This article is part of the Research Topic Proceedings of ICI Milan 2013

Original Research ARTICLE

Front. Immunol., 28 March 2014 | doi: 10.3389/fimmu.2014.00128

Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis

imageCarlo Selmi1,2*, imageFrancesca Cavaciocchi1,3, imageAna Lleo4, imageCristina Cheroni5, imageRaffaele De Francesco5, imageSimone A. Lombardi1, imageMaria De Santis1,3, imageFrancesca Meda1, imageMaria Gabriella Raimondo1, imageChiara Crotti1, imageMarco Folci1, imageLuca Zammataro1, imageMarlyn J. Mayo6, imageNancy Bach7, imageShinji Shimoda8, imageStuart C. Gordon9, imageMonica Miozzo10,11, imagePietro Invernizzi4, imageMauro Podda1, imageRossana Scavelli5, imageMichelle R. Martin12, imageJanine M. LaSalle12 and imageM. Eric Gershwin2
  • 1Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center, Milan, Italy
  • 2Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis, Davis, CA, USA
  • 3BIOMETRA Department, University of Milan, Milan, Italy
  • 4Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Milan, Italy
  • 5National Institute of Molecular Genetics (INGM), Milan, Italy
  • 6University of Texas Southwestern, Dallas, TX, USA
  • 7Mt. Sinai University, New York, NY, USA
  • 8Clinical Research Center, National Nagasaki Medical Center, Nagasaki, Japan
  • 9Henry Ford Hospital, Detroit, MI, USA
  • 10Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
  • 11Division of Pathology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
  • 12Genome Center and M.I.N.D. Institute, University of California Davis, Davis, CA, USA

Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.

Keywords: autoimmune cholangitis, epigenetics, environment

Citation: Selmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC, Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, LaSalle JM and Gershwin ME (2014) Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis. Front. Immunol. 5:128. doi: 10.3389/fimmu.2014.00128

Received: 01 November 2013; Accepted: 13 March 2014;
Published online: 28 March 2014.

Edited by:

Paola Zanovello, University of Padova, Italy

Reviewed by:

Giovanni Vazza, University of Padova, Italy
Daniele Calistri, IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori, Italy

Copyright: © 2014 Selmi, Cavaciocchi, Lleo, Cheroni, De Francesco, Lombardi, De Santis, Meda, Raimondo, Crotti, Folci, Zammataro, Mayo, Bach, Shimoda, Gordon, Miozzo, Invernizzi, Podda, Scavelli, Martin, LaSalle and Gershwin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Carlo Selmi, Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital, via A. Manzoni 56, 20089 Rozzano, Milan, Italy e-mail: carlo.selmi@unimi.it

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