Ganglioside Biosynthesis in Developing Brains and Apoptotic Cancer Cells: X

Total Page:16

File Type:pdf, Size:1020Kb

Ganglioside Biosynthesis in Developing Brains and Apoptotic Cancer Cells: X Neurochem Res (2012) 37:1245–1255 DOI 10.1007/s11064-012-0762-9 OVERVIEW Ganglioside Biosynthesis in Developing Brains and Apoptotic Cancer Cells: X. Regulation of Glyco-genes Involved in GD3 and Sialyl-Lex/a Syntheses Subhash Basu • Rui Ma • Joseph R. Moskal • Manju Basu Received: 11 November 2011 / Revised: 12 March 2012 / Accepted: 22 March 2012 / Published online: 10 April 2012 Ó Springer Science+Business Media, LLC 2012 Abstract Gangliosides, the acidic glycosphingolipids D-PDMP (inhibitor of glucosylceramide biosynthesis), (GSLs) containing N-acetylgalactosamine and sialic acid Betulinic Acid (a triterpinoid isolated from bark of certain are ubiquitous in the central nervous system. At least six trees and used for cancer treatment in China), Tamoxifen a DSL-glycosyltransferase activities (GLTs Gangliosides, drug in use in the west for treatment of early stages of the the acidic glycosphingolipids (GSLs) containing N-acety- disease in breast cancer patients), and cis-platin (an lgalactosamine and sialic acid (or NAc-Neuraminic acid) inhibitor of DNA biosynthesis used for testicular cancer are ubiquitous in the central nervous system. At least six patients) were used for induction of apoptosis in the above- GSL-glycosyltransferase activities (GLTs) of Basu-Rose- mentioned cell lines. Within 2–6 h, transcriptional modu- man pathway catalyzing the biosynthesis of these gan- lation of a number of glyco-genes was observed by DNA- gliosides have been characterized in developing chicken micro-array (containing over 300 glyco genes attached to brains. Most of these glyco-genes are expressed in the early the glass cover slips) studies. Under long incubation time stages (7–17 days) of brain development and lowered in (24–48 h) almost all of the glyco-genes were downregu- the adult stage, but the cause of reduction of enzymatic lated. The cause of these glyco-gene regulations during activities of these GLTs in the adult stages is not known. In apoptotic induction in metastatic carcinoma cells is order to study glyco-gene regulation we used four clonal unknown and needs future investigations for further metastatic cancer cells of colon and breast cancer tissue explanations. These apoptotic agents could be employed as origin (Colo-205, SKBR-3, MDA-468, and MCF-3). The a new generation of anti-cancer drugs after properly glyco-genes for synthesis of SA-LeX and SA-LeA (which delivered to the patients. contain N-acetylglucosamine, sialic acid and fucose) in these cells were modulated differently at different phases Keywords Apoptosis Á Breast cancer cells Á (between 2 and 48 h) of apoptotic inductions. L-PPMP, Ganglioside biosynthesis Á GD3 Á SA-Lex Á Glyco-gene regulation Special Issue: In Honor of Bob Leeden. Introduction S. Basu (&) Á M. Basu Department of Chemistry and Biochemistry and Cancer Drug Delivery Research Foundation, University of Notre Dame, In the field of Glycosphingolipids (GSLs), the term POBox-752, Notre Dame, IN 46556, USA ‘‘Ganglioside’’ is meant for the GSLs containing sialic e-mail: [email protected] acids (NeuAc or NeuGc). These compounds were isolated R. Ma and purified from