Characterization of human disease phenotypes associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1

Abstract

Aicardi-Goutières syndrome is an inflammatory disease occurring due to mutations in any of TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR or IFIH1. We report on 374 patients from 299 families with mutations in these seven genes. Most patients conformed to one of two fairly stereotyped clinical profiles; either exhibiting an in utero disease-onset (74 patients; 22.8% of all patients where data were available), or a post-natal presentation, usually within the first year of life (223 patients; 68.6%), characterized by a sub-acute encephalopathy and a loss of previously acquired skills. Other clinically distinct phenotypes were also observed; particularly, bilateral striatal necrosis (13 patients; 3.6%) and non-syndromic spastic paraparesis (12 patients; 3.4%). We recorded 69 deaths (19.3% of patients with follow-up data). Of 285 patients for whom data were available, 210 (73.7%) were profoundly disabled, with no useful motor, speech and intellectual function. Chilblains, glaucoma, hypothyroidism, cardiomyopathy, intracerebral vasculitis, peripheral neuropathy, bowel inflammation and systemic lupus erythematosus were seen frequently enough to be confirmed as real associations with the Aicardi-Goutieres syndrome phenotype. We observed a robust relationship between mutations in all seven genes with increased type I interferon activity in cerebrospinal fluid and serum, and the increased expression of interferon-stimulated gene transcripts in peripheral blood. We recorded a positive correlation between the level of cerebrospinal fluid interferon activity assayed within one year of disease presentation and the degree of subsequent disability. Interferon-stimulated gene transcripts remained high in most patients, indicating an ongoing disease process. On the basis of substantial morbidity and mortality, our data highlight the urgent need to define coherent treatment strategies for the phenotypes associated with mutations in the Aicardi-Goutières syndrome-related genes. Our findings also make it clear that a window of therapeutic opportunity exists relevant to the majority of affected patients and indicate that the assessment of type I interferon activity might serve as a useful biomarker in future clinical trials.

Keywords: Aicardi-Goutières syndrome; bilateral striatal necrosis; interferon signature; spastic paraparesis; type I interferon.

FIG. 1

Numbers and percentages of families with Aicardi–Goutières syndrome (AGS) with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR and IFIH1. D: denotes dominant mutation. One child with a neurological phenotype and a single heterozygous mutation in TREX1, and three children with single heterozygous mutations in RNASEH2B were also identified. In addition, four families demonstrating autosomal dominant segregation of familial chilblain lupus (FCL) with mutations in either TREX1 (two families) or SAMHD1 (one family) were ascertained. Mutations in RNASEH2B and TREX1 represent more than half of our cohort. Considering their relatively recent identification, it is possible that the proportion of patients with mutations in ADAR and IFIH1 may increase.

FIG. 2

Age at presentation by genotype. Percentage of patients with either biallelic mutations or a recognized dominant mutation in one of the known AGS-related genes, in families where at least one individual has a neurological phenotype, i.e., excluding families with only FCL. Congenital infection-like describes patients with a neurological phenotype at birth plus thrombocytopenia and hepatosplenomegaly. Most patients present within the first year of life. Mutations in TREX1 were most frequently associated with a congenital infection-like presentation, while children presenting after the age of one year were most likely to harbor mutations in ADAR or IFIH1.

FIG. 3

Development prior to presentation according to mutated gene. Percentage of patients with either biallelic mutations or a recognized dominant mutation in one of the known AGS genes, in families where at least one individual has a neurological phenotype, i.e., excluding families only with FCL. Never normal: presentation at or after birth without a period of normal development. Uncertain: presentation after birth where developmental status prior to presentation was uncertain. Normal: presentation after birth with definitely normal development prior to disease onset. Patients presenting with a period of normal development were more likely to harbor mutations in ADAR or IFIH1.

FIG. 4

Degree of disability by mutated gene. Numbers represent the sum of GMFCS (Gross Motor Function Classification System for Cerebral Palsy), MACS (Manual Ability Classification System), and CFCS (Communication Function Classification System) score at time of last contact/ death for each patient where three is normal and 15 is profoundly disabled. Number of patients with either biallelic mutations or a recognized dominant mutation in one of the known AGS-related genes, in families where at least one individual has a neurological phenotype, i.e., excluding families with only FCL. Although most patients (74%) are severely neurologically damaged, this was more likely to be the case in children with mutations in TREX1, RNASEH2A or RNASEH2C.

FIG. 5

(A) Known status of AGS patients by age at last contact/age at death. (B) Known status of AGS patients by mutated gene. Number of patients with either biallelic mutations or a recognized dominant mutation in one of the known AGS-related genes, in families where at least one individual has a neurological phenotype i.e., excluding families with FCL only. Although there is a significant mortality associated with mutations in the AGS-related genes, a number of patients have been recorded to survive into adulthood. Mutations in TREX1 were associated with a greater risk of death than mutations in the other AGS-related genes.

FIG. 6

Frequency of associated phenotypes in AGS patients. Number of patients with either biallelic mutations or a recognized dominant mutation in one of the known AGS-related genes, in families where at least one individual has a neurological phenotype, i.e., excluding families with FCL only. SLE/APLS: Systemic lupus erythematosus/antiphospholipid syndrome. Inflammatory gastrointestinal disease: Crohns disease, atrophic gastritis, coeliac disease, autoimmune hepatitis, non-specific colitis. Other autoimmune: one diabetes mellitus, one hyperparathyroidism, one growth hormone deficiency, one adrenal insufficiency.

FIG. 7

(A) Quantitative reverse transcription PCR (qPCR) showing the interferon score derived from a panel of six interferon stimulated genes (ISGs) measured in whole blood in 100 AGS patients and 29 controls. The median fold change of the six probes combined was calculated to given an interferon score for each individual. Red bars show the median RQ value for each probe in each group. Samples colored red have a positive interferon score (>2.4) whereas samples colored blue have a normal interferon score (within +2 SD of the median for the control population). For subjects with repeat samples, the median combined measurement is shown. RQ is equal to 2^−ΔΔCt, i.e., the normalized fold change relative to a control. One way ANOVA with Dunnett’s multiple comparison test. Almost all patients demonstrate a positive interferon score compared to controls, except for individuals with mutations in RNASEH2B, where 31% of patients demonstrated a normal interferon signature. (B) ISG RQ by mutated gene compared to controls. Red bars show the median RQ value for each probe in each group. One way ANOVA with Dunnett’s multiple comparison test. These data sets include some measurements published previously [Rice et al., 2013a]. These data indicate a clear upregulation of the expression of the six interferon stimulated genes assayed in patients compared to controls, with lower median values in patients with mutations in RNASEH2B.

FIG. 8

CSF interferon measurements in patients assayed within one year of disease onset, plotted against disability score. (A) CSF interferon measurements in patients with a combined GMCSF, MACS, and CFCS score of 15 compared to patients with a score less than 15. Red bars show the median CSF interferon. Unpaired t-test of log transformed data. (B) CSF interferon measurements plotted against the combined disability score. In patients with serial measurements only the first measurement is shown. These data sets include some measurements published previously [Lebon et al., 1988, Lebon et al., 2002, Rice et al., 2013a]. There is a possible association between interferon activity in the cerebrospinal fluid measured in the first year of life and disability outcome.