Dysregulation of the Ubiquitination Pathway: Insights on Autoinflammatory Conditions and Inborn Errors of Immunity in Bone Marrow Failure Disorders

Genetic variants/dysregulation of the ubiquitination pathway have been described in various autoinflammatory disorders and in inborn errors of immunity leading to broad clinical manifestations including multisystem autoimmunity and hematologic malignancies. VEXAS syndrome is an example par excellence of such a clinical diagnosis with pathognomonic mutations in UBA1, a member of the ubiquitination gene family.

While UBA1 mutation is recurrent and typical, there are patients with similar clinical constellations of autoinflammatory symptoms but in whom UBA1 mutation is not found. It is thus plausible that lesions in other genes associated with the ubiquitination pathway might be at play and produce VEXAS syndrome-like diseases. Thus, we here define the landscape of genetic defects in the ubiquitination pathway and provide clues of hemato-autoimmune genotype-phenotype associations in BMF syndromes.

Based on the symptomology and clinical scenarios reminiscent of VEXAS, we screened 80 patients for suspected presence of UBA1 mutation, of whom 13 tested positive (11 additional mutants compared to our published study¹). The remaining UBA1 negative patients were subjected to screening for the presence of other mutations in UBA1-related pathways either using whole exome or deep targeted sequencing with the hypothesis that the presence of mutations in UBA1-related genes could result in phenocopy of the classical VEXAS syndrome (VEXAS-like).

In UBA1 negative patients, we identified 16 patients (24%) with somatic mutations in other ubiquitination associated genes. 12 patients carried somatic TNFAIP3 mutations with two recurrent variants found in two patients each (p.G99R; p.Y246*). Both variants impacted the OTU-like cysteine protease domain which mediates the deubiquitinase activity. Eight additional patients carried unique TNFAIP3 variants with one impacting the OTU-like cystine protease domain, one involving a splice site, and three affecting different A20-like zinc finger domains. Two patients carried the same splice site mutation (c.757-2A>C) in RBCK1 (RanBP-type and C3HC4-type zinc finger-containing protein 1) gene. Two patients were found to have RNF31 (RING finger protein 31) mutations (p.C309S; p.R377Q).

We then combined cases with VEXAS-like syndrome associated with somatic mutations described above to search for clinical commonalities and/or differences possibly suggesting a pathogenetic ductus. UBA1 positive patients had VEXAS concomitant with MDS in 30%, CMML and T-LGL in 8% (each) of the cases while patients with other ubiquitin-related gene mutations were mostly diagnosed with immune BMF syndromes (AA, AA/PNH, PRCA [50%], T-LGL [25%]) while only 15% of the cases had a myeloid neoplasm. No vacuoles were seen in the bone marrow evaluation in UBA1 negative patients.

Of note is that 6/20 (30%) patients with somatic variants had serologic or clinical markers of autoimmune chronic disorders; 7 (35%) with Ig workup had hypergammaglobulinemia (4 mono/ 3 polyclonal) and 3 (15%) had concurrent B-cell/plasma cell neoplasia. In the case of mutations in TNFAIP3 gene, an AA/PNH with p.Y246Ter had autoimmune seropositivity, erythema nodosum and angioimmunoblastic T cell lymphoma, an AA with p.C767G had Sjogren and SLE and a T-LGL with p.T322fs was affected by rheumatoid arthritis. In the case of mutations in RBCK1 gene, a PNH patient with the splice site c.757-2A>C had rheumatoid arthritis while an AA/PNH with p.R377Q had psoriatic arthritis.

Given the implication of germline mutations in ubiquitin associated genes in defining immune imbalance leading to disease, we extended our search to germline variants. Two suspicious germline TNFAIP3 variants were noted (p.T97fs; p.D517A) with T97fs being present in a 55-y/o male patient with T-LGL, one variant in PSMB8 (p.W16*) in a 46-y/o female patient with PNH and one in the X-linked XIAP inhibitor of apoptosis (p.L284P).

Our study suggests that besides UBA1 mutation being hallmark defect in VEXAS syndrome, other genetic defects encompassing the ubiquitination associated genes are rare and might explain the pleiotropic chronic autoinflammatory manifestations of BMF disorders either in germline or somatic context. These findings provide new insights on the immunogenomic crossroads between autoimmunity, immunodeficiency, and malignancy and continue expanding the spectrum of genetic-phenotypic associations.