Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature

Abstract

Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) and thereby potentially alter the information content and structure of cellular RNAs. Notably, although the overwhelming majority of such editing events occur in transcripts derived from Alu repeat elements, the biological function of non-coding RNA editing remains uncertain. Here, we show that mutations in ADAR1 (also known as ADAR) cause the autoimmune disorder Aicardi-Goutières syndrome (AGS). As in Adar1-null mice, the human disease state is associated with upregulation of interferon-stimulated genes, indicating a possible role for ADAR1 as a suppressor of type I interferon signaling. Considering recent insights derived from the study of other AGS-related proteins, we speculate that ADAR1 may limit the cytoplasmic accumulation of the dsRNA generated from genomic repetitive elements.

Figure 1

Schematic of the human ADAR1 gene. (a) ADAR1 spans 26,191 bp of genomic sequence on chromosome 1q21.3 (154,554,533–154,580,724). Neighboring genes are also shown. Cen, centromeric; tel, telomeric. (b) Position of identified mutations within the genomic sequence of the ADAR1 long isoform (p150). The number of alleles with each mutation is shown in parentheses. *, the mutation encoding p.Gly1007Arg identified as a single heterozygous de novo change in two families; †, the same mutation identified in identical twins (therefore counted once). Numbers given above the gene indicate the relevant exons (only exons with mutations are numbered). The shorter isoform (p110) of ADAR1 starts at c.886 of the p150 isoform. (c) Position of identified variants within the ADAR1 p150 1,226-amino-acid protein. Numbers above the protein are the amino-acid count at the exon boundaries. The shorter isoform starts at amino acid 296 of p150, giving rise to a 931-amino-acid protein. (d) Schematic of the position of protein domains and their amino-acid boundaries in the p150 isoform of ADAR1. Note that the p110 isoform does not include the Zα DNA/RNA-binding domain and nuclear export signal.

Figure 2

Structural context of ADAR1 protein substitutions. (a) The surface of the ADAR domain (dark pink) with surface substitutions highlighted in bright pink. The active site contains a zinc ion (black) in the center. Arg892His, Lys999Asn, Gly1007Arg, Tyr1112Phe and Asp1113His are all on the same side of the domain as the active site, and all have the potential to alter charge and/or hydrogen bonding characteristics of the surface in the region that is likely to be responsible for RNA binding. (b,c) Models of wild-type (b) and mutant (c) residues at position 870 in the ADAR domain. Interactions between the residue and the surrounding protein structure are indicated by all-atom contact dots (blue). Green dots represent energetically favorable van der Waals interactions, whereas red and pink spikes indicate unfavorable van der Waals overlaps. The Ile872Thr substitution introduces an unsatisfied hydrogen bond donor/acceptor group, which is destabilizing but not easily depicted. (d,e) Interactions of the proline residue at position 193 (Pro193) in the Z-DNA–binding domain (d). Contact dots (blue, green, yellow) indicate favorable interactions between Pro193 and the DNA backbone (white). These interactions are absent in the mutant form (e). (f) Modeling of the deaminase domain of ADAR2 suggests contact with dsRBD2 close to Gly1007, highlighting the possibility for an arginine residue to make functionally important polyvalent interactions.

Figure 3

Protein blot of lymphoblastoid cell lines (LCLs). Protein blot analysis of ADAR1 expression in Epstein-Barr virus (EBV)-transformed LCLs from one unrelated control and two affected individuals (AGS93, AGS107). Whole-cell lysates were derived from 1 × 10⁷ cells per sample, and 10 μg of total protein was loaded per lane. To test antibody specificity and confirm IFN induction of the p150 isoform of ADAR1, unstimulated cells were compared to IFN-stimulated cells. The antibody to ADAR1 recognizes both the p110 and p150 isoforms. Immunoblotting of tubulin (50–55 kDa) was used as a loading control.

Figure 4

Site-specific and competition editing assays. (a) HEK293 cells were co-transfected with 500 ng of a plasmid expressing miR376-a2 and 500 ng of a plasmid expressing wild-type (WT) ADAR1 or ADAR1 mutants. Background editing in HEK293 cells with 500 ng of substrate plasmid is approximately 20%. As previously observed, only one monomer in an ADAR1 dimer is required to be enzymatically active, such that addition of inactive protein initially increases editing. Editing activity is expressed as a proportion of WT ADAR1 editing activity, which is 1 (y axis). Error bars, s.e.m. ***P = 0.0005. (b) Competition between ADAR1 and inactive ADAR1 mutants. HEK293 cells were co-transfected with 200 ng of a plasmid expressing miR376-a2 and 200 ng of a plasmid expressing ADAR1 p110 in the presence of increasing amounts of a plasmid expressing a catalytically inactive form of ADAR1 (Glu912Ala) or Gly1007Arg. Error bars, s.e.m. **P = 0.0026.

Figure 5

Quantitative RT-PCR of a panel of six ISGs in whole blood measured in individuals with AGS, their parents and individuals with DSH. Scatter plots showing log₁₀-transformed RQ values for a panel of 6 ISGs measured in whole blood from 10 AGS cases with mutations in ADAR1, 6 sets of parents heterozygous for mutations in ADAR1, 18 individuals with ADAR1 mutation–positive DSH and 20 healthy controls. All genes were significantly upregulated in AGS cases (P < 0.001) compared to controls. RQ is equal to 2^−ΔΔC_T, with −ΔΔC_T ± s.d., that is the normalized fold change relative to a calibrator. ***P ≤ 0.001; **P ≤ 0.01; *P < 0.05.