brain tissues [1–5] and peripheral ner- Global Assay Development, Siemens Healthcare Diagnostic vous systems [6–10]. Since discovery of GM2-ganglioside Div., Elkhart, IN 46515, USA from human Tay-Sachs brain by Klenk and his associates in 1939 [1] and GM3 from horse erythrocytes by Yama- J. R. Moskal The Falk Center for Molecular Therapeutics, Northwestern kawa and his co-workers in 1951 [11]. Structures of over University, Evanston, IL 60201, USA 180 gangliosides are documented in literature [12]. Kuhn 123 1246 Neurochem Res (2012) 37:1245–1255 and Wiegandt first established the chemical structures of acidic-GSLs were being established in different laborato- GM1, GD1a, and GD1b in 1963 [3]. Structures of all these ries around world, interest in searching the mechanism of naturally occurring gangliosides revealed they could be their synthesis in the normal tissues and cancer cells began classified in three families (Fig. 1) according to the third at almost the same time. The biosynthetic pathway-a for sugar present in the oligosaccharide chains next to cera- synthesis of GD1a ganglioside from ceramide was pro- mide: (1) Ganglio- (GalNAc-Gal-Glc-ceramide), (2) Lacto- posed by Basu and Roseman in 1975 [26–32] (Fig. 3) and (GlcNAc-Gal-Glc-ceramide), and (3) Globo- (Gal-Gal- was first established in embryonic chicken brains. All of Glc-ceramide). However, the simplest gangliosides G7 those glycosyltransferases were isolated, characterized, and (NeuAc2, 3Gal-Ceramide), GM3 (NeuAca2, 3Galb1, cloned in different laboratories. These days it is proved that 4Glc-ceramide), and GD3 (NeuAca2, 8-NeuAca2, 3Galb1, a different gene product catalyzes each enzymatic activity, 4Glc-ceramide) are free of hexosamines (Fig. 2). Sialic and isozymes are widely distributed in different animal acid-containing gangliosides were first characterized in systems. Expression of these genes in normal and diseased brain tissues; later on distribution of these acidic Glyco- stages could be studied by analysis of mRNAs, but very sphingolipids (GSLs) containing both NeuAc and NeuGc little is known about the regulation of these gene expres- has been characterized in blood and other tissues of higher sions during varied biological conditions. Recognition of eukaryotes except in marine animals. In recent years GM3, the exact regulation of these Glyco-genes would give us GD3, LD1, SA-Lex, and SA-Lea have been characterized in tools for disease control and cure in humans. many cancer cells [13–16] including breast and colon In this article an attempt is made to compare gene reg- carcinomas. In case of various neurological inherited dis- ulation of glycosyltransferases in developing brains eases, deposition of specific gangliosides in the tissues is with apoptotic cancer cells. All the enzymes of GD3 and recognized. GM2 is known to be the main ganglioside deposited in Tay-Sachs-diseased (TSD) brain, but how Abbreviated Names Structures excess deposition of this ganglioside hinders the normal Hexosamine Free α function in TSD brain [17, 18] remains unknown. Recently, G7 NeuAc 2-3Gal-Cer NeuAcα2-3Galβ1-4Glc-Cer Dwek and his associates indicated [19] using mouse GM3 GD3 NeuAca2-8NeuAca2-3Galb1-4Glc-Cer models of GM1 and GM2 gangliosidosis that inflammation may play an important role in the pathogenesis of the GalNAcβ1-4Gal-Glc-Cer