Supplementary Table S4 from BAP1 Loss Is Associated with DNA Methylomic Repatterning in Highly Aggressive Class 2 Uveal Melanomas

dataset

posted on 2023-03-31, 21:07 authored by Matthew G. Field, Jeffim N. Kuznetsov, Parker L. Bussies, Louie Z. Cai, Karam A. Alawa, Christina L. Decatur, Stefan Kurtenbach, J. William Harbour

HyperMethvsDecGE_ChrLoc: Chromosomal loci enriched (FDR < 0.05) for hypermethylated/downregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HypoMethvsIncGE_ChrLoc: Chromosomal loci enriched (FDR < 0.05) for hypomethylated/upregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HyperMethvsDecGE_KEGG_REACTOME: Functional (KEGG and REACTOME) pathways enriched (FDR < 0.05) for hypermethylated/downregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HypoMethvsIncGE_KEGG_REACTOME: Functional (KEGG and REACTOME) pathways enriched (FDR < 0.05) for hypomethylated/upregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HyperMethvsDecGE_GO: Gene ontology molecular functions enriched (FDR < 0.05) for hypermethylated/downregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HypoMethvsIncGE_GO: Gene ontology molecular functions enriched (FDR < 0.05) for hypomethylated/upregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HyperMethvsDecGE_TF: Promoter region transcription factor binding sites enriched (FDR < 0.05) for hypermethylated/downregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas HypoMethvsIncGE_TF: Promoter region transcription factor binding sites enriched (FDR < 0.05) for hypomethylated/upregulated genes in Class 2 uveal melanomas compared to Class 1 uveal melanomas

Funding

NCI

Alcon Research Institute

NIH

History

ARTICLE ABSTRACT

The strong association between BAP1 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 BAP1 loss on the DNA methylome in UM.Experimental Design: 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. Hypermethylation on chromosome 3 correlated with downregulated gene expression at several loci, including 3p21, where BAP1 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 BAP1 locus was found in all Class 2 tumors, suggesting that BAP1 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, BAP1 knockdown in UM cells induced methylomic repatterning similar to UM tumors, enriched for genes involved in axon guidance, melanogenesis, and development. 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 BAP1 on the remaining copy of chromosome 3, leading to the methylomic repatterning profile characteristic of Class 2 UMs.