Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

TLDR

Genome integrity is constantly challenged by DNA damage arising from normal metabolism, and biallelic mutations in RNase H2, the genome surveillance enzyme, cause Aicardi‑Goutières syndrome, a pediatric disorder that shares features with systemic lupus erythematosus. We found that rare RNASEH2 variants associate with systemic lupus erythematosus, that heterozygous carriers display an intermediate autoimmune phenotype, and that RNase H2‑deficient cells accumulate ribonucleotides, trigger chronic low‑level DNA damage with p53 phosphorylation and senescence, upregulate interferon‑stimulated genes, exhibit heightened type I interferon responses to poly(I:C) and UV, and show increased UV‑induced cyclobutane pyrimidine dimer formation, implicating RNase H2 dysfunction and DNA damage–associated pathways in SLE pathogenesis.

Abstract

Genome integrity is continuously challenged by the DNA damage that arises during normal cell metabolism. Biallelic mutations in the genes encoding the genome surveillance enzyme ribonuclease H2 (RNase H2) cause Aicardi-Goutières syndrome (AGS), a pediatric disorder that shares features with the autoimmune disease systemic lupus erythematosus (SLE). Here we determined that heterozygous parents of AGS patients exhibit an intermediate autoimmune phenotype and demonstrated a genetic association between rare RNASEH2 sequence variants and SLE. Evaluation of patient cells revealed that SLE- and AGS-associated mutations impair RNase H2 function and result in accumulation of ribonucleotides in genomic DNA. The ensuing chronic low level of DNA damage triggered a DNA damage response characterized by constitutive p53 phosphorylation and senescence. Patient fibroblasts exhibited constitutive upregulation of IFN-stimulated genes and an enhanced type I IFN response to the immunostimulatory nucleic acid polyinosinic:polycytidylic acid and UV light irradiation, linking RNase H2 deficiency to potentiation of innate immune signaling. Moreover, UV-induced cyclobutane pyrimidine dimer formation was markedly enhanced in ribonucleotide-containing DNA, providing a mechanism for photosensitivity in RNase H2-associated SLE. Collectively, our findings implicate RNase H2 in the pathogenesis of SLE and suggest a role of DNA damage-associated pathways in the initiation of autoimmunity.