Abstract B016: Identify DNA methylation signatures to predict chemo-resistance retinoblastoma in aqueous humor liquid biopsy
Authors: Liya Xu, Emily Lu, Daniel Weisenberger, Drishti Pandya, Hope Galarneau, Nerea Goni, David Cobrinik, Gangning Liang, Jesse L Berry
Journal: Cancer Research (2025)

Abstract Background: Retinoblastoma (RB) is the most common eye cancer in children, often leading to vision loss, enucleation, and potentially fatal outcomes if untreated. Due to the risk of cancer spread, direct tumor biopsy is not feasible, limiting opportunities for molecular diagnosis and prognosis. DNA methylation, a key epigenetic mechanism, regulates gene expression and plays a critical role in tumorigenesis by silencing tumor suppressor genes or activating oncogenes. This study aims to establish aqueous humor (AH) as a non-invasive liquid biopsy platform to capture DNA methylation markers reflective of RB tumor biology. By analyzing these profiles, we aim to identify epigenetic markers that differentiate high-risk RB cases from therapy-responsive ones, providing insights into tumor behavior and enabling precision-guided treatment strategies. Methods: Thirty-five AH samples from RB patients underwent DNA methylation profiling using the Illumina EPIC850 array, with methylation signatures correlated to clinical outcomes. Analysis included supervised clustering to identify distinct methylation patterns between salvaged and enucleated cases. Results: Supervised clustering revealed 895 significantly differentially methylated probes (∆β &amp;gt; 0.2 or &amp;lt; -0.2, p &amp;lt; 0.01) distinguishing salvaged eyes from enucleated eyes. Unsupervised clustering validated these distinct methylation signatures, with one active-treatment sample clustering with salvaged eyes and two clustering with enucleated eyes. The findings highlight AH methylation signatures that differentiate aggressive RB cases from therapy-responsive ones, correlating specific patterns with high-risk features and treatment failure. Key genes such as TFF1, BCHE, ADAM33, and PCDHB2 emerged as potential actionable targets, suggesting predictive value in stratifying patients by therapeutic response likelihood and aiding early, tailored treatment planning. Conclusions: This study highlights the critical role of DNA methylation as a regulatory mechanism in RB tumor biology, influencing gene expression and driving tumor progression or response to therapy. By leveraging AH as a liquid biopsy platform, we provide a safe and effective method for identifying methylation-based risk markers that offer both diagnostic and prognostic value. These findings advance precision medicine approaches in pediatric eye cancer, facilitating the early identification of high-risk patients and improving therapeutic strategies. Integrating methylation profiling into RB management could transform patient outcomes by enabling more personalized and targeted treatment plans. Citation Format: Liya Xu, Emily Lu, Daniel Weisenberger, Drishti Pandya, Hope Galarneau, Nerea Goni, David Cobrinik, Gangning Liang, Jesse L Berry. Identify DNA methylation signatures to predict chemo-resistance retinoblastoma in aqueous humor liquid biopsy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B016.