R-loop-associated regulator VDAC1 drives malignant phenotypes in uveal melanoma

R-loops regulate genome stability and transcription, but their roles in uveal melanoma (UVM) are unclear.

A total of 1185 R-loop regulators were analyzed across TCGA-UVM and GEO cohorts. We utilized ssGSEA to assess global R-loop activity and conducted integrative bioinformatic screening to identify key regulators associated with poor prognosis and metastasis. The study focused on the functional validation of VDAC1, a top-ranked candidate. The effects of VDAC1 on UVM cell proliferation, migration, and apoptosis were evaluated through shRNA-mediated knockdown. Mechanistically, immunofluorescence assays were employed to examine R-loop accumulation and DNA damage (γ-H2AX). A UVM mouse model was further used to assess the impact of VDAC1 on tumor growth in vivo.

Increased R-loop activity scores were significantly associated with advanced clinical stages and metastatic potential in UVM. Through systematic screening, we identified a signature of shared R-loop regulators that align with the high-risk molecular profile of UVM. Among these, VDAC1 was identified as a primary contributor to the aggressive phenotype. Experimental validation revealed that knockdown of VDAC1 significantly inhibited cell proliferation and migration while inducing apoptosis. Importantly, VDAC1 deficiency led to the aberrant accumulation of R-loops and subsequent DNA damage, both in vitro and in vivo.

Our findings demonstrate that VDAC1 is a crucial R-loop regulator in UVM. Its dysregulation contributes to genomic instability and tumor progression, suggesting that targeting VDAC1-mediated R-loop homeostasis may offer a potential therapeutic strategy for high-risk UVM patients.