Faculty of Basic Sciences, Universidad Autónoma de Occidente, Cali, Colombia. Montoya JC , Fajardo D, Peña A , Sánchez A, Domínguez MC, Satizábal JM, García-Vallejo F.. Global differential expression of genes located in the Down Syndrome Critical Region in normal human brain. Colomb Med. 2014; 45(4): 154-61. © 2014 Universidad del Valle. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Article history Abstract Resumen Background: The information of gene expression obtained from Introducción: La información de la expresión de genes consignada Received: 2 July 2014 Revised: 10 November 2014 databases, have made possible the extraction and analysis of data en bases de datos, ha permitido extraer y analizar información acerca Accepted: 19 December 2014 related with several molecular processes involving not only in procesos moleculares implicados tanto en la homeostasis cerebral y su brain homeostasis but its disruption in some neuropathologies; alteración en algunas neuropatologías.
    [Show full text]
  • NICU Gene List Generator.Xlsx
    Neonatal Crisis Sequencing Panel Gene List Genes: A2ML1 - B3GLCT A2ML1 ADAMTS9 ALG1 ARHGEF15 AAAS ADAMTSL2 ALG11 ARHGEF9 AARS1 ADAR ALG12 ARID1A AARS2 ADARB1 ALG13 ARID1B ABAT ADCY6 ALG14 ARID2 ABCA12 ADD3 ALG2 ARL13B ABCA3 ADGRG1 ALG3 ARL6 ABCA4 ADGRV1 ALG6 ARMC9 ABCB11 ADK ALG8 ARPC1B ABCB4 ADNP ALG9 ARSA ABCC6 ADPRS ALK ARSL ABCC8 ADSL ALMS1 ARX ABCC9 AEBP1 ALOX12B ASAH1 ABCD1 AFF3 ALOXE3 ASCC1 ABCD3 AFF4 ALPK3 ASH1L ABCD4 AFG3L2 ALPL ASL ABHD5 AGA ALS2 ASNS ACAD8 AGK ALX3 ASPA ACAD9 AGL ALX4 ASPM ACADM AGPS AMELX ASS1 ACADS AGRN AMER1 ASXL1 ACADSB AGT AMH ASXL3 ACADVL AGTPBP1 AMHR2 ATAD1 ACAN AGTR1 AMN ATL1 ACAT1 AGXT AMPD2 ATM ACE AHCY AMT ATP1A1 ACO2 AHDC1 ANK1 ATP1A2 ACOX1 AHI1 ANK2 ATP1A3 ACP5 AIFM1 ANKH ATP2A1 ACSF3 AIMP1 ANKLE2 ATP5F1A ACTA1 AIMP2 ANKRD11 ATP5F1D ACTA2 AIRE ANKRD26 ATP5F1E ACTB AKAP9 ANTXR2 ATP6V0A2 ACTC1 AKR1D1 AP1S2 ATP6V1B1 ACTG1 AKT2 AP2S1 ATP7A ACTG2 AKT3 AP3B1 ATP8A2 ACTL6B ALAS2 AP3B2 ATP8B1 ACTN1 ALB AP4B1 ATPAF2 ACTN2 ALDH18A1 AP4M1 ATR ACTN4 ALDH1A3 AP4S1 ATRX ACVR1 ALDH3A2 APC AUH ACVRL1 ALDH4A1 APTX AVPR2 ACY1 ALDH5A1 AR B3GALNT2 ADA ALDH6A1 ARFGEF2 B3GALT6 ADAMTS13 ALDH7A1 ARG1 B3GAT3 ADAMTS2 ALDOB ARHGAP31 B3GLCT Updated: 03/15/2021; v.3.6 1 Neonatal Crisis Sequencing Panel Gene List Genes: B4GALT1 - COL11A2 B4GALT1 C1QBP CD3G CHKB B4GALT7 C3 CD40LG CHMP1A B4GAT1 CA2 CD59 CHRNA1 B9D1 CA5A CD70 CHRNB1 B9D2 CACNA1A CD96 CHRND BAAT CACNA1C CDAN1 CHRNE BBIP1 CACNA1D CDC42 CHRNG BBS1 CACNA1E CDH1 CHST14 BBS10 CACNA1F CDH2 CHST3 BBS12 CACNA1G CDK10 CHUK BBS2 CACNA2D2 CDK13 CILK1 BBS4 CACNB2 CDK5RAP2
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Literature Mining Sustains and Enhances Knowledge Discovery from Omic Studies
    LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES by Rick Matthew Jordan B.S. Biology, University of Pittsburgh, 1996 M.S. Molecular Biology/Biotechnology, East Carolina University, 2001 M.S. Biomedical Informatics, University of Pittsburgh, 2005 Submitted to the Graduate Faculty of School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2016 UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE This dissertation was presented by Rick Matthew Jordan It was defended on December 2, 2015 and approved by Shyam Visweswaran, M.D., Ph.D., Associate Professor Rebecca Jacobson, M.D., M.S., Professor Songjian Lu, Ph.D., Assistant Professor Dissertation Advisor: Vanathi Gopalakrishnan, Ph.D., Associate Professor ii Copyright © by Rick Matthew Jordan 2016 iii LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES Rick Matthew Jordan, M.S. University of Pittsburgh, 2016 Genomic, proteomic and other experimentally generated data from studies of biological systems aiming to discover disease biomarkers are currently analyzed without sufficient supporting evidence from the literature due to complexities associated with automated processing. Extracting prior knowledge about markers associated with biological sample types and disease states from the literature is tedious, and little research has been performed to understand how to use this knowledge to inform the generation of classification models from ‘omic’ data. Using pathway analysis methods to better understand the underlying biology of complex diseases such as breast and lung cancers is state-of-the-art. However, the problem of how to combine literature- mining evidence with pathway analysis evidence is an open problem in biomedical informatics research.
