Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy

Hong-Tao Li, Liya Xu, Daniel J. Weisenberger, Meng Li, Wanding Zhou, Chen-Ching Peng, Kevin Stachelek, David Cobrinik, Gangning Liang () and Jesse L. Berry ()
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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
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
Gangning Liang: University of Southern California, Norris Comprehensive Cancer Center
Jesse L. Berry: University of Southern California

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-33248-2

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