1. Stem Cells and Regenerative Medicine
  2. Genetics and Genomics
Download icon

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

  1. Irene Gallego Romero  Is a corresponding author
  2. Bryan J Pavlovic
  3. Irene Hernando-Herraez
  4. Xiang Zhou
  5. Michelle C Ward
  6. Nicholas E Banovich
  7. Courtney L Kagan
  8. Jonathan E Burnett
  9. Constance H Huang
  10. Amy Mitrano
  11. Claudia I Chavarria
  12. Inbar Friedrich Ben-Nun
  13. Yingchun Li
  14. Karen Sabatini
  15. Trevor R Leonardo
  16. Mana Parast
  17. Tomas Marques-Bonet
  18. Louise C Laurent
  19. Jeanne F Loring
  20. Yoav Gilad
  1. University of Chicago, United States
  2. Institució Catalana de Recerca i Estudis Avançats, Spain
  3. University of Michigan, United States
  4. Lonza Walkersville, Inc., United States
  5. University of California San Diego, United States
  6. The Scripps Research Institute, United States
  7. Sanford Consortium for Regenerative Medicine, United States
Tools and Resources
  • Cited 43
  • Views 4,340
  • Annotations
Cite this article as: eLife 2015;4:e07103 doi: 10.7554/eLife.07103

Abstract

Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.

Article and author information

Author details

  1. Irene Gallego Romero

    Department of Human Genetics, University of Chicago, Chicago, United States
    For correspondence
    ireneg@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
  2. Bryan J Pavlovic

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Irene Hernando-Herraez

    Institute of Evolutionary Biology, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  4. Xiang Zhou

    Department of Biostatistics, University of Michigan, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Michelle C Ward

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Nicholas E Banovich

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Courtney L Kagan

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Jonathan E Burnett

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Constance H Huang

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Amy Mitrano

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Claudia I Chavarria

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Inbar Friedrich Ben-Nun

    n/a, Lonza Walkersville, Inc., Walkersville, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Yingchun Li

    Department of Pathology, University of California San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Karen Sabatini

    Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Trevor R Leonardo

    Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Mana Parast

    Department of Pathology, University of California San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Tomas Marques-Bonet

    Institute of Evolutionary Biology, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  18. Louise C Laurent

    n/a, Sanford Consortium for Regenerative Medicine, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  19. Jeanne F Loring

    Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  20. Yoav Gilad

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Duncan T Odom, Cancer Research UK Cambridge Institute, United Kingdom

Publication history

  1. Received: February 19, 2015
  2. Accepted: June 22, 2015
  3. Accepted Manuscript published: June 23, 2015 (version 1)
  4. Version of Record published: July 15, 2015 (version 2)

Copyright

© 2015, Gallego Romero et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,340
    Page views
  • 704
    Downloads
  • 43
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine
    Luisa F Arias Padilla et al.
    Research Article

    The production of an adequate number of gametes is necessary for normal reproduction, for which the regulation of proliferation from early gonadal development to adulthood is key in both sexes. Cystic proliferation of germline stem cells is an especially important step prior to the beginning of meiosis; however, the molecular regulators of this proliferation remain elusive in vertebrates. Here, we report that ndrg1b is an important regulator of cystic proliferation in medaka. We generated mutants of ndrg1b that led to a disruption of germ cells cystic proliferation. This loss of cystic proliferation was observed from embryogenic to adult stages, impacting the success of gamete production and reproductive parameters such as spawning and fertilization. Interestingly, the depletion of cystic proliferation also impacted male sexual behavior, with a decrease of mating vigor. These data illustrate why it is also necessary to consider gamete production capacity in order to analyze reproductive behavior.

    1. Physics of Living Systems
    2. Stem Cells and Regenerative Medicine
    Simona Hankeova et al.
    Research Article

    Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.