GalNAc-containing α2-3 gangliosides. GD3 ganglioside has been found in excess in GM2 NeuAc Galβ1-3GalNAcβ1-4Gal-Glc-Cer human meningiomas [20], gliomas [21], and melanomas α2-3 [22]. However, the relationship of these gangliosides to the GM1 NeuAc Galβ1-3GalNAcβ1-4Gal-Glc-Cer exact physiological disorders is not yet known. Both GD1a α2-3 α2-3 x a NeuAc NeuAc SA-Le and SA-Le are present on the cell surfaces of β β GlcNAc-containing Gal 1-4GlcNAc 1-3Gal-Glc-Cer α α1-3 breast and colon cancers [23–25]. A direct role of these X 2-3 SA-Le NeuAc Fuc acidic GSLs to cancer metastasis has not been established. During the last five decades while the structures of these Fig. 2 Structure of gangliosides with and without NAc-hexosamines Fig. 1 Broad classification of (Glycose)n—O—Sphingosine glycosphingolipids (GSLs) | CERAMIDE n=1 to 10 glycoses NH R=C to C | Fatty acid 13 15 CO—R ACIDIC - GSLs NEUTRAL- GSLs Glucuronyl- Sialyl- Mono- Di- Oligo-glycosyl- Gal-cer Glc-cer Gal-Glc-cer ceramide Mono- Di- Polysialo- Blood Groups Globosides Gangliosides- …. (….GlclNAc-Gal-Glc-cer) (….Gal-Gal-Glc-cer) (GalNAc-Gal-Glc-cer) (NeuAc or, NeuGc) Series—[Ganglio-Gg] —[Lacto-Lc] —[Globo-Gb] 123 Neurochem Res (2012) 37:1245–1255 1247 Fig. 3 Basu-Roseman Ceramide D-/L-PDMP ganglioside pathway and cancer GlcT D-/L-PPMP Galα1- 3Galβ1- 4GlcNAcβ1-3Lc2 GSL pathways Inhibitors Glc-Cer GalT-2 nLc5 GlcNAcT- 1 Galβ1-4Glc-Cer SAT-1 Galβ1-4Glc-Cer GlcNAcβ1-3Lc2 α GalT-5 2-3 Lc2 Lc3 SA GM3 GalT-4 SAT- 2 Galβ1-4Glc-Cer GalNAcT-1 β β SA GD3 Gal 1- 4GlcNAc 1-3Lc2 α β 2-8 nLc4 GalNAc 1-4Gal-Glc-Cer SA GalNAcT-1 SAT-3 SA GM2 GlcNAcT-2 Galβ1- 4GlcNAcβ1-3Lc2 GalT-3 β GalNAc 1-4Gal-Glc-Cer α2-3 LM1 SA GlcNAcβ1-3nLc4 β SA GD2 FucT-3 Gal 1- 3GalNAc-Gal-Glc-Cer GalT-3 inLc5 SA SAT-4 SA GM1 Galβ1- 4GlcNAcβ1-3Lc2 GlcNAcT-3 Galβ1-3GalNAc-Gal-Glc-Cer α1-3 SA Fuc Gal-GalNAc-Gal-Glc-Cer GD1b GlcNAcβ1-3 i α SA 2-3 SA-LeX nLc4 SA SA GD1a GlcNAcβ1-6 SA GT1b I Carcino-Embryonic Ii Basu-Roseman Pathway Pathway-b Antigen Ii Core GSLs (or Pathway-a) (Cancer Cells) Lymphoma Cells Embryonic Brain Sialyl-LeX/A biosynthesis are expressed in both the sys- the GlcNAc-containing nLcOse4-ceramide (the intermedi- tems (embryonic brains and breast cancer cells). The age- ate of gangliosides SA-Lex) was established in rabbit bone dependent expression studies of those glycolipid glyco- marrow [50, 51], human neuroblastoma (IMR-32) cells syltransferases raised the question whether those enzymes [52], cultured TSD cells [53], mouse T- and B-lymphomas could be modulated also under induced apoptotic condi- [54, 55], bovine spleen [56, 57], embryonic chicken brains tions of cancer cells. Of course, the expression of glyco- [58–60], and carcinoma cells of colon origin [61–63]. sphingolipids on the surfaces of both apoptotic and Complete biosynthesis of SA-Lex from nLcOse4-ceramide nonapoptotic cells has not yet been revealed exhaustively. to SA-Lex (Fig. 3) has been achieved in colo-205 and However, our finding on the activity and DNA-microarrays embryonic chicken brains [60, 61]. Biosynthesis in studies suggested these could be different at different time vitro of Ii-core glycosphingolipids (GlcNAcbeta1,6(Glc- points (2 and 24 h) and with different concentrations of NAcbeta1,3)Galbeta1,4Glc-R) was achieved in mouse the apoptotic agents (L-PPMP; 2–16 lmol).
