Cytoplasmic synthesis of endogenous Alu complementary DNA via reverse transcription and implications in age-related macular degeneration

Abstract

Alu retroelements propagate via retrotransposition by hijacking long interspersed nuclear element-1 (L1) reverse transcriptase (RT) and endonuclease activities. Reverse transcription of Alu RNA into complementary DNA (cDNA) is presumed to occur exclusively in the nucleus at the genomic integration site. Whether Alu cDNA is synthesized independently of genomic integration is unknown. Alu RNA promotes retinal pigmented epithelium (RPE) death in geographic atrophy, an untreatable type of age-related macular degeneration. We report that Alu RNA-induced RPE degeneration is mediated via cytoplasmic L1–reverse-transcribed Alu cDNA independently of retrotransposition. Alu RNA did not induce cDNA production or RPE degeneration in L1-inhibited animals or human cells. Alu reverse transcription can be initiated in the cytoplasm via self-priming of Alu RNA. In four health insurance databases, use of nucleoside RT inhibitors was associated with reduced risk of developing atrophic macular degeneration (pooled adjusted hazard ratio, 0.616; 95% confidence interval, 0.493–0.770), thus identifying inhibitors of this Alu replication cycle shunt as potential therapies for a major cause of blindness.

Alu complementary DNA is enriched in atrophic macular degeneration and triggers retinal pigmented epithelium toxicity via cytosolic innate immunity

“…Endogenous Alu cDNA in human geographic atrophy Previously, we demonstrated that Alu RNA-induced RPE degeneration and inflammation are mediated via cytoplasmic L1-reverse-transcribed Alu cDNA independently of retrotransposition in human RPE cells and mice (11). In geographic atrophy, an untreatable, advanced vision-threatening form of AMD (2), Alu RNA expressed from endogenous Alu retrotransposons by RNA polymerase III accumulates in the RPE (3,4).…”

Cytoplasmic DNA: sources, sensing, and role in aging and disease

“…Although TPRT occurs in the nucleus, L1 cDNA has also been found in the cytosol in certain conditions, such as autoimmunity (Stetson et al, 2008;Thomas et al, 2017), and others that will be discussed in more detail below. There are two possible mechanisms by which L1 cDNA might exist in the cytoplasm: one possibility is that accumulation of high amounts of L1 mRNA and L1 proteins in the cytosol might enable reverse transcription to occur without a standard DNA template, resulting in increased cytosolic cDNA elements (Fukuda et al, 2021). Alternatively, it is also possible that during TPRT, the resulting cDNA does not re-integrate into the genome and instead leaves the nucleus into the cytosol by an unknown process (Thomas et al, 2017).…”

Sensing of transposable elements by the antiviral innate immune system

“…For instance, senescent cells could be retrotranscribing LINE-1 in the cytoplasm, if cytoplasmic RNA/DNA molecules could act as primer. Only recently, Alu elements have been shown to be retrotranscribed in the cytoplasm by the LINE-1-encoded machinery independently of its retrotransposition, bringing closer the possibility that LINE-1 RNA could be also used as template to generate LINE-1 cDNA in the cytoplasm (Fukuda et al 2021). Alternatively, LINE-1 cDNA could also be recognised by cGAS in the nucleus, as a significant proportion of this sensor has been found in the nuclear compartment of specific cell types (Xia et al 2018;Volkman et al 2019;Gentili et al 2019).…”