Integrative omics approach identifies druggable BAP1-dependencies in Uveal Melanoma

Abstract

Purpose : Uveal melanoma (UM) is the most common intraocular cancer; 50% of patients develop metastases, usually to the liver, that prove fatal within 2-years due to lack of successful therapies. BAP1 mutations are frequently associated with metastatic UM (mUM), and also with malignant pleural mesothelioma (MPM). Through multi-omics analysis to identify common BAP1-dependencies in UM and a gene-edited model of MPM, we tested the hypothesis that adaptation to BAP1 alteration creates therapeutic vulnerabilities in UM.

Methods : A novel function-driven multi-omics analysis, which included pathway-based and gene-based approaches, was used to integrate mRNA, protein and miRNA datasets from isogenic BAP1-mutant mesothelial MeT5A cells with in-house and publicly available UM patient sample transcriptome datasets (Fig 1A). Genes were then filtered (Fig 1B) and candidates validated by qRT-PCR in MeT5A cells and FFPE primary UM (pUM) samples (n=19). Statistical analyses used one-sample or Wilcoxon t-test for MeT5A and two-tailed t-test or Mann Whitney test for UM, depending on whether data were normally distributed.

Results : Multi-omics integration and filtering identified 24 BAP1-dependent candidates: 14 from pathway-based and 17 from gene-based approaches, with 7 in common (Fig 1B). 16 candidates were validated by qRT-PCR (p<0.05) in MeT5A cells, whilst qRT-PCR in pUM samples highlighted 3 lead candidates: BIRC3 significantly increased 9.3-fold in BAP1 altered (4.38±5.66x10^-2 relative to actin) compared to BAP1 normal pUM (4.69±7.57x10^-3;p=0.02), HSP90AB1 decreased 2.3-fold in BAP1 altered (3.81±0.87x10^-1) compared to BAP1 normal pUM (8.75±2.85x10^-1;p=0.0001), and KCND3 increased 13.2-fold in BAP1 altered (1.73±1.73x10^-1) compared to BAP1 normal pUM (1.32±1.56x10^-2;p=0.0015).

Conclusions : This function-driven approach identified novel BAP1-dependent adaptations in UM that may provide therapeutic targets for mUM: increase in BIRC3, an anti-apoptotic gene, decrease in HSP90AB1, a pro-apoptotic gene, and increase in KCND3 which has been shown to promote migration. Assessment of protein expression in UM cell lines and UM patient samples is underway. UM cell line viability will be tested in response to drugs targeting these candidates: LCL-161 (BIRC3), polaprezinc (HSP90AB1 agonist) and dronedarone (KCND3).

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

 

Fig 1. Integration of datasets. A: Venn diagram; circle size reflects size of each dataset. B: Filtering gene candidates.