title: Selective demethylation and altered gene expression are associated with ICF syndrome in human-induced pluripotent stem cells and mesenchymal stem cells.
abstract: Immunodeficiency, centromeric instability and facial anomalies type I (ICF1) syndrome is a rare genetic disease caused by mutations in DNA methyltransferase (DNMT) 3B, a de novo DNA methyltransferase. However, the molecular basis of how DNMT3B deficiency leads to ICF1 pathogenesis is unclear. Induced pluripotent stem cell (iPSC) technology facilitates the study of early human developmental diseases via facile in vitro paradigms. Here, we generate iPSCs from ICF Type 1 syndrome patient fibroblasts followed by directed differentiation of ICF1-iPSCs to mesenchymal stem cells (MSCs). By performing genome-scale bisulfite sequencing, we find that DNMT3B-deficient iPSCs exhibit global loss of non-CG methylation and select CG hypomethylation at gene promoters and enhancers. Further unbiased scanning of ICF1-iPSC methylomes also identifies large megabase regions of CG hypomethylation typically localized in centromeric and subtelomeric regions. RNA sequencing of ICF1 and control iPSCs reveals abnormal gene expression in ICF1-iPSCs relevant to ICF syndrome phenotypes, some directly associated with promoter or enhancer hypomethylation. Upon differentiation of ICF1 iPSCs to MSCs, we find virtually all CG hypomethylated regions remained hypomethylated when compared with either wild-type iPSC-derived MSCs or primary bone-marrow MSCs. Collectively, our results show specific methylome and transcriptome defects in both ICF1-iPSCs and differentiated somatic cell lineages, providing a valuable stem cell system for further in vitro study of the molecular pathogenesis of ICF1 syndrome. GEO accession number: GSE46030.
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine.
authors.forename: Kevin
authors.initials: K
authors.lastname: Huang
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine, Translational Stem Cell Center, Tongji Hospital and Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China.
authors.forename: Zhourui
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine, Translational Stem Cell Center, Tongji Hospital and Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China.
authors.forename: Zhenshan
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine, Translational Stem Cell Center, Tongji Hospital and Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China.
authors.forename: Ganlu
authors.initials: G
authors.lastname: Hu
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine.
authors.forename: Juehua
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine.
authors.forename: Kai H
authors.initials: KH
authors.lastname: Chang
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine.
authors.forename: Kee-Pyo
authors.initials: KP
authors.lastname: Kim
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine.
authors.forename: Thuc
authors.initials: T
authors.lastname: Le
authors.affiliation: Pasarow Mass Spectrometry Laboratory, The Semel Institute for Neuroscience and Human Behavior and the Department of Psychiatry & Biobehavioral Sciences, University of California Los Angeles, CA 90024, USA and.
authors.forename: Kym F
authors.initials: KF
authors.lastname: Faull
authors.affiliation: Department of Pathology.
authors.forename: Nagesh
authors.initials: N
authors.lastname: Rao
authors.affiliation: Department of Paediatric Immunology, Great North Children's Hospital, Queen Victoria Road, Newcastle upon Tyne NE1 4LP, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Gennery
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine, Translational Stem Cell Center, Tongji Hospital and Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Xue
authors.affiliation: Laboratory of Molecular Signaling, Division of Oral Biology and Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Cun-Yu
authors.initials: CY
authors.lastname: Wang
authors.affiliation: Department of Molecular, Cell and Developmental Biology, gfan@mednet.ucla.edu matteop@mcdb.ucla.edu.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Department of Human Genetics, Broad Stem Cell Research Center, David Geffen School of Medicine, gfan@mednet.ucla.edu matteop@mcdb.ucla.edu.
authors.forename: Guoping
authors.initials: G
authors.lastname: Fan
mesh_terms: D002454:Cell Differentiation; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000172:deficiency / Q000235:genetics*; D019175:DNA Methylation; D004742:Enhancer Elements, Genetic; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000201:enzymology / Q000473:pathology; D015894:Genome, Human; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000201:enzymology / Q000235:genetics* / Q000473:pathology; D057026:Induced Pluripotent Stem Cells / Q000201:enzymology* / Q000473:pathology; D059630:Mesenchymal Stem Cells / Q000201:enzymology* / Q000473:pathology; D011401:Promoter Regions, Genetic; D000097584:DNA Methyltransferase 3B
chemical_list: D004248:DNA (Cytosine-5-)-Methyltransferases; D000097584:DNA Methyltransferase 3B