Recommended publications
  • Seq2pathway Vignette
    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
    [Show full text]
  • Genome-Wide Analysis of Thyroid Hormone Receptors Shared and Specific Functions in Neural Cells
    Genome-wide analysis of thyroid hormone receptors shared and specific functions in neural cells Fabrice Chatonneta, Romain Guyota, Gérard Benoîtb, and Frederic Flamanta,1 aInstitut de Génomique Fonctionnelle de Lyon, Université de Lyon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique, École Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France; and bCentre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS, Université Lyon 1, Unité Mixte de Recherche 5334, Villeurbanne F-69622, France Edited by Pierre Chambon, Institut de Génétique et de Biologie Moléculaire et Cellulaire (Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U596, Université de Strasbourg, College de France), Illkirch-Cedex, France, and approved January 4, 2013 (received for review June 25, 2012) TRα1 and TRβ1, the two main thyroid hormone receptors in mam- issue. It would help to develop new selective ligands (6). It might mals, are transcription factors that share similar properties. How- also help to predict the possible detrimental side effects of these ever, their respective functions are very different. This functional synthetic ligands in heart and brain (7) and the toxicity of some divergence might be explained in two ways: it can reflect different environmental contaminants supposed to interfere with TR expression patterns or result from different intrinsic properties of functions (8). The primary sequence and 3D structure of TRα1 β the receptors. We tested this second hypothesis by comparing the and TR 1 are very similar, although differences are observed for – repertoires of 3,3′,5-triiodo-L-thyronine (T3)-responsive genes of key amino acids in the DNA-binding domain (9 12).
    [Show full text]
  • Investigation of Adiposity Phenotypes in AA Associated with GALNT10 & Related Pathway Genes
    Investigation of Adiposity Phenotypes in AA Associated With GALNT10 & Related Pathway Genes By Mary E. Stromberg A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVERSITY GRADUATE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY In Molecular Genetics and Genomics December 2018 Winston-Salem, North Carolina Approved by: Donald W. Bowden, Ph.D., Advisor Maggie C.Y. Ng, Ph.D., Advisor Timothy D. Howard, Ph.D., Chair Swapan Das, Ph.D. John P. Parks, Ph.D. Acknowledgements I would first like to thank my mentors, Dr. Bowden and Dr. Ng, for guiding my learning and growth during my years at Wake Forest University School of Medicine. Thank you Dr. Ng for spending so much time ensuring that I learn every detail of every protocol, and supporting me through personal difficulties over the years. Thank you Dr. Bowden for your guidance in making me a better scientist and person. I would like to thank my committee for their patience and the countless meetings we have had in discussing this project. I would like to say thank you to the members of our lab as well as the Parks lab for their support and friendship as well as their contributions to my project. Special thanks to Dean Godwin for his support and understanding. The umbrella program here at WFU has given me the chance to meet some of the best friends I could have wished for. I would like to also thank those who have taught me along the way and helped me to get to this point of my life, with special thanks to the late Dr.
