Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy

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.

Children's Oncology Group's 2023 blueprint for research: Rare tumors

“…D2. This difference is also seen in the MDS plot of the cluster A (green) and cluster B (red) samples 72 …”

“…63 An ongoing trial, ARET2121, is evaluating the role of intravitreal CHLA AH samples and 97 enucleated RB tumors shows a difference in methylation profile of cluster A (less aggressive) and cluster B (more aggressive) tumors based on 1092 probes. 72 D2. This difference is also seen in the MDS plot of the cluster A (green) and cluster B (red) samples.…”

“…This difference is also seen in the MDS plot of the cluster A (green) and cluster B (red) samples. 72 retinoblastoma. Trans-scleral diffusion using an episcleral depot has encouraging initial results (NCT04156347 and NCT04428879).…”

“…Identification of specific DNA methylation clusters from AH cfDNAs. Unsupervised clustering of the 12 CHLA AH samples and 97 enucleated RB tumors shows a difference in methylation profile of cluster A (less aggressive) and cluster B (more aggressive) tumors based on 1092 probes 72 . D2.…”

“…Circulating blood RB1‐ mutant DNA may be associated with extraocular disease 71 . Aberrant methylation portends aggressive tumor behavior 72 …”