Hypoxia‐mediated regulation of DDX5 through decreased chromatin accessibility and post‐translational targeting restricts R‐loop accumulation

• Published in: Molecular oncology 2023-07, Vol.17 (7), p.1173-1191
• Main Authors: Leszczynska, Katarzyna B., Dzwigonska, Monika, Estephan, Hala, Moehlenbrink, Jutta, Bowler, Elizabeth, Giaccia, Amato J., Mieczkowski, Jakub, Kaminska, Bozena, Hammond, Ester M.
• Format: Article
• Language: English
• Subjects: ATACseq; Cancer; Cancer and Oncology; Cell Line; Chromatin; DDX5; Dehydrogenases; Disease resistance; DNA helicase; DNA methylation; DNA repair; Epigenetics; Gene expression; Gene loci; Humans; Hypoxia; Hypoxia - genetics; Plasmids; Post-translation; Proteins; R-Loop Structures; RNA helicase; R‐loops; Short Report; Solid tumors; Tumor cell lines
• ISSN: 1574-7891; 1878-0261
• DOI: 10.1002/1878-0261.13431

Local hypoxia occurs in most solid tumors and is associated with aggressive disease and therapy resistance. Widespread changes in gene expression play a critical role in the biological response to hypoxia. However, most research has focused on hypoxia‐inducible genes as opposed to those that are decreased in hypoxia. We demonstrate that chromatin accessibility is decreased in hypoxia, predominantly at gene promoters and specific pathways are impacted including DNA repair, splicing, and the R‐loop interactome. One of the genes with decreased chromatin accessibility in hypoxia was DDX5, encoding the RNA helicase, DDX5, which showed reduced expression in various cancer cell lines in hypoxic conditions, tumor xenografts, and in patient samples with hypoxic tumors. Most interestingly, we found that when DDX5 is rescued in hypoxia, replication stress and R‐loop levels accumulate further, demonstrating that hypoxia‐mediated repression of DDX5 restricts R‐loop accumulation. Together these data support the hypothesis that a critical part of the biological response to hypoxia is the repression of multiple R‐loop processing factors; however, as shown for DDX5, their role is specific and distinct. Regions of hypoxia occur in solid tumors and are associated with cancer progression and therapy resistance. The repression of specific pathways in response to hypoxia like DNA repair and splicing factors was described previously. Here, we find that genes encoding proteins with roles in the R‐loop interactome are repressed in hypoxia and link this to decreased chromatin accessibility. DDX5 expression was decreased under hypoxia in cell lines (cancer and normal), tumor xenografts and hypoxic tumors from cancer patients leading to reduced R‐loop accumulation and replication stress.