    [Show full text]
  • Down Syndrome Congenital Heart Disease: a Narrowed Region and a Candidate Gene Gillian M
    March/April 2001 ⅐ Vol. 3 ⅐ No. 2 article Down syndrome congenital heart disease: A narrowed region and a candidate gene Gillian M. Barlow, PhD1, Xiao-Ning Chen, MD1, Zheng Y. Shi, BS1, Gary E. Lyons, PhD2, David M. Kurnit, MD, PhD3, Livija Celle, MS4, Nancy B. Spinner, PhD4, Elaine Zackai, MD4, Mark J. Pettenati, PhD5, Alexander J. Van Riper, MS6, Michael J. Vekemans, MD7, Corey H. Mjaatvedt, PhD8, and Julie R. Korenberg, PhD, MD1 Purpose: Down syndrome (DS) is a major cause of congenital heart disease (CHD) and the most frequent known cause of atrioventricular septal defects (AVSDs). Molecular studies of rare individuals with CHD and partial duplications of chromosome 21 established a candidate region that included D21S55 through the telomere. We now report human molecular and cardiac data that narrow the DS-CHD region, excluding two candidate regions, and propose DSCAM (Down syndrome cell adhesion molecule) as a candidate gene. Methods: A panel of 19 individuals with partial trisomy 21 was evaluated using quantitative Southern blot dosage analysis and fluorescence in situ hybridization (FISH) with subsets of 32 BACs spanning the region defined by D21S16 (21q11.2) through the telomere. These BACs span the molecular markers D21S55, ERG, ETS2, MX1/2, collagen XVIII and collagen VI A1/A2. Fourteen individuals are duplicated for the candidate region, of whom eight (57%) have the characteristic spectrum of DS-CHD. Results: Combining the results from these eight individuals suggests the candidate region for DS-CHD is demarcated by D21S3 (defined by ventricular septal defect), through PFKL (defined by tetralogy of Fallot). Conclusions: These data suggest that the presence of three copies of gene(s) from the region is sufficient for the production of subsets of DS-CHD.
    [Show full text]
  • Glycosyltransferase B4GALNT2 As a Predictor of Good Prognosis in Colon Cancer: Lessons from Databases
    International Journal of Molecular Sciences Article Glycosyltransferase B4GALNT2 as a Predictor of Good Prognosis in Colon Cancer: Lessons from Databases Michela Pucci, Nadia Malagolini and Fabio Dall’Olio * Department of Experimental, Diagnostic and Specialty Medicine (DIMES), General Pathology Building, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy; [email protected] (M.P.); [email protected] (N.M.) * Correspondence: [email protected]; Tel.: +39-051-2094704 Abstract: Background: glycosyltransferase B4GALNT2 and its cognate carbohydrate antigen Sda are highly expressed in normal colon but strongly downregulated in colorectal carcinoma (CRC). We previously showed that CRC patients expressing higher B4GALNT2 mRNA levels displayed longer survival. Forced B4GALNT2 expression reduced the malignancy and stemness of colon cancer cells. Methods: Kaplan–Meier survival curves were determined in “The Cancer Genome Atlas” (TCGA) COAD cohort for several glycosyltransferases, oncogenes, and tumor suppressor genes. Whole expression data of coding genes as well as miRNA and methylation data for B4GALNT2 were downloaded from TCGA. Results: the prognostic potential of B4GALNT2 was the best among the glycosyltransferases tested and better than that of many oncogenes and tumor suppressor genes; high B4GALNT2 expression was associated with a lower malignancy gene expression profile; differential methylation of an intronic B4GALNT2 gene position and miR-204-5p expression play major roles in B4GALNT2 regulation. Conclusions: high B4GALNT2 expression is a strong predictor of good prognosis in CRC as a part of a wider molecular signature that includes ZG16, ITLN1, BEST2, and Citation: Pucci, M.; Malagolini, N.; GUCA2B. Differential DNA methylation and miRNA expression contribute to regulating B4GALNT2 Dall’Olio, F.
