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Reprogramming roadmap reveals route to human induced trophoblast stem cells

Author

Listed:
  • Xiaodong Liu

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • John F. Ouyang

    (Duke-National University of Singapore Medical School)

  • Fernando J. Rossello

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University
    University of Melbourne Centre For Cancer Research, The University of Melbourne)

  • Jia Ping Tan

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Kathryn C. Davidson

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Daniela S. Valdes

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Jan Schröder

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Yu B. Y. Sun

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Joseph Chen

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Anja S. Knaupp

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Guizhi Sun

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Hun S. Chy

    (Monash University
    Commonwealth Scientific and Industrial Research Organisation)

  • Ziyi Huang

    (Monash University
    Commonwealth Scientific and Industrial Research Organisation)

  • Jahnvi Pflueger

    (The University of Western Australia
    The Harry Perkins Institute of Medical Research)

  • Jaber Firas

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Vincent Tano

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Sam Buckberry

    (The University of Western Australia
    The Harry Perkins Institute of Medical Research)

  • Jacob M. Paynter

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Michael R. Larcombe

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Daniel Poppe

    (The University of Western Australia
    The Harry Perkins Institute of Medical Research)

  • Xin Yi Choo

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • Carmel M. O’Brien

    (Monash University
    Commonwealth Scientific and Industrial Research Organisation)

  • William A. Pastor

    (University of California Los Angeles
    University of California Los Angeles
    McGill University)

  • Di Chen

    (University of California Los Angeles
    University of California Los Angeles)

  • Anna L. Leichter

    (University of Melbourne Centre For Cancer Research, The University of Melbourne)

  • Haroon Naeem

    (Monash University)

  • Pratibha Tripathi

    (Monash University
    Monash Biomedicine Discovery Institute)

  • Partha P. Das

    (Monash University
    Monash Biomedicine Discovery Institute)

  • Alexandra Grubman

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

  • David R. Powell

    (Monash University)

  • Andrew L. Laslett

    (Monash University
    Commonwealth Scientific and Industrial Research Organisation)

  • Laurent David

    (Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR1064, ITUN, F-44000
    Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS016, CNRS UMS3556, F-44000)

  • Susan K. Nilsson

    (Monash University
    Commonwealth Scientific and Industrial Research Organisation)

  • Amander T. Clark

    (University of California Los Angeles
    University of California Los Angeles
    University of California Los Angeles
    University of California Los Angeles)

  • Ryan Lister

    (The University of Western Australia
    The Harry Perkins Institute of Medical Research)

  • Christian M. Nefzger

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University
    University of Queensland)

  • Luciano G. Martelotto

    (University of Melbourne Centre For Cancer Research, The University of Melbourne)

  • Owen J. L. Rackham

    (Duke-National University of Singapore Medical School)

  • Jose M. Polo

    (Monash University
    Monash Biomedicine Discovery Institute
    Monash University)

Abstract

The reprogramming of human somatic cells to primed or naive induced pluripotent stem cells recapitulates the stages of early embryonic development1–6. The molecular mechanism that underpins these reprogramming processes remains largely unexplored, which impedes our understanding and limits rational improvements to reprogramming protocols. Here, to address these issues, we reconstruct molecular reprogramming trajectories of human dermal fibroblasts using single-cell transcriptomics. This revealed that reprogramming into primed and naive pluripotency follows diverging and distinct trajectories. Moreover, genome-wide analyses of accessible chromatin showed key changes in the regulatory elements of core pluripotency genes, and orchestrated global changes in chromatin accessibility over time. Integrated analysis of these datasets revealed a role for transcription factors associated with the trophectoderm lineage, and the existence of a subpopulation of cells that enter a trophectoderm-like state during reprogramming. Furthermore, this trophectoderm-like state could be captured, which enabled the derivation of induced trophoblast stem cells. Induced trophoblast stem cells are molecularly and functionally similar to trophoblast stem cells derived from human blastocysts or first-trimester placentas7. Our results provide a high-resolution roadmap for the transcription-factor-mediated reprogramming of human somatic cells, indicate a role for the trophectoderm-lineage-specific regulatory program during this process, and facilitate the direct reprogramming of somatic cells into induced trophoblast stem cells.

