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Cell reprogramming promises to make characterization of the impact of human genetic variation on health and disease experimentally tractable by enabling the bridging of genotypes to phenotypes in developmentally relevant human cell lineages. Here we apply this paradigm to two disorders caused by symmetrical copy number variations of 7q11.23, which display a striking combination of shared and symmetrically opposite phenotypes—Williams-Beuren syndrome and 7q-microduplication syndrome. Through analysis of transgene-free patient-derived induced pluripotent stem cells and their differentiated derivatives, we find that 7q11.23 dosage imbalance disrupts transcriptional circuits in disease-relevant pathways beginning in the pluripotent state. These alterations are then selectively amplified upon differentiation of the pluripotent cells into disease-relevant lineages. A considerable proportion of this transcriptional dysregulation is specifically caused by dosage imbalances in GTF2I, which encodes a key transcription factor at 7q11.23 that is associated with the LSD1 repressive chromatin complex and silences its dosage-sensitive targets.

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Change history

  • 09 January 2015

    In the version of this article initially published online, GTF1I knockdown was incorrectly referred to in the legend for Figure 4c. GTF2I is the correct shRNA target in this experiment. The error has been corrected for the print, PDF and HTML versions of this article.


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We thank the AFSW (Associazione Famiglie Sindrome di Williams) and AISW (Associazione Italiana Sindrome di Williams) for agreeing to participate and making this study possible and the Genomic and Genetic Disorder Biobank, Galliera Genetic Bank and members of the Telethon Network of Genetic Biobanks (project numbers GTB12001G and GTB12001A), along with the EuroBioBank network, for providing us with specimens. We also thank scientists at the Drug Discovery Unit, Drug Development Program (DDU-DDP) of the European Institute of Oncology (IEO) for sharing with us the two LSD1 inhibitors used in this study; A. Bachi, A. Cattaneo and P. Soffiantini from the Mass Spectrometry service of the FIRC (Fondazione Italiana per la Ricerca sul Cancro) Institute of Molecular Oncology (IFOM); F. Pisati for processing of the teratomas; P. Andrews (University of Sheffield) for sharing two control iPSC lines (CTL2-C1 and CTL2-C2; reprogrammed from CRL-2429 fibroblasts); G. Mostoslavsky and the Center for Regenerative Medicine of Boston University for sharing the BU1Cr3-1 line; G. Barbagiovanni for help with FACS profiling and analysis; and L. Marelli along with all other members of the Testa laboratory for discussion. This work was funded by the European Research Council (consolidator grant number 616441-DISEASEAVATARS to G.T.), the Italian Ministry of Health (Ricerca Corrente to G.T. and G.M. and Bando Giovani Ricercatori 2008 and 2009 to G.T.), the EPIGEN Flagship Project of the Italian National Research Council (G.T.), the Jerome-Lejeune Foundation (G.T. and G.M.), the ERA-NET Neuron Program (G.T.), the Umberto Veronesi Foundation (S.A. and G.D.) and the Federation of European Biochemical Societies (FEBS; fellowship awarded to A.A. to work in the laboratory of G.T.).

Author information

Author notes

    • Antonio Adamo
    • , Sina Atashpaz
    •  & Pierre-Luc Germain

    These authors contributed equally to this work.


  1. Department of Experimental Oncology, European Institute of Oncology (Istituto di Ricovero e Cura a Carattere Scientifico, IRCCS), Milan, Italy.

    • Antonio Adamo
    • , Sina Atashpaz
    • , Pierre-Luc Germain
    • , Matteo Zanella
    • , Giuseppe D'Agostino
    • , Veronica Albertin
    • , Giancarlo Pruneri
    •  & Giuseppe Testa
  2. Lieber Institute for Brain Development, Baltimore, Maryland, USA.

    • Josh Chenoweth
    •  & Ronald McKay
  3. Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy.

