TY - JOUR
T1 - BAP1 loss is associated with DNA methylomic repatterning in highly aggressive class 2 uveal melanomas
AU - Field, Matthew G.
AU - Kuznetsov, Jeffim N.
AU - Bussies, Parker L.
AU - Cai, Louie Z.
AU - Alawa, Karam A.
AU - Decatur, Christina L.
AU - Kurtenbach, Stefan
AU - Harbour, J. William
N1 - Funding Information:
The authors are grateful to the patients who generously contributed samples for this research. The authors acknowledge the support of the Biostatistics & Bioinformatics and Oncogenomics Shared Resources at the Sylvester Comprehensive Cancer Center (Miami, FL), and the University of Miami Center for Computational Science (Coral Gables, FL). This work was supported by NCI grants R01 CA125970 (to J.W. Harbour) and F30 CA206430 (to M.G. Field), Alcon Research Institute (to J.W. Harbour), Research to Prevent Blindness, Inc. Senior Scientific Investigator Award (to J.W. Harbour), the University of Miami Sheila and David Fuente Graduate Program in Cancer Biology (to M.G. Field), the Center for Computational Science Fellowship (to M.G. Field), and a generous gift from Dr. Mark J. Daily (to J.W. Harbour). The Bascom Palmer Eye Institute also received funding from NIH Core Grant P30EY014801 and a Research to Prevent Blindness Unrestricted Grant.
Publisher Copyright:
© 2019 American Association for Cancer Research.
PY - 2019/9/15
Y1 - 2019/9/15
N2 - Purpose: 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 primaryUMsand inUMcells engineered to inducibly deplete BAP1. RNA-Seq was analyzed in 80 UM samples and engineered UM cells. Results: 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 inUMcells induced methylomic repatterning similar to UM tumors, enriched for genes involved in axon guidance, melanogenesis, and development. Conclusions: 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.
AB - Purpose: 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 primaryUMsand inUMcells engineered to inducibly deplete BAP1. RNA-Seq was analyzed in 80 UM samples and engineered UM cells. Results: 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 inUMcells induced methylomic repatterning similar to UM tumors, enriched for genes involved in axon guidance, melanogenesis, and development. Conclusions: 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.
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U2 - 10.1158/1078-0432.CCR-19-0366
DO - 10.1158/1078-0432.CCR-19-0366
M3 - Article
C2 - 31285370
AN - SCOPUS:85072234311
SN - 1078-0432
VL - 25
SP - 5663
EP - 5673
JO - Clinical Cancer Research
JF - Clinical Cancer Research
IS - 18
ER -