    [Show full text]
  • A Chromosome Level Genome of Astyanax Mexicanus Surface Fish for Comparing Population
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.06.189654; this version posted July 6, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Title 2 A chromosome level genome of Astyanax mexicanus surface fish for comparing population- 3 specific genetic differences contributing to trait evolution. 4 5 Authors 6 Wesley C. Warren1, Tyler E. Boggs2, Richard Borowsky3, Brian M. Carlson4, Estephany 7 Ferrufino5, Joshua B. Gross2, LaDeana Hillier6, Zhilian Hu7, Alex C. Keene8, Alexander Kenzior9, 8 Johanna E. Kowalko5, Chad Tomlinson10, Milinn Kremitzki10, Madeleine E. Lemieux11, Tina 9 Graves-Lindsay10, Suzanne E. McGaugh12, Jeff T. Miller12, Mathilda Mommersteeg7, Rachel L. 10 Moran12, Robert Peuß9, Edward Rice1, Misty R. Riddle13, Itzel Sifuentes-Romero5, Bethany A. 11 Stanhope5,8, Clifford J. Tabin13, Sunishka Thakur5, Yamamoto Yoshiyuki14, Nicolas Rohner9,15 12 13 Authors for correspondence: Wesley C. Warren ([email protected]), Nicolas Rohner 14 ([email protected]) 15 16 Affiliation 17 1Department of Animal Sciences, Department of Surgery, Institute for Data Science and 18 Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MO 19 2 Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 20 3 Department of Biology, New York University, New York, NY 21 4 Department of Biology, The College of Wooster, Wooster, OH 22 5 Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 23 6 Department of Genome Sciences, University of Washington, Seattle, WA 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.06.189654; this version posted July 6, 2020.
    [Show full text]
  • Biosynthesis and Deficiencies of Glycosylphosphatidylinositol
    130 Proc. Jpn. Acad., Ser. B 90 (2014) [Vol. 90, Review Biosynthesis and deficiencies of glycosylphosphatidylinositol † By Taroh KINOSHITA*1, (Communicated by Kunihiko SUZUKI, M.J.A.) Abstract: At least 150 different human proteins are anchored to the outer leaflet of the plasma membrane via glycosylphosphatidylinositol (GPI). GPI preassembled in the endoplasmic reticulum is attached to the protein’s carboxyl-terminus as a post-translational modification by GPI transamidase. Twenty-two PIG (for Phosphatidyl Inositol Glycan) genes are involved in the biosynthesis and protein-attachment of GPI. After attachment to proteins, both lipid and glycan moieties of GPI are structurally remodeled in the endoplasmic reticulum and Golgi apparatus. Four PGAP (for Post GPI Attachment to Proteins) genes are involved in the remodeling of GPI. GPI- anchor deficiencies caused by somatic and germline mutations in the PIG and PGAP genes have been found and characterized. The characteristics of the 26 PIG and PGAP genes and the GPI deficiencies caused by mutations in these genes are reviewed. Keywords: glycosylphosphatidylinositol, glycolipid, post-translational modification, somatic mutation, germline mutation, deficiency glycolipid membrane anchors. GPI-APs are typical Introduction raft-associated proteins and tend to form homo- At least 150 different human proteins are post- dimers.3),4) GPI-APs can be released from the translationally modified by glycosylphosphatidylino- cell after cleavage by GPI-cleaving enzymes or sitol (GPI) at the carboxyl (C)-terminus.1),2) These GPIases.5)–8) These characteristics are critical for proteins are expressed on the cell surface by being the functions of individual GPI-APs and for embryo- anchored to the outer leaflet of the plasma membrane genesis, neurogenesis, fertilization, and the immune via the phosphatidylinositol (PI) moiety and termed system.5),8)–11) GPI-anchored proteins (GPI-APs).