    [Show full text]
  • Precise Integration of Inducible Transcriptional Elements (Priite
    Published online 4 May 2017 Nucleic Acids Research, 2017, Vol. 45, No. 13 e123 doi: 10.1093/nar/gkx371 Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of gene expression Rita Pinto1,2,3,4, Lars Hansen4, John Hintze4, Raquel Almeida1,2,3,5, Sylvester Larsen6,7, Mehmet Coskun8,9, Johanne Davidsen6, Cathy Mitchelmore6, Leonor David1,2,3, Jesper Thorvald Troelsen6 and Eric Paul Bennett4,* 1i3S, Instituto de Investigac¸ao˜ e Inovac¸ao˜ em Saude,´ Universidade do Porto, Porto, Portugal, 2Ipatimup, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal, 3Faculty of Medicine of the University of Porto, Porto, Portugal, 4Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark, 5Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal, 6Department of Science and Environment, Roskilde University, Roskilde, Denmark, 7Department of Clinical Immunology, Naestved Hospital, Naestved, Denmark, 8Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark and 9The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Received October 03, 2016; Revised March 30, 2017; Editorial Decision April 10, 2017; Accepted April 27, 2017 ABSTRACT INTRODUCTION Tetracycline-based inducible systems provide pow- Historically, analysis of the molecular genetic mechanisms erful methods for functional studies where gene ex- underlying cell fate and animal phenotypes has been studied pression can be controlled. However, the lack of tight by abrogating gene function in cellular and animal model control of the inducible system, leading to leakiness systems.
    [Show full text]
  • The Intriguing Case of the B3GALT5 Gene and Its Distinct Promoters
    Biology 2014, 3, 484-497; doi:10.3390/biology3030484 OPEN ACCESS biology ISSN 2079-7737 www.mdpi.com/journal/biology Review Control of Glycosylation-Related Genes by DNA Methylation: the Intriguing Case of the B3GALT5 Gene and Its Distinct Promoters Marco Trinchera 1,*, Aida Zulueta 2, Anna Caretti 2 and Fabio Dall’Olio 3 1 Department of Medicine Clinical and Experimental (DMCS), University of Insubria, 21100 Varese, Italy 2 Department of Health Sciences, San Paolo Hospital, University of Milan, 20142 Milano, Italy; E-Mails: [email protected] (A.Z.); [email protected] (A.C.) 3 Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-0332-39-7160; Fax: +39-0332-39-7119. Received: 28 April 2014; in revised form: 22 July 2014 / Accepted: 25 July 2014 / Published: 4 August 2014 Abstract: Glycosylation is a metabolic pathway consisting of the enzymatic modification of proteins and lipids through the stepwise addition of sugars that gives rise to glycoconjugates. To determine the full complement of glycoconjugates that cells produce (the glycome), a variety of genes are involved, many of which are regulated by DNA methylation. The aim of the present review is to briefly describe some relevant examples of glycosylation-related genes whose DNA methylation has been implicated in their regulation and to focus on the intriguing case of a glycosyltransferase gene (B3GALT5). Aberrant promoter methylation is frequently at the basis of their modulation in cancer, but in the case of B3GALT5, at least two promoters are involved in regulation, and a complex interplay is reported to occur between transcription factors, chromatin remodelling and DNA methylation of typical CpG islands or even of other CpG dinucleotides.
    [Show full text]
  • Chromosome-Wide Assessment of Replication Timing for Human Chromosomes 11Q and 21Q: Disease-Related Genes in Timing-Switch Regions
    © 2002 Oxford University Press Human Molecular Genetics, 2002, Vol. 11, No. 1 13–21 ARTICLE Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions Yoshihisa Watanabe1, Asao Fujiyama2,3, Yuta Ichiba1, Masahira Hattori3, Tetsushi Yada3, Yoshiyuki Sakaki3 and Toshimichi Ikemura1,* 1Division of Evolutionary Genetics, Department of Population Genetics and 2Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka-ken 411-8540, Japan and 3Human Genome Research Group, RIKEN Genomic Sciences Center, RIKEN, Suehiro-cho 1-7-22, Turumi-ku, Yokohama, Kanagawa-ken 230-0045, Japan Received August 15, 2001; Revised and Accepted November 2, 2001 The completion of the human genome sequence will greatly accelerate development of a new branch of bioscience and provide fundamental knowledge to biomedical research. We used the sequence information to measure replication timing of the entire lengths of human chromosomes 11q and 21q. Megabase-sized zones that replicate early or late in S phase (thus early/late transition) were defined at the sequence level. Early zones were more GC-rich and gene-rich than were late zones, and early/late transitions occurred primarily at positions identical to or near GC% transitions. We also found the single nucleotide polymorphism (SNP) frequency was high in the late-replicating and replication-transition regions. In the early/late transition regions, concentrated occurrence of cancer-related genes that include CCND1 encoding cyclin D1 (BCL1), FGF4 (KFGF), TIAM1 and FLI1, was observed. The transition regions contained other disease-related genes including APP associated with familial Alzheimer’s disease (AD1), SOD1 associated with familial amyotrophic lateral sclerosis (ALS1) and PTS associated with phenylketonuria.
