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Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation

Author

Listed:
  • Deblina Banerjee

    (National Cancer Institute)

  • Sukriti Bagchi

    (National Cancer Institute)

  • Zhihui Liu

    (National Cancer Institute)

  • Hsien-Chao Chou

    (National Cancer Institute)

  • Man Xu

    (National Cancer Institute)

  • Ming Sun

    (National Cancer Institute)

  • Sara Aloisi

    (Case Western Reserve University
    University of Bologna)

  • Zalman Vaksman

    (New York Genome Center)

  • Sharon J. Diskin

    (Perelman School of Medicine)

  • Mark Zimmerman

    (Dana-Farber Cancer Institute)

  • Javed Khan

    (National Cancer Institute)

  • Berkley Gryder

    (Case Western Reserve University)

  • Carol J. Thiele

    (National Cancer Institute)

Abstract

Temporal regulation of super-enhancer (SE) driven transcription factors (TFs) underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify SEs driving TF regulators, we use all-trans retinoic acid (ATRA) to induce NB growth arrest and differentiation. Time-course H3K27ac ChIP-seq and RNA-seq reveal ATRA coordinated SE waves. SEs that decrease with ATRA link to stem cell development (MYCN, GATA3, SOX11). CRISPR-Cas9 and siRNA verify SOX11 dependency, in vitro and in vivo. Silencing the SOX11 SE using dCAS9-KRAB decreases SOX11 mRNA and inhibits cell growth. Other TFs activate in sequential waves at 2, 4 and 8 days of ATRA treatment that regulate neural development (GATA2 and SOX4). Silencing the gained SOX4 SE using dCAS9-KRAB decreases SOX4 expression and attenuates ATRA-induced differentiation genes. Our study identifies oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.

Suggested Citation

  • Deblina Banerjee & Sukriti Bagchi & Zhihui Liu & Hsien-Chao Chou & Man Xu & Ming Sun & Sara Aloisi & Zalman Vaksman & Sharon J. Diskin & Mark Zimmerman & Javed Khan & Berkley Gryder & Carol J. Thiele, 2024. "Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47166-y
    DOI: 10.1038/s41467-024-47166-y
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