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]
  • Chromosome 21 Leading Edge Gene Set
    Chromosome 21 Leading Edge Gene Set Genes from chr21q22 that are part of the GSEA leading edge set identifying differences between trisomic and euploid samples. Multiple probe set IDs corresponding to a single gene symbol are combined as part of the GSEA analysis. Gene Symbol Probe Set IDs Gene Title 203865_s_at, 207999_s_at, 209979_at, adenosine deaminase, RNA-specific, B1 ADARB1 234539_at, 234799_at (RED1 homolog rat) UDP-Gal:betaGlcNAc beta 1,3- B3GALT5 206947_at galactosyltransferase, polypeptide 5 BACE2 217867_x_at, 222446_s_at beta-site APP-cleaving enzyme 2 1553227_s_at, 214820_at, 219280_at, 225446_at, 231860_at, 231960_at, bromodomain and WD repeat domain BRWD1 244622_at containing 1 C21orf121 240809_at chromosome 21 open reading frame 121 C21orf130 240068_at chromosome 21 open reading frame 130 C21orf22 1560881_a_at chromosome 21 open reading frame 22 C21orf29 1552570_at, 1555048_at_at, 1555049_at chromosome 21 open reading frame 29 C21orf33 202217_at, 210667_s_at chromosome 21 open reading frame 33 C21orf45 219004_s_at, 228597_at, 229671_s_at chromosome 21 open reading frame 45 C21orf51 1554430_at, 1554432_x_at, 228239_at chromosome 21 open reading frame 51 C21orf56 223360_at chromosome 21 open reading frame 56 C21orf59 218123_at, 244369_at chromosome 21 open reading frame 59 C21orf66 1555125_at, 218515_at, 221158_at chromosome 21 open reading frame 66 C21orf7 221211_s_at chromosome 21 open reading frame 7 C21orf77 220826_at chromosome 21 open reading frame 77 C21orf84 239968_at, 240589_at chromosome 21 open reading frame 84
    [Show full text]
  • An Isogenic Cell Line Panel Identi Es Major Regulators of Aberrant Astrocyte Proliferation in Down Syndrome
    An isogenic cell line panel identies major regulators of aberrant astrocyte proliferation in Down syndrome Keiji Kawatani Osaka University Toshihiko Nambara Osaka University Nobutoshi Nawa Tokyo Medical and Dental University https://orcid.org/0000-0001-6785-7867 Hidetaka Yoshimatsu Osaka University Haruna Kusakabe Osaka University Katsuya Hirata Osaka University https://orcid.org/0000-0003-3148-9892 Akira Tanave RIKEN Center for Biosystems Dynamics Research Kenta Sumiyama RIKEN https://orcid.org/0000-0001-8785-5439 Kimihiko Banno Nara Medical University Hidetoshi Taniguchi Osaka University https://orcid.org/0000-0002-1015-7760 Hitomi Arahori Osaka University Keiichi Ozono Osaka University Graduate School of Medicine Yasuji Kitabatake ( [email protected] ) Osaka University Article Keywords: Down syndrome, isogenic cell line panel, aberrant astrocyte proliferation Page 1/33 Posted Date: October 12th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-79293/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/33 Abstract Astrocytes exert adverse effects on the brains of individuals with Down syndrome (DS). Although a neurogenic-to-gliogenic shift in the fate-specication step has been reported, the mechanisms and key regulators underlying the accelerated proliferation of astrocyte precursor cells (APCs) in DS remain elusive. Here, we established an isogenic cell line panel, based on DS-specic induced pluripotent stem cells, the XIST-mediated transcriptional silencing system in trisomic chromosome 21, and genome/chromosome-editing technologies to eliminate phenotypic uctuations caused by genetic variation. The transcriptional responses of genes observed upon XIST induction and/or downregulation were not uniform, and only a small subset of genes showed a characteristic expression pattern, which is consistent with the proliferative phenotypes of DS APCs.
