The zinc finger (ZnF) protein A20 is a ubiquitin-editing enzyme encoded by the TNFAIP3 (tumor necrosis factor a-induced protein 3) gene that contains an amino-terminal ovarian tumor (OTU) domain followed by seven ZnF domains. Due to its E3 ligase activity (ZnF4), its deubiquitinase function (OTU) and its ubiquitin-binding domain (ZnF7), A20 regulates the fate of several substrates such as RIPK1 (receptor-interacting serine/threonine-protein kinase 1), NEMO (NF-kappa-B essential modulator), and TRAF6 (TNF receptor-associated factor 6), all converging to the canonical NF-κB pathway (Boone et al., 2004; De et al., 2014; Tokunaga et al., 2012; Wertz et al., 2004). Owing to these various functions, A20 plays a pivotal role in the regulation of inflammation and immunity by inhibiting the canonical NF-κB signaling pathway and by preventing cell death (Lork et al., 2017; Martens and van Loo, 2020). Abnormal expression or function of A20 therefore contributes to the onset of several autoimmune or inflammatory disorders such as Crohn’s disease, systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes mellitus, psoriasis, and atherosclerosis as shown by genome-wide association studies (reviewed in Malynn and Ma, 2019). Furthermore, germline variations in TNFAIP3 lead to an autoinflammatory disease of autosomal dominant inheritance referred to as A20 haploinsufficiency (HA20; MIM#616744), where insufficient suppression of NF-κB activity is observed (Zhou et al., 2016). HA20 is a Behçet-like autoinflammatory syndrome of early onset associated with variable clinical signs. The hallmark features of HA20 are recurrent fever, painful oral, genital and/or gastrointestinal ulcers with diarrhea, arthralgia, or polyarthritis (Aeschlimann and Laxer, 2019). Since the first description of HA20 (Zhou et al., 2016), more than 25 TNFAIP3 truncating variations have been reported (reviewed in Yu et al., 2020) whereas the pathogenic significance has been confirmed for only a part of the 12 reported missense variations (Aslani et al., 2022; Chen et al., 2020a; Dong et al., 2019; Jiang et al., 2022; Kadowaki et al., 2021; Mulhern et al., 2019; Niwano et al., 2022; Shigemura et al., 2016; Tian et al., 2022). Indeed, a body of genetic and experimental evidence is necessary to determine non-ambiguously the deleterious character of missense variations.

In this study, we report a non-previously described TNFAIP3 missense variation, c.707T>C, p.(Leu236Pro), identified in three patients from the same family. We provide a phenotypic description of all affected patients, as well as cytokine and A20 level quantification in patient-derived samples. Furthermore, we assessed the pathogenicity of this variant, as well as that of previously reported TNFAIP3 missense variations, through in vitro molecular and cellular assays. Notably, by studying the location and the intra-molecular amino acid interactions of Leu236 with the other amino acids involved in pathogenic TNFAIP3 missense variations, we identified a critical region within the OTU domain of A20 where the pathogenic TNFAIP3 missense variations are in close proximity and where the affected residues share common amino acid interactions on the 3D protein structure.

The diagnosis of HA20 is highly challenging due to its heterogeneous clinical presentation and the lack of pathognomonic symptoms. The non-ambiguous pathogenic significance of TNFAIP3 variations is necessary for the confirmation of HA20 diagnosis and adaptation of the clinical care. While in the case of TNFAIP3 nonsense or frameshift variations the deleterious impact is most often established, the pathogenic effect of missense variations is difficult to determine.

Herein, we studied a family in which three patients had a disease phenotype compatible with the diagnosis of HA20 and in whom we identified a novel TNFAIP3 missense variation, the c.707T>C, p.(Leu236Pro) variation. In the current work, we provide solid proof for the pathogenicity of this variation through an in-depth study relying on the analysis of the clinical and biological features of the patients, the intrafamilial segregation of the variation with the disease, the absence of occurrence of the identified variation in the general population, the conservation of the affected residue, and most importantly, on the functional evaluation of the variant through a combination of different assays: expression and stability of the variant protein, study of its ability to inhibit the NF-κB pathway and of its deubiquitination activity. By assessing, through dedicated in silico and in vitro assays, the pathogenicity of other missense variations located in the OTU domain of A20 and that fulfill the same criteria, we identified a critical region in the OTU domain in which residues involved in pathogenic missense variations establish common interactions.

