Mapping the future of oxidative RNA damage in neurodegeneration: Rethinking the status quo with new tools

Abstract

Over two decades ago, increased levels of RNA oxidation were reported in postmortem patients with ALS, Alzheimer's, Parkinson's, and other neurodegenerative diseases. Interestingly, not all cell types and transcripts were equally oxidized. Furthermore, it was shown that RNA oxidation is an early phenomenon, altogether indicating that oxidative RNA damage could be a driver, and not a consequence, of disease. Despite all these exciting observations, the field appears to have stagnated since then. We argue that this is a consequence of the shortcomings of technologies to model these diseases, limiting our understanding of which transcripts are being oxidized, which RNA-binding proteins are interacting with these RNAs, what their implications are in RNA processing, and as a result, what their potential role is in disease onset and progression. Here, we discuss the limits of previous technologies and propose ways by which advancements in iPSC-derived disease modeling, proteomics, and sequencing technologies can be combined and leveraged to answer new and decades-old questions.

Keywords: RNA-binding proteins; induced pluripotent stem cells; neurodegeneration; oxidative RNA damage; oxidative stress.

Fig. 1.

Proposed link between oxidative RNA lesion-driven defects in RNA processing and other hallmarks of neurodegenerative disease. Donor fibroblasts or PBMCs can be reprogrammed to iPSCs and subsequently differentiated into disease-relevant cell types. iPSC-derived neuronal systems have been shown to closely recapitulate the eight hallmarks of neurodegenerative disease (5) and can be leveraged to elucidate disease-associated mechanisms. The interplay between oxidative RNA damage, impaired RNA processing, and the manifestation of one or more of the shared neurodegenerative phenotypes has yet to be explored. A deeper understanding of converging phenotypes will aid in determining the role of RNA oxidation on dysregulated processes and neurodegenerative disease. Created with BioRender.com.

Fig. 2.

Novel detection methodologies for identification of RNA oxidation and their protein interacting partners. Oxidative RNA lesions (in red) can be recognized by RBPs (in dark yellow). To determine the identity of damaged transcripts two approaches can be used. Immunoprecipitation (IP) with anti-lesion antibodies followed by sequencing, or alternatively sequencing (without IP) with a focus on damage signatures introduced during reverse transcription. Lesion-binding RBPs can be identified by novel interactome phase separation methods (OOPS, XRNAX, and LEAP-RBP) via LC–MS. Their RNA targets can be further determined via eCLIP or other recent interactome technologies such as TRIBE, STAMP, and REMORA. The table on the right shows a comparison of previous (1.0) and novel (2.0) methods used for antibody isolation of damaged RNAs, identification of these transcripts, and identification of their interacting RBPs as well as these RBPs’ targets. Created with BioRender.com.

Fig. 3.

Knowledge gap in the interactions between neurodegeneration, RNA oxidation, and RBPs. To date, research in the three shown disciplines has focused either on a single discipline or the interactions between two of them. The nature and main takeaways from these interactions are highlighted for each of the three combinations. This work postulates the idea that all three disciplines must be combined, together with novel technological advancements, to explore the potential role that oxidative RNA damage plays in neurodegeneration through RNA processing. Created with BioRender.com.