DNA damage and repair in age-related inflammation

Abstract

Genomic instability is an important driver of ageing. The accumulation of DNA damage is believed to contribute to ageing by inducing cell death, senescence and tissue dysfunction. However, emerging evidence shows that inflammation is another major consequence of DNA damage. Inflammation is a hallmark of ageing and the driver of multiple age-related diseases. Here, we review the evidence linking DNA damage, inflammation and ageing, highlighting how premature ageing syndromes are associated with inflammation. We discuss the mechanisms by which DNA damage induces inflammation, such as through activation of the cGAS-STING axis and NF-κB activation by ATM. The triggers for activation of these signalling cascades are the age-related accumulation of DNA damage, activation of transposons, cellular senescence and the accumulation of persistent R-loops. We also discuss how epigenetic changes triggered by DNA damage can lead to inflammation and ageing via redistribution of heterochromatin factors. Finally, we discuss potential interventions against age-related inflammation.

Figure 1:. DNA damage as an inducer of inflammation.

Multiple mechanisms connect DNA damage to inflammation. DNA damage may result in chromosome fragments that do not segregate properly during subsequent cell division. These chromosome fragments become surrounded by nuclear envelope forming. When the micronuclei undergo nuclear envelope rupture, the chromosome DNA is exposed to the DNA sensor cGAS. Alternatively, during DNA damage or subsequent resection and repair, DNA fragments may directly leak into the cytoplasm through a less understood mechanism (dashed line). ssDNA fragments may form double-stranded secondary structures, which can also be recognized by cGAS. DNA-bound cGAS converts GTP and ATP into cGAMP, which activates STING. Activated STING through TBK1-IRF3 and TRAF6-NF-κB, induces transcription of IFN genes and other cytokines. Additionally, proteins involved in DNA damage response can directly trigger inflammation. Depending on the type of DNA damage, ATM or ATR are activated and recruited to the DNA break sites. Activated ATM or ATR can activate NF-κB by stabilizing GATA4 protein. ATM can also stimulate NF-κB by activating TRAF6. Senescence inducing stimuli, including sustained DNA damage and telomere defects, may activate p38 pathway. p38 induces inflammation through NF-κB; it also inhibits STING-dependent IFN response through USP21-mediated K27/63 linked polyubiquitination. NE: nuclear envelope. Image was generated using biorender.com.

Figure 2:. RTE mobilization triggers inflammation via cytoplasmic DNA.

Ageing-related loss of heterochromatin marks on RTEs results in their transcriptional activation and retrotransposition. In the cytoplasm, Alu elements produce ssDNA via self-priming utilizing LINE1 RT machinery. Simar process may take place for L1s. In the nucleus, RNPs initiate RTE integration by generating DNA nicks and reverse transcription, which induces DNA damage. Additionally, unsuccessful integration produces DNA flaps, which are processed to RNA-DNA hybrid fragments. The RTE RNA-DNA hybrids resulting from reverse transcription either in the nucleus or cytoplasm and DNA fragments resulting from genomic damage are recognized by cytoplasmic cGAS, triggering the cGAS-STING signaling, leading to IFN production and sterile inflammation. Dashed lines indicate steps that require further experimental evidence.

Figure 3:. Mechanisms of senescence induced inflammation.

Cellular senescence induces inflammation via cytoplasmic nucleic acid sensing pathway. Three major events participate in the generation of cytoplasmic DNA. One of the hallmarks of senescence is the loss of lamin B1. The autophagy-related protein LC3 interacts with lamina and lamina-associated domains (LADs) of the chromatin and directs lamin B1 to autophagy. This process results in the loss of nuclear membrane integrity, contributing to the leaking of chromatin to the cytoplasm. Sustained DNA damage response (DDR) is another hallmark of senescence. The cytoplasmic DNA is positive for γH2AX and negative of 53BP1, suggesting that the formation of cytoplasmic DNA is associated with DDR. Two cytoplasmic DNases, DNase 2α and Trex1, are responsible for degrading excessive cytoplasmic DNA. Both enzymes are down-regulated in senescence through a negative transcriptional regulation. Therefore, in senescence, loss of nuclear membrane integrity promotes the accumulation of cytoplasmic DNA, which is further stabilized by the down-regulation of DNases. Cytoplasmic DNA is sensed by the DNA the sensor cGAS, which triggers STING and its downstream pathways, including IRF3-IFN and NF-κB-SASP pathways.

Figure 4:. R-loops accumulate with age and drive inflammation.

R-loops form in healthy young cells during regular cellular processes, including transcription and DNA replication. Proteins such as BRCA1 and SETX ensure RNA displacement and R-loops resolution. FA complex proteins and BRCA2 also ensure that R-loops remain transitory. In older cells, R-loops accumulate and persist within the genome, due to failure of processes responsible for their resolution. Secondary DNA structures, such as G-quadraplexes, contribute to unresolved R-loop accumulation. Persistent R-loops leave displaced ssDNA strands exposed to endonucleases, such as XPF, XPG and FEN1, leading to genomic instability and inflammation. Persistent R-loops can also be recognized by cGAS-STING and trigger sterile inflammation.

Figure 5:. Epigenetic changes triggered by life-long DNA damage lead to induction of RTEs and inflammaging.

DNA damage can induce redistribution of heterochromatin modifiers such as proteins of the Sirtuin family, SIRT1 and SIRT6. In young cells, these Sirtuins silence RTEs and other repetitive elements by maintaining heterochromatin. Upon DNA damage, Sirtuins re-localize to DSB sites, leading to the activation of RTEs. Activated RTEs result in the formation of cytoplasmic RNA or DNA, which trigger the RNA or DNA sensing pathway to induce inflammation. This mechanism provides a link between DNA damage and inflammation through chromatin change.