The clinical features and the cytokine profile of the patients presented in our study are in line with those exhibited by previously reported HA20 patients. Indeed, elevated levels of pro-inflammatory cytokines in the plasma and supernatants of LPS-stimulated PBMCs of the patients presented in our study resemble that of previously reported patients harboring TNFAIP3 pathogenic truncating variations (Rajamäki et al., 2018; Zhou et al., 2016). Accordingly, the patients reported herein exhibit typical HA20 phenotypic features: early-onset, recurrent fever, articular symptoms, recurrent oral, genital and/or gastrointestinal manifestations. Nevertheless, HA20 clinical manifestations can vary considerably among patients even among those who carry the same variation (Aeschlimann and Laxer, 2019). Depending on disease severity, colchicine treatment, corticosteroids, or cytokine antagonists can be required for HA20 treatment. Colchicine treatment was satisfactory for the control of the symptoms of individuals II.1 and II.2, suggesting a less severe disease presentation, whereas corticosteroids and azathioprine were required for individual I.1. The difference in disease severity observed in these patients cannot be attributed to the missense nature of the variation. In fact, other HA20 patients carrying pathogenic missense variations were shown to be resistant to colchicine and required steroid therapy (Dong et al., 2019; Kadowaki et al., 2021; Shigemura et al., 2016). Disease management of the patients reported in our study did not require cytokine antagonists. Nevertheless, in light of the elevated IL6 levels in PBMCs supernatant prior to LPS stimulation, the use of IL6 antagonist for the control of the patients’ symptoms could be of therapeutic interest in case the patients develop resistance to their current treatments, as previously reported for the treatment of two HA20 patients (Lawless et al., 2018; Zhou et al., 2016).

Further findings supporting the pathogenic significance of the p.(Leu236Pro) variation include enhanced UPS-dependent degradation of the A20_Leu236Pro protein, which is most likely responsible for the HA20 observed in the patients’ PBMCs. We show that this abnormally enhanced degradation is also observed for another missense variant (p.(Leu275Pro), Aslani et al., 2022) for which functional assays have not been reported yet. Interestingly, the in silico tools predicted high destabilizing effects for both A20_Leu236Pro and A20_Leu275Pro. Altogether, the flow cytometry-based functional assay, in combination with the in silico approach, identifies enhanced recognition by the protein quality control machinery and thus increased degradation as one of the mechanisms explaining the pathogenicity of TNFAIP3 missense variants. Our study thus provides a valuable approach that can be used for assessing newly identified missense variations.

Moreover, our experiments indicate that, in addition to reduced levels of the variant protein, the function of A20_Leu236Pro is altered. Indeed, in an attempt to bypass the decreased protein expression in vitro, we doubled the amounts of mutant A20 plasmid used for transfection in the NF-κB luciferase assay. Although this allowed for an increased inhibition of the canonical NF-κB pathway, the inhibitory function of A20_Leu236Pro was not restored up to the levels of the WT protein. Interestingly, such functional deregulation has also been observed for the pathogenic p.(Cys243Tyr) and p.(Glu192Lys) variants (Kadowaki et al., 2021; Shigemura et al., 2016): a 10-fold protein expression increase was required to compensate the loss-of-function of the p.(Cys243Tyr) variant (Shigemura et al., 2016). As for the p.(Glu192Lys) variant, it does not exhibit reduced expression compared to the WT protein but it loses the ability to sufficiently inhibit the NF-κB pathway (Kadowaki et al., 2021), in line with its location at the putative ubiquitin-binding site of A20 (Lin et al., 2008).

The consequences on the native structure of A20 of the three pathogenic missense variations of the OTU domain (p.(Leu236Pro), p.(Glu192Lys), and p.(Cys243Tyr)) converge. Although Glu192 and Cys243 are distant, Leu236 bridges the interactions between the two regions they belong to on the tertiary structure of A20. Moreover, p.(Leu236Pro) and p.(Cys243Tyr) have common consequences on interactions established by surrounding amino acids such as Asn201, Pro235, Trp238, and Tyr306, suggesting a putative importance of these residues for proper protein expression and/or function.

