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Clonal evolution of the 3D chromatin landscape in patients with relapsed pediatric B-cell acute lymphoblastic leukemia

Author

Listed:
  • Sonali Narang

    (NYU Langone Health)

  • Yohana Ghebrechristos

    (NYU Langone Health
    NYU Langone Health)

  • Nikki A. Evensen

    (NYU Langone Health)

  • Nina Murrell

    (NYU Langone Health
    NYU Langone Health)

  • Sylwia Jasinski

    (NYU Langone Health
    NYU Langone Health)

  • Talia H. Ostrow

    (NYU Langone Health)

  • David T. Teachey

    (Children’s Hospital of Philadelphia)

  • Elizabeth A. Raetz

    (NYU Langone Health
    NYU Langone Health)

  • Timothee Lionnet

    (NYU Langone Health
    NYU Tandon School of Engineering)

  • Matthew Witkowski

    (University of Colorado Anschutz Medical Campus)

  • Iannis Aifantis

    (NYU Langone Health
    NYU Langone Health)

  • Aristotelis Tsirigos

    (NYU Langone Health
    NYU Langone Health)

  • William L. Carroll

    (NYU Langone Health
    NYU Langone Health)

Abstract

Relapsed pediatric B-cell acute lymphoblastic leukemia (B-ALL) remains one of the leading causes of cancer mortality in children. We performed Hi-C, ATAC-seq, and RNA-seq on 12 matched diagnosis/relapse pediatric leukemia specimens to uncover dynamic structural variants (SVs) and 3D chromatin rewiring that may contribute to relapse. While translocations are assumed to occur early in leukemogenesis and be maintained throughout progression, we discovered novel, dynamic translocations and confirmed several fusion transcripts, suggesting functional and therapeutic relevance. Genome-wide chromatin remodeling was observed at all organizational levels: A/B compartments, TAD interactivity, and chromatin loops, including some loci shared by 25% of patients. Shared changes were found to drive the expression of genes/pathways previously implicated in resistance as well as novel therapeutic candidates, two of which (ATXN1 and MN1) we functionally validated. Overall, these results demonstrate chromatin reorganization under the selective pressure of therapy and offer the potential for discovery of novel therapeutic interventions.

Suggested Citation

  • Sonali Narang & Yohana Ghebrechristos & Nikki A. Evensen & Nina Murrell & Sylwia Jasinski & Talia H. Ostrow & David T. Teachey & Elizabeth A. Raetz & Timothee Lionnet & Matthew Witkowski & Iannis Aifa, 2024. "Clonal evolution of the 3D chromatin landscape in patients with relapsed pediatric B-cell acute lymphoblastic leukemia," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51492-6
    DOI: 10.1038/s41467-024-51492-6
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    1. Jesse R. Dixon & Siddarth Selvaraj & Feng Yue & Audrey Kim & Yan Li & Yin Shen & Ming Hu & Jun S. Liu & Bing Ren, 2012. "Topological domains in mammalian genomes identified by analysis of chromatin interactions," Nature, Nature, vol. 485(7398), pages 376-380, May.
    2. Jie Li & Phillip M. Galbo & Weida Gong & Aaron J. Storey & Yi-Hsuan Tsai & Xufen Yu & Jeong Hyun Ahn & Yiran Guo & Samuel G. Mackintosh & Ricky D. Edmondson & Stephanie D. Byrum & Jason E. Farrar & Sh, 2021. "ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    3. William A. Flavahan & Yotam Drier & Brian B. Liau & Shawn M. Gillespie & Andrew S. Venteicher & Anat O. Stemmer-Rachamimov & Mario L. Suvà & Bradley E. Bernstein, 2016. "Insulator dysfunction and oncogene activation in IDH mutant gliomas," Nature, Nature, vol. 529(7584), pages 110-114, January.
    4. Elphège P. Nora & Bryan R. Lajoie & Edda G. Schulz & Luca Giorgetti & Ikuhiro Okamoto & Nicolas Servant & Tristan Piolot & Nynke L. van Berkum & Johannes Meisig & John Sedat & Joost Gribnau & Emmanuel, 2012. "Spatial partitioning of the regulatory landscape of the X-inactivation centre," Nature, Nature, vol. 485(7398), pages 381-385, May.
    5. Charles G. Mullighan & Jinghui Zhang & Lawryn H. Kasper & Stephanie Lerach & Debbie Payne-Turner & Letha A. Phillips & Sue L. Heatley & Linda Holmfeldt & J. Racquel Collins-Underwood & Jing Ma & Kenne, 2011. "CREBBP mutations in relapsed acute lymphoblastic leukaemia," Nature, Nature, vol. 471(7337), pages 235-239, March.
    6. Jie Xu & Fan Song & Huijue Lyu & Mikoto Kobayashi & Baozhen Zhang & Ziyu Zhao & Ye Hou & Xiaotao Wang & Yu Luan & Bei Jia & Lena Stasiak & Josiah Hiu-yuen Wong & Qixuan Wang & Qi Jin & Qiushi Jin & Yi, 2022. "Subtype-specific 3D genome alteration in acute myeloid leukaemia," Nature, Nature, vol. 611(7935), pages 387-398, November.
    7. Caryn S. Ross-Innes & Rory Stark & Andrew E. Teschendorff & Kelly A. Holmes & H. Raza Ali & Mark J. Dunning & Gordon D. Brown & Ondrej Gojis & Ian O. Ellis & Andrew R. Green & Simak Ali & Suet-Feung C, 2012. "Differential oestrogen receptor binding is associated with clinical outcome in breast cancer," Nature, Nature, vol. 481(7381), pages 389-393, January.
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