    [Show full text]
  • Human Chromosome 21 Gene Expression Atlas in the Mouse
    letters to nature Microarray data analysis .............................................................. We identified all of the positive oligonucleotides with the threshold values R ¼ 13 and D ¼ 12Q (ref. 21). R and D are threshold values for the ratio and the difference between Human chromosome 21 gene perfect match intensity and mismatch intensity, respectively. Thus varying these values gives different measures of sensitivity and specificity. We then used BLAST to identify expression atlas in the mouse conserved blocks that corresponded to at least two positive oligonucleotides so as to reduce the number of false positives. Alexandre Reymond*†, Valeria Marigo†‡, Murat B. Yaylaoglu†§, Received 16 September; accepted 30 October 2002; doi:10.1038/nature01251. Antonio Leoni‡, Catherine Ucla*, Nathalie Scamuffa*, 1. Hardison, R. C., Oeltjen, J. & Miller, W. Long human–mouse sequence alignments reveal novel Cristina Caccioppoli‡, Emmanouil T. Dermitzakis*, Robert Lyle*, regulatory elements: a reason to sequence the mouse genome. Genome Res. 7, 959–966 (1997). Sandro Banfi , Gregor Eichele , Stylianos E. Antonarakis 2. O’Brien, S. J. et al. The promise of comparative genomics in mammals. Science 286, 458–462 (1999) ‡ § * 479–481. & Andrea Ballabio‡k 3. Shabalina, S. A., Ogurtsov, A. Y., Kondrashov, V. A. & Kondrashov, A. S. Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17, 373–376 (2001). * Division of Medical Genetics, University of Geneva Medical School and 4. Hardison, R. C. Conserved noncoding sequences are reliable guides to regulatory elements. Trends University Hospital of Geneva, CMU, 1, rue Michel Servet, 1211 Geneva, Genet. 16, 369–372 (2000). Switzerland 5. Dermitzakis, E. T. & Clark, A. G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover.
    [Show full text]
  • Mapping Pathogenic Regulatory Regions and Genes
    Mapping pathogenic regulatory regions and genes Chris Cotsapas Yale/Broad Mapping pathogenic regulatory regions Chris Cotsapas Yale/Broad Mapping pathogenic regulatory regions Chris Cotsapas Yale/Broad cotsapaslab.info/positions http://biorxiv.org/content/early/2016/05/19/054361 Common risk variants localize to DHS Maurano et. al, Science 2012 Gusev et. al, AJHG 2014 Trynka et al, AJHG 2015 over loci shown for 9 AID). and adjusted forIdentifying the correlation specific structure regulatory in the gene elements expression driving data (see risk supplementary to the disease, and the materials forgenes more that details). they control: We called any DHS cluster harboring a CI SNP (⇢d > 0) a We convertedpathogenic P values DHS of correlationcluster. For to chi-squareeach lead test SNP, statistics we defined as an a intermediate 2 Mbp region step centered on it, required toand measure identified posterior all pathogenic of association DHS transmitted clusters and from genes a pathogenic overlapping DHS the cluster region to using intersect a gene. Asfunction shown in of Supplementary BEDTools [45]. Figure We reasoned 7 34, P values that if of a correlationDHS cluster follow controls a uniform expression of a gene, distribution;its therefore, presence/absence this conversion should is be valid. correlated We showed to the the expression proportion of the of associationtarget gene over matched posterior transmittedsamples. We from therefore, DHS cluster measuredd to P gene valueg ofby correlationβd,g, and computed between all it pairs using of the pathogenic DHS following formula.clusters and genes in the locus using paired expression and DHS data over 22 cell types from 2 2 χ /2 χd,g /2 Roadmap Epigenomeβ Projectd,g = e d,g (see/ supplementarye i materials), and asked whether expression g of any gene in the locus changed conditionalXi on presence of a pathogenic DHS cluster.
