Induction of viral mimicry upon loss of DHX9 and ADAR1 in breast cancer cells

Abstract

Detection of viral double-stranded RNA (dsRNA) is an important component of innate immunity. However, many endogenous RNAs containing double-stranded regions can be misrecognized and activate innate immunity. The interferon inducible ADAR1-p150 suppresses dsRNA sensing, an essential function for ADAR1 in many cancers, including breast. Although ADAR1-p150 has been well established in this role, the functions of the constitutively expressed ADAR1-p110 isoform are less understood. We used proximity labeling to identify putative ADAR1-p110 interacting proteins in breast cancer cell lines. Of the proteins identified, the RNA helicase DHX9 was of particular interest. Knockdown of DHX9 in ADAR1-dependent cell lines caused cell death and activation of the dsRNA sensor PKR. In ADAR1-independent cell lines, combined knockdown of DHX9 and ADAR1, but neither alone, caused activation of multiple dsRNA sensing pathways leading to a viral mimicry phenotype. Together, these results reveal an important role for DHX9 in suppressing dsRNA sensing by multiple pathways.

Activation of PKR by a short-hairpin RNA

“…Using proximity labeling, we had previously identified the RNA helicase DDX54 as an ADAR1 interacting protein 22 . This led us to study the role of DDX54 in the regulation of dsRNA sensing, a role that has been well established for ADAR1.…”

Adenosine deaminases that act on RNA, then and now

“…Posttranslational modifications of the ADAR enzymes themselves can alter their activity, and as discussed in more detail below, localization of ADARs to the nucleus or cytoplasm plays a large role in which dsRNAs are edited ( Vesely and Jantsch 2021 ); indeed, examples of factors that affect localization exist ( Deffit and Hundley 2016 ). Finally, and importantly, the story is not over yet, and recent genome-wide and proximity-labeling experiments reveal candidate accessory factors ( Hong et al 2018 ; Quinones-Valdez et al 2019 ; Freund et al 2020 ; Cottrell et al 2023 ). While identifying a number of interesting proteins whose effects on ADARs are yet to be explored, these studies also emphasize that other dsRBPs, by competing for binding to ADAR's dsRNA substrates, can regulate levels of editing.…”