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Comparative functional genomics identifies unique molecular features of EPSCs

View ORCID ProfileVikas Malik, Ruge Zang, Alejandro Fuentes-Iglesias, Xin Huang, Dan Li, Miguel Fidalgo, Hongwei Zhou, View ORCID ProfileJianlong Wang  Correspondence email
Vikas Malik
1Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
Roles: Data curation, Formal analysis, Validation, Investigation, Methodology, Writing—original draft, Writing—review and editing
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  • ORCID record for Vikas Malik
Ruge Zang
1Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
Roles: Data curation, Investigation, Methodology, Writing—review and editing
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Alejandro Fuentes-Iglesias
2Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC)-Health Research Institute (IDIS), Santiago de Compostela, Spain
Roles: Data curation, Formal analysis, Investigation, Writing—review and editing
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Xin Huang
1Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
Roles: Data curation, Formal analysis, Investigation, Methodology, Writing—review and editing
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Dan Li
1Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
Roles: Data curation, Investigation, Methodology, Writing—review and editing
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Miguel Fidalgo
2Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela (USC)-Health Research Institute (IDIS), Santiago de Compostela, Spain
Roles: Writing—review and editing
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Hongwei Zhou
1Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
Roles: Data curation, Investigation, Methodology, Project administration, Writing—review and editing
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Jianlong Wang
1Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
Roles: Conceptualization, Supervision, Funding acquisition, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing
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  • ORCID record for Jianlong Wang
  • For correspondence: jw3925@cumc.columbia.edu
Published 12 August 2022. DOI: 10.26508/lsa.202201608
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Abstract

Extended pluripotent or expanded potential stem cells (EPSCs) possess superior developmental potential to embryonic stem cells (ESCs). However, the molecular underpinning of EPSC maintenance in vitro is not well defined. We comparatively studied transcriptome, chromatin accessibility, active histone modification marks, and relative proteomes of ESCs and the two well-established EPSC lines to probe the molecular foundation underlying EPSC developmental potential. Despite some overlapping transcriptomic and chromatin accessibility features, we defined sets of molecular signatures that distinguish EPSCs from ESCs in transcriptional and translational regulation as well as metabolic control. Interestingly, EPSCs show similar reliance on pluripotency factors Oct4, Sox2, and Nanog for self-renewal as ESCs. Our study provides a rich resource for dissecting the regulatory network that governs the developmental potency of EPSCs and exploring alternative strategies to capture totipotent stem cells in culture.

  • Received July 15, 2022.
  • Revision received July 19, 2022.
  • Accepted July 20, 2022.
  • © 2022 Malik et al.
Creative Commons logoCreative Commons logohttps://creativecommons.org/licenses/by/4.0/

This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/).

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Defining expanded/extended pluripotent stem cells
Vikas Malik, Ruge Zang, Alejandro Fuentes-Iglesias, Xin Huang, Dan Li, Miguel Fidalgo, Hongwei Zhou, Jianlong Wang
Life Science Alliance Aug 2022, 5 (11) e202201608; DOI: 10.26508/lsa.202201608

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Defining expanded/extended pluripotent stem cells
Vikas Malik, Ruge Zang, Alejandro Fuentes-Iglesias, Xin Huang, Dan Li, Miguel Fidalgo, Hongwei Zhou, Jianlong Wang
Life Science Alliance Aug 2022, 5 (11) e202201608; DOI: 10.26508/lsa.202201608
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Volume 5, No. 11
November 2022
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