Inherited deficiency of stress granule ZNFX1 in patients with monocytosis and mycobacterial disease

Abstract

Human inborn errors of IFN-γ underlie mycobacterial disease, due to insufficient IFN-γ production by lymphoid cells, impaired myeloid cell responses to this cytokine, or both. We report four patients from two unrelated kindreds with intermittent monocytosis and mycobacterial disease, including bacillus Calmette–Guérin-osis and disseminated tuberculosis, and without any known inborn error of IFN-γ. The patients are homozygous for ZNFX1 variants (p.S959* and p.E1606Rfs*10) predicted to be loss of function (pLOF). There are no subjects homozygous for pLOF variants in public databases. ZNFX1 is a conserved and broadly expressed helicase, but its biology remains largely unknown. It is thought to act as a viral double-stranded RNA sensor in mice, but these patients do not suffer from severe viral illnesses. We analyze its subcellular localization upon overexpression in A549 and HeLa cell lines and upon stimulation of THP1 and fibroblastic cell lines. We find that this cytoplasmic protein can be recruited to or even induce stress granules. The endogenous ZNFX1 protein in cell lines of the patient homozygous for the p.E1606Rfs*10 variant is truncated, whereas ZNFX1 expression is abolished in cell lines from the patients with the p.S959* variant. Lymphocyte subsets are present at normal frequencies in these patients and produce IFN-γ normally. The hematopoietic and nonhematopoietic cells of the patients tested respond normally to IFN-γ. Our results indicate that human ZNFX1 is associated with stress granules and essential for both monocyte homeostasis and protective immunity to mycobacteria.

Biallelic ZNFX1 variants are associated with a spectrum of immuno‐hematological abnormalities

“…The ZNFX1 protein is a 1918 amino-acid-long member of RNA helicase superfamily-1 8 that functions in antiviral immunity by sensing the nucleic acids of pathogens and inhibiting their replication. 9 ZNFX1 is predominantly localized to RNA-rich ribonucleoprotein granules (stress granules), 3 and it contains three distinct domains: the armadillo, helicase, and zinc-finger domain (Figure 1), the first two of which are responsible for the recognition of viral RNA. 8 Importantly, ZNFX1 is an ISG, and its expression is upregulated by the JAK-STAT signaling pathway.…”

“…Recently, ZNFX1 (zinc finger NFX1-type containing 1) was reported as a novel gene for recessively inherited immunodeficiency, characterized by severe viral infections or MSMD, and accompanied by monocytosis, neutrophilia, thrombocytopenia, hepatomegaly, and splenomegaly in 19 patients from 10 unrelated families. 3,4 To further investigate the role of variants in ZNFX1 in primary immunodeficiencies, we queried our in-house bio-databank 5 for rare homozygous/compound heterozygous changes in ZNFX1 and the relevant Human Phenotype Ontology (HPO) terms. We report nine additional patients from seven unrelated families with biallelic variants in ZNFX1 that share a broader immunological and hematological phenotype.…”

Two parallel sRNA amplification cycles contribute to RNAi inheritance in C. elegans

“…By maintaining a transcript pool in nuage, ZNFX-1 prevents self-extinction of the RNAi response that might arise as a consequence of rapid transcript turn over in the cytoplasm. ZNFX-1 homologs in mice and humans function in the primary immune response against RNA viruses and bacteria (Wang et al, 2019; Le Voyer et al, 2021; Vavassori et al, 2021). We do not yet know how these functions relate to those described here for C. elegans ZNFX-1 and described previously for S. pombe Hrr1 (Motamedi et al, 2004).…”

E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

“…The ZF2 domain is predicted to be a functional zinc finger, highly similar to an uncharacterized zinc finger in the C-terminal region of the human helicase ZNFX1 (Figure 3c). ZNFX1 was shown to associate with stress granules (28), and is involved in the immune response against both viral (29) and bacterial (28) infections. Ultraviolet-visible spectroscopy (UV-VIS) revealed that RNF213 ZF2 is indeed a canonical zinc finger (30,31) that can bind divalent transition metals, with a preference for Zn 2+ (Figure 3-figure supplement 1b).…”