title: DNA methylation profiling of the X chromosome reveals an aberrant demethylation on CXCR3 promoter in primary biliary cirrhosis.
abstract: BACKGROUND
  Although the etiology of primary biliary cirrhosis (PBC) remains enigmatic, there are several pieces of data supporting the thesis that a strong genetic predisposition and environmental factors interact to produce a selective loss of tolerance. The striking female predominance of PBC has suggested that this sex predisposition may be secondary to epigenetic alterations on the X chromosome. In the present study, we rigorously defined the X chromosome methylation profile of CD4, CD8, and CD14 cells from 30 PBC patients and 30 controls. Genomic DNA from sorted CD4, CD8, and CD14 subpopulations was isolated, sonicated, and immunoprecipitated for analysis of methylation. All products were hybridized to a custom-tiled four-plex array containing 27,728 CpG islands annotated by UCSC and 22,532 well-characterized RefSeq promoter regions. Furthermore, bisulfite sequencing was then used for validation on a subsequent group of independent samples from PBC patients and controls. Thence, expression levels of selected X-linked genes were evaluated by quantitative real-time PCR with cDNA samples from all subjects.
  
  
  RESULTS
  We report herein that a total of 20, 15, and 19 distinct gene promoters reflected a significant difference in DNA methylation in CD4+ T, CD8+ T, and CD14+ cells in patients with PBC. Interestingly, there was hypermethylation of FUNDC2 in CD8+ T cells and a striking demethylation of CXCR3 in CD4+ T cells, which inversely correlated with CXCR3 expression levels in CD4+ T cells from early-stage PBC patients.
  
  
  CONCLUSIONS
  Our data provides a set of genes with epigenetic alteration likely to be indicators of autoimmunity and emphasizes the role of CXCR3 in the natural history of PBC.
authors.affiliation: Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Milan Italy.
authors.forename: Ana
authors.initials: A
authors.lastname: Lleo
authors.affiliation: Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616 USA.
authors.forename: Weici
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Ming
authors.initials: M
authors.lastname: Zhao
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Yixin
authors.initials: Y
authors.lastname: Tan
authors.affiliation: Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Milan Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Bernuzzi
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Bochen
authors.initials: B
authors.lastname: Zhu
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Qiqun
authors.initials: Q
authors.lastname: Tan
authors.affiliation: Migliavacca Center for the Study of Liver Disease, 1st Division of Gastroenterology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milan, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Malinverno
authors.affiliation: Internal Medicine, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca' Granda - Ospedale Maggiore Policlinico Milano, Milan, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Valenti
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Jiang
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Lina
authors.initials: L
authors.lastname: Tan
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liao
authors.affiliation: Department of Microbiology, Monash University, Clayton, Victoria Australia.
authors.forename: Ross
authors.initials: R
authors.lastname: Coppel
authors.affiliation: Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Milan Italy.|Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616 USA.
authors.forename: Pietro
authors.initials: P
authors.lastname: Invernizzi
authors.affiliation: Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, Hunan People's Republic of China.
authors.forename: Qianjin
authors.initials: Q
authors.lastname: Lu
authors.affiliation: Centre for Liver Research and NIHR Biomedical Research Unit for Liver Disease, University of Birmingham, Edgbaston, Birmingham, England UK.
authors.forename: David H
authors.initials: DH
authors.lastname: Adams
authors.affiliation: Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Suite 6510, Davis, CA 95616 USA.
authors.forename: M Eric
authors.initials: ME
authors.lastname: Gershwin
keywords: CXCR3; Primary biliary cirrhosis; X chromosome