Gain of chromosome 6p is a molecular biomarker for prognostication of retinoblastoma ocular survival: The aqueous humor surrogate tumor biopsy

Abstract

Purpose : Aqueous humor (AH) is a novel source of tumor-derived cell-free DNA (cfDNA) and can serve as a surrogate or liquid biopsy, for retinoblastoma (RB). We previously identified a somatic copy number alteration (SCNA) gain of chromosome 6p as associated with a 10-fold increased risk of enucleation. In this study, we provide a 2-year extended updates to further explore 6p gain as a prognostic biomarker for ocular survival.

Methods : Patients diagnosed with RB from 12/2014-7/2019 from whom AH was sampled were included. AH was extracted via clear corneal paracentesis at diagnosis, during intravitreal injection of chemotherapy or enucleation. CfDNA was extracted; shallow whole genome sequencing performed to assess for highly recurrent RB SCNAs (gain of 1q, 2p, 6p, loss of 13q, 16q). Patient demographics, treatment and globe salvage were recorded.

Results : 50 eyes from 46 patients were included: 27 eyes were salvaged and 23 were enucleated. 116 samples of AH were analyzed. There were no cases of orbital relapse or metastatic spread. The median follow-up was 30 months (range 6-64 mos). 33/50 eyes (66%) demonstrated one or more highly-recurrent RB SCNAs. Gain of 6p was the most prevalent RB SCNA (50%), followed by 1q gain(38%), 16q loss(30%), 2p gain(including focal MYCN;18%), and 13q loss(16%).
RB SCNAs were significantly more prevalent in enucleated eyes (21/23,91.3%) than salvaged eyes (12/27,44.4%; Fisher’s exact,P=0.0007). Of these, 6p gain was particularly more prevalent in enucleated eyes (17/23,73.9%) than in salvaged eyes (8/27,29.6%; Chi-squared,P=0.002) The presence of 6p gain in the cfDNA in the AH portended nearly 10 times greater odds of enucleation (OR=9.87,95% CI=1.75-55.65,P=0.009). No single other SCNA had a statistically significant power to predict enucleation although there was a trend towards significance for 2p/focal MYCN gain (P=0.09) limited by the number of eyes with this SCNA.

Conclusions : Although we previously identified chromosomal gain of 6p as a potential indicator of aggressive phenotype in RB, the study included a smaller cohort of patients and limited follow-up. With extended follow-up and nearly double the eyes and AH samples, the data continue to demonstrate that AH is a high-yield surrogate tumor biopsy, and the presence of RB-specific SCNAs—specifically gain of 6p—has the potential to serve as a prognostic biomarker for RB.

This is a 2020 ARVO Annual Meeting abstract.