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Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy

Author

Listed:
  • Hong-Tao Li

    (University of Southern California, Norris Comprehensive Cancer Center)

  • Liya Xu

    (University of Southern California)

  • Daniel J. Weisenberger

    (University of Southern California, Norris Comprehensive Cancer Center
    Keck School of Medicine, University of Southern California)

  • Meng Li

    (University of Southern California)

  • Wanding Zhou

    (University of Pennsylvania, Children’s Hospital of Philadelphia)

  • Chen-Ching Peng

    (University of Southern California)

  • Kevin Stachelek

    (University of Southern California)

  • David Cobrinik

    (University of Southern California
    University of Southern California, Norris Comprehensive Cancer Center
    Keck School of Medicine, University of Southern California
    Children’s Hospital Los Angeles)

  • Gangning Liang

    (University of Southern California, Norris Comprehensive Cancer Center
    Keck School of Medicine, University of Southern California)

  • Jesse L. Berry

    (University of Southern California
    Keck School of Medicine, University of Southern California
    Children’s Hospital Los Angeles)

Abstract

Retinoblastoma (RB) is a cancer that forms in the developing retina of babies and toddlers. The goal of therapy is to cure the tumor, save the eye and maximize vision. However, it is difficult to predict which eyes are likely to respond to therapy. Predictive molecular biomarkers are needed to guide prognosis and optimize treatment decisions. Direct tumor biopsy is not an option for this cancer; however, the aqueous humor (AH) is an alternate source of tumor-derived cell-free DNA (cfDNA). Here we show that DNA methylation profiling of the AH is a valid method to identify the methylation status of RB tumors. We identify 294 genes directly regulated by methylation that are implicated in p53 tumor suppressor (RB1, p53, p21, and p16) and oncogenic (E2F) pathways. Finally, we use AH to characterize molecular subtypes that can potentially be used to predict the likelihood of treatment success for retinoblastoma patients.

Suggested Citation

  • Hong-Tao Li & Liya Xu & Daniel J. Weisenberger & Meng Li & Wanding Zhou & Chen-Ching Peng & Kevin Stachelek & David Cobrinik & Gangning Liang & Jesse L. Berry, 2022. "Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33248-2
    DOI: 10.1038/s41467-022-33248-2
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    References listed on IDEAS

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    1. Jinghui Zhang & Claudia A. Benavente & Justina McEvoy & Jacqueline Flores-Otero & Li Ding & Xiang Chen & Anatoly Ulyanov & Gang Wu & Matthew Wilson & Jianmin Wang & Rachel Brennan & Michael Rusch & Am, 2012. "A novel retinoblastoma therapy from genomic and epigenetic analyses," Nature, Nature, vol. 481(7381), pages 329-334, January.
    2. Dvir Aran & Marina Sirota & Atul J. Butte, 2015. "Systematic pan-cancer analysis of tumour purity," Nature Communications, Nature, vol. 6(1), pages 1-12, December.
    3. Hyo-Jin Park & Mi-Jung Kim & Christina Rothenberger & Ashok Kumar & Edith M. Sampson & Dalian Ding & Chul Han & Karessa White & Kevin Boyd & Senthilvelan Manohar & Yong-Hwan Kim & Maria S. Ticsa & Aar, 2019. "GSTA4 mediates reduction of cisplatin ototoxicity in female mice," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    4. Ilya Kupershmidt & Qiaojuan Jane Su & Anoop Grewal & Suman Sundaresh & Inbal Halperin & James Flynn & Mamatha Shekar & Helen Wang & Jenny Park & Wenwu Cui & Gregory D Wall & Robert Wisotzkey & Satnam , 2010. "Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-13, September.
    5. Jing Liu & Daniela Ottaviani & Meriem Sefta & Céline Desbrousses & Elodie Chapeaublanc & Rosario Aschero & Nanor Sirab & Fabiana Lubieniecki & Gabriela Lamas & Laurie Tonon & Catherine Dehainault & Cl, 2021. "A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
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    Cited by:

    1. Grayson A. Herrgott & James M. Snyder & Ruicong She & Tathiane M. Malta & Thais S. Sabedot & Ian Y. Lee & Jacob Pawloski & Guilherme G. Podolsky-Gondim & Karam P. Asmaro & Jiaqi Zhang & Cara E. Cannel, 2023. "Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas," Nature Communications, Nature, vol. 14(1), pages 1-19, December.

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