Charna Albert
August 2024—The recently discovered VEXAS syndrome is caused by somatic mutations in the UBA1 gene arising in bone marrow stem cells.
VEXAS (vacuoles, E1-ubiquitin-activating enzyme, X-linked, autoinflammatory, somatic) syndrome was discovered when National Institutes of Health researchers identified deleterious mutations in ubiquitin-related genes (Beck DB, et al. N Engl J Med. 2020;383[27]:2628–2638). In a retrospective observational study published last year, Beck, et al., evaluated UBA1 variants in exome data from the Geisinger MyCode Community Health Initiative, a health-system-based cohort of patients who provide samples for broad research use (Beck DB, et al. JAMA. 2023;329[4]:318–324). Clinical phenotypes were determined from Geisinger EHR data spanning four to 25 years. UBA1 variants were found in one in 13,591 unrelated individuals, one in 4,269 men older than 50, and one in 26,238 women older than 50.
“This is not a rare mutation in the community. VEXAS is increasingly recognized in older white men with a wide variety of symptoms,” said Neal S. Young, MD, chief of the Hematology Branch at the NIH National Heart, Lung, and Blood Institute, speaking at the AMP annual meeting last year. The disease is “predominantly rheumatologic and hematologic in its manifestations, although we think every organ system can be affected and the full spectrum of clinical manifestations is not yet defined.”
Of 163,096 Geisinger participants, 11 harbored likely somatic variants at known pathogenic UBA1 positions, with all 11 having clinical manifestations consistent with VEXAS (nine men, two women). Five of 11 did not meet criteria for rheumatologic and/or hematologic diagnoses previously associated with VEXAS; however, all patients had anemia (hemoglobin: mean, 7.8 g/dL; median, 7.5 g/dL), which was mostly macrocytic (10/11), with concomitant thrombocytopenia (10/11). “Macrocytic anemia,” Dr. Young said, “is the major feature of the genetic defect when it’s detected by screening large databases.”
The authors write: “At an occurrence of one in 13,591 across all age groups, UBA1 pathogenic variants may be more common than the reported prevalence of clinical diagnoses comprising VEXAS syndrome, including most vasculitides (granulomatosis with polyangiitis: approximately 1/18,000; polyarteritis nodosa: approximately 1/33,000), with a prevalence similar to Behçet disease (approximately 1/10,000) and MDS (approximately 1/14,000). Thus, given the current understanding of VEXAS syndrome, many of these patients may not have been identified using phenotype-based ascertainment.”
In a study that examined the translation of cytoplasmic UBA1 and how it contributes to VEXAS syndrome pathogenesis, Ferrada, et al., analyzed 83 patients with somatic pathogenic variants in UBA1 at p.Met41 (p.Met41Leu/Thr/Val), the start codon for translation of the cytoplasmic isoform of UBA1 (UBA1b).
Patients with the p.Met41Val genotype, which supports less UBA1b translation than either p.Met41Leu or p.Met41Thr, were most likely to have an undifferentiated inflammatory syndrome. The authors concluded that regulation of residual UBA1b translation is fundamental to the pathogenesis of VEXAS syndrome and contributes to disease prognosis (Ferrada MA, et al. Blood. 2022;140[13]:1496–1506).
“VEXAS syndrome is due to discrete mutations in the methionine start codon that eliminate or reduce the transcription and translation of the UBA1 gene products,” Dr. Young said. UBA1 catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation, and in subsequent steps as Ub carrier. “So it’s quite critical,” Dr. Young said. “And the screening that led to the discovery of VEXAS was for this particular pathway, based on genetic syndromes.”
Protein ubiquitylation marks proteins for proteasome degradation. VEXAS arises with acquired hematopoietic stem cell mutations in UBA1 Enzyme1 in protein ubiquitylation. “Its manifestations in the bone marrow are striking,” Dr. Young said. “They can be recognized easily as prominent vacuoles in both myeloid and erythroid cells, which we call myelodysplasia because it does look dysplastic. But it probably doesn’t represent a typical form of MDS” or other diseases that occur in cartilage and joint tissue, such as polychondritis and arthritis.
VEXAS is appearing now as a diagnosis in many rheumatologic diseases, including relapsing polychondritis, Sweet syndrome, vasculitis, polyarteritis nodosa, and others (Koster MJ, et al. Semin Hematol. 2021;58[4]:218–225). “VEXAS has major hematologic features,” Dr. Young said. Multifactorial anemia is one of the first manifestations. MDS is another, though “it’s probably a distinct subset” of MDS, he said. “It also leads to monoclonal gammopathy of undetermined significance or smoldering myeloma occasionally, frank myeloid malignancy, and multiple myeloma.” And it has a high prevalence of venous thrombosis, which also can be the first manifestation of the disease. “So this is a hematologic disease in many of its forms,” Dr. Young said.
In a study of VEXAS pathophysiology, Dr. Young and others performed transcriptome sequencing of single bone marrow mononuclear cells and hematopoietic stem and progenitor cells from nine VEXAS patients (Wu Z, et al. Cell Rep Med. 2023;4[8]:101160). “These patients have a marked myeloid-based differentiation—high neutrophil counts, low lymphocyte counts,” Dr. Young said. He and his coauthors found that activation of multiple inflammatory pathways (interferons and tumor necrosis factor alpha) occurs ontogenically early in primitive hematopoietic cells and particularly in the myeloid lineage in VEXAS, and inflammation is prominent in UBA1-mutated cells.
