Nuclear DNA Damage Response Triggers Reorganization of Mitochondrial Nucleic Acids

Abstract

Mitochondria are subcellular organelles responsible for energy production, and a hub for several cellular signaling pathways that ultimately control cellular processes ranging from cell death to innate immunity. Genotoxic stress, including cellular irradiation, has been shown to cause the mitochondrial-dependent activation of innate immunity via release of mitochondrial nucleic acids in the cytosol. Yet, how the other cellular events triggered by genotoxic stress affects mitochondria and mitochondrial immunity is largely unexplored. Nuclear DNA damage responses (DDR) are a set of well-described responses to genotoxic stressors that allow the cells to, through characterized mechanisms including transcriptional responses and checkpoint activation, survive or die. Whether canonical DDR directly influence mitochondrial structure and activation of downstream pathways of immunity remains unclear. Here, we identify mito-blobs: enlarged TOMM20-positive mitochondrial structures induced by genotoxic stress that are enriched for TFAM-marked mitochondrial DNA nucleoids, FASTKD2-positive mitochondrial RNA granules, and immunogenic double-stranded RNA. While structurally resembling other mitochondria stress responsive rearrangements, mito-blobs carry the distinctive feature of being induced by nuclear DNA double-stranded breaks alone. Strikingly, mitochondrial double-stranded breaks failed to induce mito-blobs, indicating nuclear-to-mitochondrial signaling rather than an autonomous response to mitochondrial genome damage. Mechanistically, we show that mito-blobs formation strictly requires MFN1/2- and OPA1-dependent fusion machinery, while nuclear DNA damage invokes a classical ATM-p53 response, which lead to cell cycle block in the G1 phase that reduce DRP1 S616 phosphorylation and shifting mitochondrial morphology toward a low-fission pro-fusion state. Strikingly, the use of the standard of care CDK4/6 inhibitor palbociclib, was sufficient to trigger mito-blobs without nuclear DNA damage. Considering the mito-blobs high content in nucleic acids, we additionally investigated if affecting their life cycle could perturb inflammatory and interferon-associated gene expression downstream of genotoxic stress. We describe how autophagic-lysosomal clearance triggered upon cell cycle block limited mito-blob persistence, and blocking autophagy disposal unmasked a strong inflammatory response. Taken together, these findings suggest mito-blobs are the product of an active mitochondrial remodeling process elicited in response to nuclear genotoxic stress and that concentrate immunogenic mitochondrial nucleic acids in defined structures for their correct disposal via autophagy and avoid aberrant activation of innate immunity. HighlightsO_LIGenotoxic stress induces enlarged mitochondrial structures called mito-blobs. C_LIO_LIMito-blobs concentrate mitochondrial DNA, RNA granules, and double-stranded RNA. C_LIO_LINuclear DNA damage, but not mitochondrial, is sufficient to induce mito-blobs. C_LIO_LICDK4 Inhibitors Trigger Mito-blob Formation. C_LIO_LIMito-blob formation and clearance alter inflammatory gene expression. C_LI eTOC blurbYu et al. identify mito-blobs as enlarged mitochondrial structures that form after genotoxic stress. They show that nuclear DNA breaks - as opposed to mitochondrial DNA breaks - trigger mito-blob formation through nuclear-to-mitochondrial signaling involving altered DRP1 phosphorylation and mitochondrial fusion machinery. Mito-blob persistence is limited by autophagic clearance and is associated with inflammatory and interferon-associated gene expression after stress.