The OTU domain of A20 harbors the active site essential for the DUB activity of A20, which encompasses the catalytic Cys103, His256, and a third residue for which Asp70 or Thr97 are possible candidates (Komander and Barford, 2008; Lin et al., 2008). Study of the crystal structure of the A20 OTU domain shows that the ubiquitin-binding site of A20 may require the surface formed by α-helices (α4, α7, and α8) and β sheets (β2, β3, β4, and β5) and the loops between them; Glu192 is among the surface residues identified in the ubiquitin-binding region, whereas Leu236 and Cys243 are in the loop between β3 and β4 (Lin et al., 2008). Ubiquitin binding requires interactions between hydrophobic residues of ubiquitin and hydrophobic A20 amino acid, making Leu236 a very suitable candidate for surface amino acids in the ubiquitin-binding domain. Overall, the HA20-causing missense variations in the OTU domain, which alter the proper function and/or expression of the protein, are located in a critical region outside the DUB active site but close to the ubiquitin-binding domain.

Figure 3 - Source Data 1 to 5 contain the original western blots used for figure 3Figure 4 - Source Data 1 to 3 contain the original flow cytometry original data used for figure 4.

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Author details

1. Elma El Khouri

   Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France

   Contribution

   Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing – original draft

   Competing interests

   No competing interests declared

2. Farah Diab

   Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France

   Contribution

   Conceptualization, Formal analysis, Investigation, Writing – original draft

   Competing interests

   No competing interests declared

3. Camille Louvrier

   1. Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France
   2. Département de Génétique Médicale, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France

   Contribution

   Conceptualization, Formal analysis, Methodology, Writing – review and editing

   Competing interests

   No competing interests declared

4. Eman Assrawi

   Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France

   Contribution

   Conceptualization, Formal analysis, Methodology, Writing – review and editing

   Competing interests

   No competing interests declared

5. Aphrodite Daskalopoulou

   Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France

   Contribution

   Investigation

   Competing interests

   No competing interests declared

6. Alexandre Nguyen

   Département de Médecine Interne et Immunologie Clinique, Normandie Univ, UNICAEN, UR4650 PSIR, CHU de Caen Normandie, Caen, France

   Contribution

   Resources

   Competing interests

   No competing interests declared

7. William Piterboth

   Département de Génétique Médicale, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France

   Contribution

   Formal analysis, Investigation

   Competing interests

   No competing interests declared

8. Samuel Deshayes

   Département de Médecine Interne et Immunologie Clinique, Normandie Univ, UNICAEN, UR4650 PSIR, CHU de Caen Normandie, Caen, France

   Contribution

   Resources, Writing – review and editing

   Competing interests

   No competing interests declared

9. Alexandra Desdoits

   Service de chirurgie pédiatrique, CHU de Caen Normandie, Caen, France

   Contribution

   Resources

   Competing interests

   No competing interests declared

10. Bruno Copin

    Département de Génétique Médicale, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France

    Contribution

    Software, Methodology

    Competing interests

    No competing interests declared

11. Florence Dastot Le Moal

    Département de Génétique Médicale, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France

    Contribution

    Investigation, Methodology

    Competing interests

    No competing interests declared

12. Sonia Athina Karabina

    Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France

    Contribution

    Conceptualization, Funding acquisition, Methodology, Writing – review and editing

    Competing interests

    No competing interests declared

13. Serge Amselem

    1. Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France
    2. Département de Génétique Médicale, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France

    Contribution

    Conceptualization, Resources, Data curation, Supervision, Funding acquisition, Methodology, Project administration, Writing – review and editing

    Competing interests

    No competing interests declared

14. Achille Aouba

    Département de Médecine Interne et Immunologie Clinique, Normandie Univ, UNICAEN, UR4650 PSIR, CHU de Caen Normandie, Caen, France

    Contribution

    Conceptualization, Resources, Writing – review and editing

    Contributed equally with

    Irina Giurgea

    Competing interests

    No competing interests declared

15. Irina Giurgea

    1. Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), "Maladies génétiques d’expression pédiatrique", Paris, France
    2. Département de Génétique Médicale, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France

    Contribution

    Conceptualization, Resources, Data curation, Supervision, Funding acquisition, Validation, Methodology, Project administration, Writing – review and editing

    Contributed equally with

    Achille Aouba

    For correspondence

    irina.giurgea@inserm.fr

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-5035-2958

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