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

Abstract

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.

Role of the DEAD-box RNA helicase DDX5 (p68) in cancer DNA repair, immune suppression, cancer metabolic control, virus infection promotion, and human microbiome (microbiota) negative influence

“…2 H). Consistently, decreased DDX5 expression is associated with R-loops accumulation in cancer cells [ 40 ]. This finding suggests that DDX5 also plays a critical role in hypoxia response by increasing R-loop-associated DNA damage resulting from hypoxia-mediated inhibition of DDX5.…”

“…Additionally, Leszczynska et al found that hypoxia decreases DDX5 expression and chromatin accessibility at gene promoters and impacts specific pathways [ 40 ]. This may include mRNA stability, DNA topological regulation, DNA repair, RNA splicing, and ribosome biogenesis (Fig.…”

“…The literature discussions above [ 29 – 40 ] highlight the role of DDX5 as a center protein molecule and a partner for multiple other proteins to control R-loop formation/accumulation resolution and gene transcription, being involved in their individual signaling pathways in a very similar manner (Fig. 2 A-H).…”

DDX5 enhances HIF‐1 activity by promoting the interaction of HIF‐1α with HIF‐1β and recruiting the resulting heterodimer to its target gene loci

“…A recent study showed that DDX5 expression levels were reduced under hypoxic conditions in various cancer cell lines, including RKO and HCT116, and so on (Leszczynska et al., 2023). However, under our experimental setup and hypoxic conditions, we observed no apparent change in the expression levels of DDX5.…”

Helicases in R-loop Formation and Resolution

“…Several helicases belonging to the DEAD/H-box family have been reported to prevent R-loop accumulation. DDX5 has been reported to resolve R-loops by different groups ( 37 , 76 , 77 , 78 , 79 ). DDX18 can inhibit the accumulation of R-loops mediated by PARP-1 (poly[ADP-ribose] polymerase-1).…”