    [Show full text]
  • Morphology, Behavior, and the Sonic Hedgehog Pathway in Mouse Models of Down Syndrome
    MORPHOLOGY, BEHAVIOR, AND THE SONIC HEDGEHOG PATHWAY IN MOUSE MODELS OF DOWN SYNDROME by Tara Dutka A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2014 © 2014 Tara Dutka All Rights Reserved Abstract Down Syndrome (DS) is caused by a triplication of human chromosome 21 (Hsa21). Ts65Dn, a mouse model of DS, contains a freely segregating extra chromosome consisting of the distal portion of mouse chromosome 16 (Mmu16), a region orthologous to part of Hsa21, and a non-Hsa21 orthologous region of mouse chromosome 17. All individuals with DS display some level of craniofacial dysmorphology, brain structural and functional changes, and cognitive impairment. Ts65Dn recapitulates these features of DS and aspects of each of these traits have been linked in Ts65Dn to a reduced response to Sonic Hedgehog (SHH) in trisomic cells. Dp(16)1Yey is a new mouse model of DS which has a direct duplication of the entire Hsa21 orthologous region of Mmu16. Dp(16)1Yey’s creators found similar behavioral deficits to those seen in Ts65Dn. We performed a quantitative investigation of the skull and brain of Dp(16)1Yey as compared to Ts65Dn and found that DS-like changes to brain and craniofacial morphology were similar in both models. Our results validate examination of the genetic basis for these phenotypes in Dp(16)1Yey mice and the genetic links for these phenotypes previously found in Ts65Dn , i.e., reduced response to SHH. Further, we hypothesized that if all trisomic cells show a reduced response to SHH, then up-regulation of the SHH pathway might ameliorate multiple phenotypes.
    [Show full text]
  • PIGP (N-Term) Rabbit Polyclonal Antibody – AP53299PU-N | Origene
    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 AP53299PU-N PIGP (N-term) Rabbit Polyclonal Antibody Product data: Product Type: Primary Antibodies Applications: WB Recommended Dilution: Western blot: 1/1000. Reactivity: Human Host: Rabbit Isotype: Ig Clonality: Polyclonal Immunogen: Synthetic peptide - KLH conjugated - corresponding to the N-terminal region (between 2-30 aa) of human PIGP. Specificity: This antibody recognizes PIGP at N-term. Formulation: PBS with 0.09% (W/V) Sodium azide State: Aff - Purified State: Liquid purified Ig fraction Concentration: lot specific Purification: Purified through a Protein A column followed by peptide affinity purification Conjugation: Unconjugated Storage: Store undiluted at 2-8°C for one month or (in aliquots) at -20°C for longer. Avoid repeated freezing and thawing. Stability: Shelf life: one year from despatch. Gene Name: Homo sapiens phosphatidylinositol glycan anchor biosynthesis class P (PIGP), transcript variant 1 Database Link: Entrez Gene 51227 Human P57054 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 / 2 PIGP (N-term) Rabbit Polyclonal Antibody – AP53299PU-N Background: The PIGP gene encodes an enzyme involved in the first step of glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells that serves to anchor proteins to the cell surface. The encoded protein is a component of the GPI- N-acetylglucosaminyltransferase complex that catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI).
    [Show full text]
  • University of Southern Denmark the Correlation of Copy Number
    University of Southern Denmark The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese Zhao, Xin; Liu, Xiaomin; Zhang, Aiping; Chen, Huashuai; Huo, Qing; Li, Weiyang; Ye, Rui; Chen, Zhihua; Liang, Liping; Liu, Qiong A; Shen, Juan; Jin, Xin; Li, Wenwen; Nygaard, Marianne; Liu, Xiao; Hou, Yong; Ni, Ting; Bolund, Lars; Gottschalk, William; Tao, Wei; Gu, Jun; Tian, Xiao-Li; Yang, Huanming; Wang, Jian; Xu, Xun; Lutz, Michael W; Min, Junxia; Zeng, Yi; Nie, Chao Published in: Aging DOI: 10.18632/aging.101461 Publication date: 2018 Document version: Final published version Document license: CC BY Citation for pulished version (APA): Zhao, X., Liu, X., Zhang, A., Chen, H., Huo, Q., Li, W., Ye, R., Chen, Z., Liang, L., Liu, Q. A., Shen, J., Jin, X., Li, W., Nygaard, M., Liu, X., Hou, Y., Ni, T., Bolund, L., Gottschalk, W., ... Nie, C. (2018). The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese. Aging, 10(6), 1206-1222. https://doi.org/10.18632/aging.101461 Go to publication entry in University of Southern Denmark's Research Portal Terms of use This work is brought to you by the University of Southern Denmark. Unless otherwise specified it has been shared according to the terms for self-archiving. If no other license is stated, these terms apply: • You may download this work for personal use only. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying this open access version If you believe that this document breaches copyright please contact us providing details and we will investigate your claim.
    [Show full text]