Suggested Citation

  • Xiaodong Liu & John F. Ouyang & Fernando J. Rossello & Jia Ping Tan & Kathryn C. Davidson & Daniela S. Valdes & Jan Schröder & Yu B. Y. Sun & Joseph Chen & Anja S. Knaupp & Guizhi Sun & Hun S. Chy & Z, 2020. "Reprogramming roadmap reveals route to human induced trophoblast stem cells," Nature, Nature, vol. 586(7827), pages 101-107, October.
  • Handle: RePEc:nat:nature:v:586:y:2020:i:7827:d:10.1038_s41586-020-2734-6
    DOI: 10.1038/s41586-020-2734-6
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    Citations

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    Cited by:

    1. Liang-Jie Wang & Chie-Pein Chen & Yun-Shien Lee & Pui-Sze Ng & Geen-Dong Chang & Yu-Hsuan Pao & Hsiao-Fan Lo & Chao-Hsiang Peng & Mei-Leng Cheong & Hungwen Chen, 2022. "Functional antagonism between ΔNp63α and GCM1 regulates human trophoblast stemness and differentiation," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Mohammad Jaber & Ahmed Radwan & Netanel Loyfer & Mufeed Abdeen & Shulamit Sebban & Areej Khatib & Hazar Yassen & Thorsten Kolb & Marc Zapatka & Kirill Makedonski & Aurelie Ernst & Tommy Kaplan & Yosef, 2022. "Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    3. Dasol Han & Guojing Liu & Yujeong Oh & Seyoun Oh & Seungbok Yang & Lori Mandjikian & Neha Rani & Maria C. Almeida & Kenneth S. Kosik & Jiwon Jang, 2023. "ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Chen Dong & Shuhua Fu & Rowan M. Karvas & Brian Chew & Laura A. Fischer & Xiaoyun Xing & Jessica K. Harrison & Pooja Popli & Ramakrishna Kommagani & Ting Wang & Bo Zhang & Thorold W. Theunissen, 2022. "A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Kaela M. Varberg & Esteban M. Dominguez & Boryana Koseva & Joseph M. Varberg & Ross P. McNally & Ayelen Moreno-Irusta & Emily R. Wesley & Khursheed Iqbal & Warren A. Cheung & Carl Schwendinger-Schreck, 2023. "Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    6. Magnus Zethoven & Luciano Martelotto & Andrew Pattison & Blake Bowen & Shiva Balachander & Aidan Flynn & Fernando J. Rossello & Annette Hogg & Julie A. Miller & Zdenek Frysak & Sean Grimmond & Lauren , 2022. "Single-nuclei and bulk-tissue gene-expression analysis of pheochromocytoma and paraganglioma links disease subtypes with tumor microenvironment," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    7. Yan Bi & Zhifen Tu & Jianfeng Zhou & Xuehao Zhu & Hong Wang & Shaorong Gao & Yixuan Wang, 2022. "Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Francesco Panariello & Onelia Gagliano & Camilla Luni & Antonio Grimaldi & Silvia Angiolillo & Wei Qin & Anna Manfredi & Patrizia Annunziata & Shaked Slovin & Lorenzo Vaccaro & Sara Riccardo & Valenti, 2023. "Cellular population dynamics shape the route to human pluripotency," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Yueli Yang & Wenqi Jia & Zhiwei Luo & Yunpan Li & Hao Liu & Lixin Fu & Jinxiu Li & Yu Jiang & Junjian Lai & Haiwei Li & Babangida Jabir Saeed & Yi Zou & Yuan Lv & Liang Wu & Ting Zhou & Yongli Shan & , 2024. "VGLL1 cooperates with TEAD4 to control human trophectoderm lineage specification," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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