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Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia

Author

Listed:
  • Han Wang

    (Shanghai Jiao Tong University)

  • Huiying Sun

    (Shanghai Jiao Tong University)

  • Bilin Liang

    (Shanghai Jiao Tong University)

  • Fang Zhang

    (Shanghai Jiao Tong University)

  • Fan Yang

    (Shanghai Jiao Tong University)

  • Bowen Cui

    (Shanghai Jiao Tong University)

  • Lixia Ding

    (Shanghai Jiao Tong University)

  • Xiang Wang

    (Shanghai Jiao Tong University)

  • Ronghua Wang

    (Shanghai Jiao Tong University)

  • Jiaoyang Cai

    (Shanghai Jiao Tong University)

  • Yanjing Tang

    (Shanghai Jiao Tong University)

  • Jianan Rao

    (Shanghai Jiao Tong University)

  • Wenting Hu

    (Shanghai Jiao Tong University)

  • Shuang Zhao

    (Shanghai Jiao Tong University)

  • Wenyan Wu

    (Shanghai Jiao Tong University)

  • Xiaoxiao Chen

    (Shanghai Jiao Tong University)

  • Kefei Wu

    (Shanghai Jiao Tong University)

  • Junchen Lai

    (Shanghai Jiao Tong University)

  • Yangyang Xie

    (Shanghai Jiao Tong University)

  • Benshang Li

    (Shanghai Jiao Tong University)

  • Jingyan Tang

    (Shanghai Jiao Tong University)

  • Shuhong Shen

    (Shanghai Jiao Tong University
    Fujian Children’s Hospital, Fujian Branch of Shanghai Children’s Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine)

  • Yu Liu

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University
    Fujian Children’s Hospital, Fujian Branch of Shanghai Children’s Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine)

Abstract

For around half of the pediatric B-lineage acute lymphoblastic leukemia (B-ALL) patients, the molecular mechanism of relapse remains unclear. To fill this gap in knowledge, here we characterize the chromatin accessibility landscape in pediatric relapsed B-ALL. We observe rewired accessible chromatin regions (ACRs) associated with transcription dysregulation in leukemia cells as compared with normal B-cell progenitors. We show that over a quarter of the ACRs in B-ALL are in quiescent regions with high heterogeneity among B-ALLs. We identify subtype-specific and allele-imbalanced chromatin accessibility by integrating multi-omics data. By characterizing the differential ACRs between diagnosis and relapse in B-ALL, we identify alterations in chromatin accessibility during drug treatment. Further analysis of ACRs associated with relapse free survival leads to the identification of a subgroup of B-ALL which show early relapse. These data provide an advanced and integrative portrait of the importance of chromatin accessibility alterations in tumorigenesis and drug responses.

Suggested Citation

  • Han Wang & Huiying Sun & Bilin Liang & Fang Zhang & Fan Yang & Bowen Cui & Lixia Ding & Xiang Wang & Ronghua Wang & Jiaoyang Cai & Yanjing Tang & Jianan Rao & Wenting Hu & Shuang Zhao & Wenyan Wu & Xi, 2023. "Chromatin accessibility landscape of relapsed pediatric B-lineage acute lymphoblastic leukemia," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42565-z
    DOI: 10.1038/s41467-023-42565-z
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    as
    1. Di Zhang & Zhanyun Tang & He Huang & Guolin Zhou & Chang Cui & Yejing Weng & Wenchao Liu & Sunjoo Kim & Sangkyu Lee & Mathew Perez-Neut & Jun Ding & Daniel Czyz & Rong Hu & Zhen Ye & Maomao He & Y. Ge, 2019. "Metabolic regulation of gene expression by histone lactylation," Nature, Nature, vol. 574(7779), pages 575-580, October.
    2. Xiaotu Ma & Yu Liu & Yanling Liu & Ludmil B. Alexandrov & Michael N. Edmonson & Charles Gawad & Xin Zhou & Yongjin Li & Michael C. Rusch & John Easton & Robert Huether & Veronica Gonzalez-Pena & Mark , 2018. "Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours," Nature, Nature, vol. 555(7696), pages 371-376, March.
    3. Carsten Bahr & Lisa von Paleske & Veli V. Uslu & Silvia Remeseiro & Naoya Takayama & Stanley W. Ng & Alex Murison & Katja Langenfeld & Massimo Petretich & Roberta Scognamiglio & Petra Zeisberger & Ame, 2018. "A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies," Nature, Nature, vol. 553(7689), pages 515-520, January.
    4. James B. Studd & Jayaram Vijayakrishnan & Minjun Yang & Gabriele Migliorini & Kajsa Paulsson & Richard S. Houlston, 2017. "Genetic and regulatory mechanism of susceptibility to high-hyperdiploid acute lymphoblastic leukaemia at 10q21.2," Nature Communications, Nature, vol. 8(1), pages 1-9, April.
    5. Robert E. Thurman & Eric Rynes & Richard Humbert & Jeff Vierstra & Matthew T. Maurano & Eric Haugen & Nathan C. Sheffield & Andrew B. Stergachis & Hao Wang & Benjamin Vernot & Kavita Garg & Sam John &, 2012. "The accessible chromatin landscape of the human genome," Nature, Nature, vol. 489(7414), pages 75-82, September.
    6. Matthew J. Niederst & Lecia V. Sequist & John T. Poirier & Craig H. Mermel & Elizabeth L. Lockerman & Angel R. Garcia & Ryohei Katayama & Carlotta Costa & Kenneth N. Ross & Teresa Moran & Emily Howe &, 2015. "RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer," Nature Communications, Nature, vol. 6(1), pages 1-10, May.
    7. 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.
    8. André F. Rendeiro & Christian Schmidl & Jonathan C. Strefford & Renata Walewska & Zadie Davis & Matthias Farlik & David Oscier & Christoph Bock, 2016. "Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks," Nature Communications, Nature, vol. 7(1), pages 1-12, September.
    9. Carsten Bahr & Lisa Paleske & Veli V. Uslu & Silvia Remeseiro & Naoya Takayama & Stanley W. Ng & Alex Murison & Katja Langenfeld & Massimo Petretich & Roberta Scognamiglio & Petra Zeisberger & Amelie , 2018. "Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies," Nature, Nature, vol. 558(7711), pages 4-4, June.
    10. Carles A. Boix & Benjamin T. James & Yongjin P. Park & Wouter Meuleman & Manolis Kellis, 2021. "Regulatory genomic circuitry of human disease loci by integrative epigenomics," Nature, Nature, vol. 590(7845), pages 300-307, February.
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