    [Show full text]
  • Transcriptional Control of the B3GALT5 Gene by a Retroviral Promoter and Methylation of Distant Regulatory Elements
    The FASEB Journal • Research Communication Transcriptional control of the B3GALT5 gene by a retroviral promoter and methylation of distant regulatory elements Aida Zulueta,* Anna Caretti,* Paola Signorelli,* Fabio Dall’Olio,† and Marco Trinchera‡,1 *Department of Health Sciences, San Paolo Hospital, University of Milan, Milan, Italy; †Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; and ‡Department of Medicine Clinical and Experimental (DMCS), University of Insubria, Varese, Italy ABSTRACT We focused on transcription factors and Key Words: hepatocyte nuclear factor 1 ⅐ colon cancer ⅐ type 1 epigenetic marks that regulate the B3GALT5 gene chain carbohydrates ⅐ transposon through its retroviral long terminal repeat (LTR) pro- moter. We compared the expression levels of the The B3GALT5 gene codes for ␤1,3 galactosyltrans- B3GALT5 LTR transcript, quantitated by competitive ferase 5, an enzyme responsible for the synthesis of type RT-PCR, with those of the candidate transcription 1 chain carbohydrates in mammals. In humans, in ␣ ␤ factors HNF1 / and Cdx1/2, determined by Western particular, it participates in the biosynthesis of the blot analysis, in colon cancer biopsies, various cell lines, histo-blood group antigens Lewis a (Gal␤1–3[Fuc␣1– and cell models serving as controls. We found that 4]GlcNAc), Lewis b (Fuc␣1-2Gal␤1–3[Fuc␣1– ␣ ␤ HNF1 / were easily detected, irrespective of the 4]GlcNAc), and sialyl-Lewis a (NeuAc␣2-3Gal␤1– amount of LTR transcript expressed by the source, 3[Fuc␣1–4]GlcNAc) (1). The latter is a specific selectin whereas Cdx1/2 were undetectable, and no sample ligand (2, 3) constituting the epitope of the CA19.9 lacking HNF1␣/␤ expressed the LTR transcript.
    [Show full text]
  • Differential Chromatin Accessibility Landscape of Gain-Of-Function Mutant P53 Tumours
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.24.395913; this version posted November 24, 2020. 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. Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours Bhavya Dhaka and Radhakrishnan Sabarinathan* National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India. * To whom correspondence should be addressed. Email: [email protected] Abstract Mutations in TP53 not only affect its tumour suppressor activity but also exerts oncogenic gain-of-function activity. While the genome-wide mutant p53 binding sites have been identified in cancer cell lines, the chromatin accessibility landscape driven by mutant p53 in primary tumours is unknown. Here, we leveraged the chromatin accessibility data of primary tumours from TCGA to identify differentially accessible regions in mutant p53 tumours compared to wild p53 tumours, especially in breast and colon cancers. We found 1587 lost and 984 gained accessible regions in breast, and 1143 lost and 640 gained regions in colon. However, less than half of those regions in both cancer types contain sequence motifs for wild-type or mutant p53 binding. Whereas, the remaining showed enrichment for master transcriptional regulators, such as FOX-Family TFs and NF-kB in lost and SMAD and KLF TFs in gained regions of breast. In colon, ATF3 and FOS/JUN TFs were enriched in lost, and CDX family TFs and HNF4A in gained regions.
    [Show full text]