Data from BAP1 Loss Is Associated with DNA Methylomic Repatterning in Highly Aggressive Class 2 Uveal Melanomas

Abstract

<div>AbstractPurpose:<p>The strong association between <i>BAP1</i> mutations and metastasizing Class 2 uveal melanoma (UM) suggests that epigenetic alterations may play a significant role in tumor progression. Thus, we characterized the impact of <i>BAP1</i> loss on the DNA methylome in UM.</p><p><b>Experimental Design:</b> Global DNA methylation was analyzed in 47 Class 1 and 45 Class 2 primary UMs and in UM cells engineered to inducibly deplete BAP1. RNA-Seq was analyzed in 80 UM samples and engineered UM cells.</p>Results:<p>Hypermethylation on chromosome 3 correlated with downregulated gene expression at several loci, including 3p21, where <i>BAP1</i> is located. Gene set analysis of hypermethylated and downregulated genes identified axon guidance and melanogenesis as deregulated pathways, with several of these genes located on chromosome 3. A novel hypermethylated site within the <i>BAP1</i> locus was found in all Class 2 tumors, suggesting that <i>BAP1</i> itself is epigenetically regulated. Highly differentially methylated probes were orthogonally validated using bisulfite sequencing, and they successfully distinguished Class 1 and Class 2 tumors in 100% of cases. In functional validation experiments, <i>BAP1</i> knockdown in UM cells induced methylomic repatterning similar to UM tumors, enriched for genes involved in axon guidance, melanogenesis, and development.</p>Conclusions:<p>This study, coupled with previous work, suggests that the initial event in the divergence of Class 2 UM from Class 1 UM is loss of one copy of chromosome 3, followed by mutation of <i>BAP1</i> on the remaining copy of chromosome 3, leading to the methylomic repatterning profile characteristic of Class 2 UMs.</p></div>