FOXD1 is involved in uveal melanocyte development and associated with high-risk uveal melanoma

Abstract

Purpose : Uveal melanoma (UM) arises from melanocytes located in the uveal tract and is the most common primary intraocular malignancy. Driver mutations are mainly found in GNAQ and GNA11, followed by mutually exclusive mutations in BAP1, SF3B1 and EIF1AX which predicts prognosis. (Fig.1A) BAP1-UM is known to be highly aggressive, although the mechanism remains unclear. Multiple studies used transcriptomics to study BAP1-UM and implicate a more stem-like profile in BAP1-UM with an unique immune-landscape compared to SF3B1- and EIF1AX-UM. We hypothesized that BAP1-UM reactivate genes involved in uveal melanocyte development to increase aggressiveness. To identify transcripts involved in uveal melanocyte development, we used public scRNA-seq datasets of zebrafish and human and validated our finding in RNA-seq datasets of UM

Methods : To gain insights in uveal melanocyte transcriptomes, we utilized embryonic zebrafish scRNA-seq datasets lacking the eyes and used genes found in melanocytes as a filter against whole zebrafish scRNA-seq. Similarly, we used postnatal human skin scRNA-seq dataset as a filter against human eye to identify uveal melanocyte genes. Uniquely found transcripts in ocular melanocytes were then validated in 106 UM samples (Fig.1B)

Results : After filtering the zebrafish dataset, cluster 199 was identified as uveal melanocytes. Expression of melanocyte core genes (Fig.2A) and ocular genes pmelb and otx1 (Fig.2B) were expected, yet interestingly we uniquely found foxd1 to be involved in this cluster. We were unable to detect FOXD1 in healthy human scRNA-seq, suggesting spatial expression during embryonic vertebrate development. This prompted us to study FOXD1 in UM and found near exclusive expression in the BAP1-UM (Fig.2C), which is correlated to poor prognosis (Fig.2D)

Conclusions : Using a multi-species scRNA-seq approach we found genes involved ocular pigmentation and identified foxd1 in embryonic zebrafish melanocytes. Absence of FOXD1 transcripts in healthy human ocular melanocytes suggested spatial expression of FOXD1 as the human dataset consists of postnatal tissue. In UM we found expression of FOXD1 in BAP1-UM, which is correlated to poor prognosis. This study identified FOXD1 as a novel gene involved in high-risk UM

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

 

A)KM-survival curve of UM specific mutations B)Overview of study method

 

A,B)Melanocytic gene expression in zebrafish C)FOXD1 expression in UM D)FOXD1 based KM survival curve