    • Lucia Micale
    • , Carmela Fusco
    • , Bartolomeo Augello
    • , Orazio Palumbo
    • , Massimo Carella
    •  & Giuseppe Merla
  4. Department of Biomedical Sciences, University of Sheffield, Sheffield, UK.

    • Christian Unger
  5. Stemgent, Cambridge, Massachusetts, USA.

    • Brad Hamilton
  6. Medical Genetics Unit, Hospital Santa Maria della Misericordia, University of Perugia, Perugia, Italy.

    • Emilio Donti
    •  & Paolo Prontera
  7. Unità Operativa Semplice (UOS) Genetica Clinica Pediatrica, Fondazione Monza e Brianza per il Bambino e la sua Mamma (Fondazione MBBM), Azienda Ospedaliera San Gerardo, Monza, Italy.

    • Angelo Selicorni
  8. Department of Pediatrics, University of Turin, Turin, Italy.

    • Elisa Biamino
  9. Department of Health Sciences, University of Milan, Milan, Italy.

    • Giuseppe Testa


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S.A. initiated this project and set up human iPSC reprogramming and culture, including mRNA-based reprogramming. S.A. and A.A. reprogrammed the lines presented in this study. A.A., S.A., G.D. and M.Z. cultured and characterized iPSC lines and profiled transcriptomes. A.A. performed the biochemical characterization of the GTF2I complex and GTF2I and LSD1 ChIP-seq. A.A. performed the Nanostring experiment. A.A. and V.A. generated the GTF2I RNAi lines. S.A. established human iPSC differentiation into the cortical neural and neural crest lineages. S.A. and A.A. differentiated human iPSCs into cortical neural progenitors. S.A. analyzed NPCs and NCSCs by microarray. S.A. and M.Z. differentiated human iPSCs into NCSCs and MSCs. P.-L.G. performed the computational analysis for the microarray, Nanostring, RNA-seq and ChIP-seq data sets. P.-L.G. created the WikiWilliams-7qGeneBase web platform. G.M. organized the recruitment of patients, including molecular diagnostics and derivation of fibroblast cultures (with L.M., C.F. and B.A.). O.P., M.C. and G.M. performed aCGH analysis. G.P. performed histopathological analysis of teratomas. A.S. diagnosed and recruited patient AtWBS1, E.B. diagnosed and recruited patient WBS4, and P.P. and E.D. diagnosed and recruited patient 7dupASD1. R.M. and J.C. performed RNA-seq on a subset of samples. C.U. provided two control iPSC lines. B.H. provided mRNA reprogramming kits and expertise. P.-L.G., S.A., A.A. and G.T. wrote the manuscript. G.T. conceived, designed and supervised the study.

Competing interests

B.H. is the director of research and development for Stemgent and Asterand. All other authors declare no competing financial interests.

Corresponding author

Correspondence to Giuseppe Testa.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–9 and Supplementary Tables 1 and 10

Excel files

  1. 1.

    Supplementary Table 2

    Summary of the copy number variations (CNVs) identified through aCGH.

  2. 2.

    Supplementary Table 3

    GO biological processes enriched among linear DEGs, defined as mean (control) within a 20–80% range between mean (WBS) and mean (7dupASD), and abs(Pearson correlation) > 0.5 with WBS copy number.

  3. 3.

    Supplementary Table 4

    Proportion of DEGs, in each comparison between genotypes, attributable to GTF2I.

  4. 4.

    Supplementary Table 5

    GTF2I interactors identified through mass spectrometry analysis.

  5. 5.

    Supplementary Table 6

    GTF2I target classification according to ChIP analysis.

  6. 6.

    Supplementary Table 7

    GO biological processes enriched among the union of NCSC DEGs.

  7. 7.

    Supplementary Table 8

    Comparison of GO biological processes enriched among MSC DEGs and in MSC shuffling.

  8. 8.

    Supplementary Table 9

    List of performed experiments (Nat. Biotechnol. 25, 681–686, 2007).

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