“If we look at the hematopoietic stem cell,” Dr. Young said, “there’s upregulation of tumor necrosis factor alpha, interferon alpha, interferon gamma, there’s T-cell expansion as well as B-cell expansion, and enhanced cell-cell interactions” between activated myeloid cells and hematopoietic stem and progenitor cells. And there’s an unfolded protein response, he said, “because proteins are not being ubiquitylated.” He and coauthors say their results suggest that a dysregulated protein ubiquitination/proteasome pathway due to UBA1 mutations and a lack of compensatory pathways for protein degradation leads to an increased unfolded protein stress, which might contribute to enhanced inflammation in VEXAS hematopoietic stem and progenitor cells.
They determined that genes involved in the inflammatory pathways were upregulated in both UBA1-mutated bone marrow mononuclear cells and UBA1-mutated hematopoietic stem and progenitor cells. To obtain direct evidence that loss of UBA1-wildtype resulted in major alterations in transcription, the authors “knocked down” in vitro UBA1 expression in two myeloid (U937 and THP1) and two lymphoid (Raji and Jurkat) cell lines. Expression of inflammation genes, including genes involved in the TNF-alpha and IFN-gamma pathways, increased in all four perturbed myeloid and lymphoid cell lines. “We think this is not secondary,” Dr. Young said, “because when we knock down this gene . . . we see the same shift to hyperinflammation.”
“It sounds as if we’ve explained everything,” he continued, “but we don’t know how the protein misfolding response and the mutation that causes it, the various immunological pathways upregulated, lead to what seems to be a clonal proliferative event in these patients.”
VEXAS is an acquired disease, and “there are somatic mutations, in addition to UBA1, that accompany it,” Dr. Young said.
“And they’re quite stereotypical—not random in terms of their clonal expansion.” What dominates, he said, are DNMT3A clones—almost always large, highly prevalent—and small TET2 clones.
Gutierrez-Rodrigues, et al., studied the spectrum of clonal hematopoiesis in VEXAS syndrome, retrospectively screening 80 patients with VEXAS for clonal hematopoiesis in peripheral blood and correlating the findings with clinical outcomes in 77 patients (Gutierrez-Rodrigues F, et al. Blood. 2023;142[3]:244–259). Typical clonal hematopoiesis mutations co-occurred with mutated UBA1 in 60 percent of patients, mostly in DNMT3A and TET2, and were not associated with inflammatory or hematologic manifestations.
“There’s little else in the way of clonal expansion,” Dr. Young said. “And interestingly, these do not lead to myeloproliferative neoplasm. They can lead to a diagnosis of MDS, based on the presence of the clone and funny-looking cells in the bone marrow, but it’s not classic MDS in its progression.” The effect on survival is low, though measurable, he said, but mortality is not due to the development of MDS or hematologic complications; rather, it is due to the high doses of corticosteroids required to control the disabling inflammatory symptoms. Cytopenia and MDS do not impact survival in VEXAS.
The single-cell DNA and single-cell RNA sequencing make it possible to track the occurrence of the various mutations, and “the bottom line for these experiments is that UBA1 mutations always come first,” he said. “DNMT3A and TET2 may arise out of that mutated clone or may occur in parallel, but this is not a progression from the common CHIP clones to UBA1.” DNMT3A and TET2, then, are secondary and nonprognostic. “The same pattern of clonal hematopoiesis, DNMT3A, and TET2 clones occurs in a wide range of vasculitides, in childhood, middle age, and adulthood. Not associated with MDS, not associated with leukemia. So from our perspective, these mutated clones are expanding in inflamed environments, not causative of inflamed environments.”
When should physicians diagnose MDS in the setting of VEXAS? “Calling it VEXAS MDS is the safest at this point,” Dr. Young said, noting it’s an important but unsettled question. “But VEXAS appears as a distinct disease entity.”
The meaning of DNMT3A and CHIP-type mutations is context dependent, he said. “When you see these clones, they need to be interpreted in the context of the disease, whether immune aplastic anemia, VEXAS, or telomere disease—or what we think is that disease pathophysiology.”
VEXAS likely explains much of the literature on the coupling of rheumatoid arthritis and MDS, he said. “There are older case series of relapsing polychondritis and abnormal bone marrow findings with MDS. That’s all due to VEXAS. A transplanter with a good memory may recall a patient with red ears,” he said, noting one of the clinical manifestations, “or Sweet syndrome, or vasculitis, and it all got better after replacing the marrow. The VEXAS diagnosis can be made years later by identifying a UBA1 mutation in banked tissue.”
Mayo Clinic and the NIH have a prospective trial to transplant patients who have VEXAS, and he has no doubt, he said, that it will be curative. The patients are older and have comorbidities, in large part owing to the yearslong steroid treatment. “Getting patients completely off steroids is hard,” Dr. Young said. “Transplant works. We just have to see how well it works.”
Charna Albert is CAP TODAY associate contributing editor.