Potential of aqueous humor as a liquid biopsy for uveal melanoma

Abstract

Purpose : Tumor biopsy can identify prognostic biomarkers for metastatic uveal melanoma (UM). Aqueous humor (AH) biopsy is less invasive and repeatable, and thus facilitates longitudinal monitoring of disease. We investigated if the AH of UM eyes had sufficient tumor-derived cell free DNA (cfDNA) to perform genetic analysis of the tumor.

Methods : A case series of 37 AH samples from 12 choroidal and 8 ciliary body (CB) tumor patients were studied. From 12 choroidal tumor patients, there were 9 paired pre- and post-radiation, 2 post-radiation only and 1 at enucleation AH samples. One CB tumor biopsy wash sample was collected. AH was analyzed for nucleic acids (Qubit Assay Kits). Whole-genome sequencing was done on DNA samples isolated from the AH samples and cells from tumor wash via 150bp paired-end Illumina sequencing to detect somatic copy number alterations (SCNAs). Hybridization-based capturing and targeted sequencing were subsequently done using a custom gene panel that covers all exonic regions of the BAP1 and GNAQ genes.

Results : Comparing paired pre- and post-radiation AH samples revealed significantly higher nucleic acid concentrations post-radiation. Most significant increases within choroidal and CB groups respectively were seen in miRNA (n=9 pairs, P=0.016 and n=8 pairs, P=0.008). Among post-radiation AH samples, there was a significantly higher concentration of dsDNA (P=0.033), ssDNA (P=0.033) and RNA (P=0.018) in CB compared to choroidal. Highly recurrent UM SCNAs were identified in 0/11 post- choroidal and 5/8 (62.5%) post- CB samples. Of those 5 SCNA-containing post- AH samples that underwent targeted resequencing, BAP1 or GNAQ somatic mutations were detected in 3/5 (60%). The DNA profile of the only available tumor sample was highly concordant with its corresponding post- AH sample (r=0.978).

Conclusions : AH is a source of cfDNA in UM eyes, with a higher yield of nucleic acids post-radiation. This is the first-time that UM SCNAs and mutations were identified in cfDNA isolated from the AH. This suggests that AH can serve as a liquid biopsy for UM.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.