Enhanced cGAS-STING–dependent interferon signaling associated with mutations in ATAD3A

Abstract

Mitochondrial DNA (mtDNA) has been suggested to drive immune system activation, but the induction of interferon signaling by mtDNA has not been demonstrated in a Mendelian mitochondrial disease. We initially ascertained two patients, one with a purely neurological phenotype and one with features suggestive of systemic sclerosis in a syndromic context, and found them both to demonstrate enhanced interferon-stimulated gene (ISG) expression in blood. We determined each to harbor a previously described de novo dominant-negative heterozygous mutation in ATAD3A, encoding ATPase family AAA domain–containing protein 3A (ATAD3A). We identified five further patients with mutations in ATAD3A and recorded up-regulated ISG expression and interferon α protein in four of them. Knockdown of ATAD3A in THP-1 cells resulted in increased interferon signaling, mediated by cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Enhanced interferon signaling was abrogated in THP-1 cells and patient fibroblasts depleted of mtDNA. Thus, mutations in the mitochondrial membrane protein ATAD3A define a novel type I interferonopathy.

The type I interferonopathies: 10 years on

“…The clustering of mutant genotypes implicated in nucleic acid metabolism and sensing and in negative regulation of type I interferon signalling — in some cases, for example, DNASE2 deficiency and ATAD3A-related disease, identified through agnostic screening for type I interferon upregulation — provides compelling evidence in support of the type I interferonopathy hypothesis. Notable recent insights derived from the definition and study of this rare disease grouping include the identification of physiologically important Golgi apparatus to ER transport of STING involving COPA 72 – 74 , the implication of innate immune system activation as a contributor to the phenotype of certain monogenic mitochondrial diseases 38 , 61 , the characterization of a separation-of-function mutation in STAT2 specifically affecting its role in limiting IFNAR2 signalling 78 , 79 and the observation that disturbed histone stoichiometry due to mutations in LSM11 and RNU7-1 enhances the immunostimulatory potential of nuclear DNA 53 . All of these findings inform possible novel drug targets relevant to the future treatment of diseases associated with enhanced type I interferon signalling.…”

“…These tests have proven highly useful in directing genetic analysis, the interpretation of sequence variants 31 and the identification of novel type I interferonopathy genotypes 32 , including where a link to interferon signalling had not been previously recognized. Important examples of the latter situation include the demonstration of type I interferon induction due to dysfunction of PSMB8 (refs 33 , 34 ), coatomer subunit-α (COPA) 35 , 36 and ATAD3A 37 , 38 2, 3 and 5 years, respectively, after the initial description of disease-associated mutations in the genes encoding these proteins. Tests of type I interferon signalling status are still not included in mainstream clinical medicine assessment, although the use of digital enzyme-linked immunosorbent assay, Nanostring 39 and other 40 technologies may change this situation, particularly as the (early) recognition of phenotypes associated with enhanced type I interferon signalling becomes more important with the introduction of anti-interferon treatments.…”

“…Loss of function of NGLY1, a conserved deglycosylation enzyme, has also been reported to result in chronic activation of cytosolic nucleic acid sensing, this time as a result of mitochondrial fragmentation and the release of immunostimulatory nucleic acid into the cytoplasm 62 , with increased ISG expression observed in patient-derived lymphoblastoid cell lines. More recently, pathogenic mutations in ATAD3A , which encodes the ubiquitously expressed ATPase ATAD3A, have been shown to cause mitochondrial DNA-dependent upregulation of type I interferon signalling in the context of autoimmunity (specifically, features of systemic sclerosis) and neurological disease 38 . Ex vivo, there was a marked and persistent elevation of the expression of ISGs and IFNα in the blood, CSF and primary fibroblasts of patients with mutations in ATAD3A .…”

Cooperative sensing of mitochondrial DNA by ZBP1 and cGAS promotes cardiotoxicity

“…Cardiac complications are frequently associated with both inherited mitochondrial disorders and autoimmune diseases such type I interferonopathies and Lupus (Crow et al, 2015;Frazier et al, 2021;Kim et al, 2017;Meyers et al, 2013). Recently, mutations in the mtDNA maintenance factor ATAD3A have been demonstrated to cause a novel type I interferonopathy characterized by mtDNA release and enhanced cGAS-STING signaling (Lepelley et al, 2021b). Cardiac failure has been observed in some patients with ATAD3-mediated mitochondrial disease, as well as in other interferonopathies (Crow and Stetson, 2021;Frazier et al, 2021;Lei et al, 2021;Lepelley et al, 2021bLepelley et al, , 2021a.…”

Molecular Mechanisms of mtDNA-Mediated Inflammation

“…By analyzing two patients with a different phenotype but a common enhanced expression of ISGs, Lepelley and coworkers have recently identified the mitochondrial membrane protein ATPase family AAA domain-containing protein 3A (ATAD3A) as a player in the regulation of mtDNA release from mitochondria and cGAS activation [ 63 ]. Indeed, dominant negative mutations of ATAD3A or knockdown of the gene resulted in increased activation of cGAS pathway.…”