Dataset Information

Heterozygous NFKB1 variant causes inflammatory dysregulation shaped by broader genetic context in common variable immunodeficiency

ABSTRACT: Common variable immunodeficiency (CVID) is the most prevalent symptomatic primary antibody deficiency. For unclear reasons, inflammatory complications, like gastrointestinal (GI) disease, occur in ~50% of CVID cases, worsening morbidity and mortality. NFKB1 variants are among the most frequent genetic variants in CVID. While impact of NFKB1 variants is not well understood, we previously found frameshift heterozygous NFKB1 variants to increase cytokines, monocytes, and inflammatory complications in CVID. In this report, we used induced pluripotent stem cell (iPSC)-derived monocytes (iMONOs) with CRISPR/Cas9-mediated gene editing to study a heterozygous NFKB1 frameshift found in a CVID patient with severe GI disease. The heterozygous NFKB1 variant similarly reduced NFKB1 protein in CVID patient and healthy donor derived iMONOs, but elevated lipopolysaccharide-induced IL-1β release and expression of inflammatory genes, including IL1B, IL6, TNF, and neutrophil chemoattractants only in CVID patient iMONOs. CVID patient iMONOs also had elevations of IL-12, CCL4, and CCL12 unaffected by presence or absence of the NFKB1 variant. TNF antagonism improved the patient’s GI disease, diminishing neutrophilic gastritis, circulating neutrophils, and the neutrophil chemoattractant CXCL1 in the blood. While the biology remains complex, our approach found heterozygous NFKB1 variant-induced inflammatory changes intensified in CVID iMONOs, corresponding with clinical response to TNF antagonism.

ORGANISM(S): Homo sapiens

PROVIDER: GSE311471 | GEO | 2026/02/02

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:ETS Variant 6 (ETV6) encodes an essential transcriptional repressor abundantly expressed in hematopoietic stem and progenitor cells (HSPCs), where it is required for adult hematopoiesis. Heterozygous pathogenic germline ETV6 variants are associated with Thrombocytopenia 5 (T5), a poorly-understood genetic condition predisposing to thrombocytopenia and hematologic malignancies. To elucidate how germline ETV6 variants impact the HSPC compartment and contribute to disease, we generated a knock-in mouse harboring an Etv6R355X loss-of-function variant, which represents the mouse equivalent to the T5-associated variant ETV6R359X. All HSPC subpopulations are present in the bone marrow (BM) of Etv6R355X/+ mice under homeostatic conditions; however, these animals exhibit subtle shifts in the proportions and/or numbers of specific progenitor subtypes. To examine whether the Etv6R355X/+ mutation impacts HSPC function, we carried out serial competitive transplantation and observed that Etv6R355X/+ lineagesca1+cKit+ (LSK) cells exhibit significantly impaired reconstitution, with near complete failure to repopulate irradiated-recipients by the tertiary transplant. Mechanistic studies incorporating CUT&RUN, ATAC-Seq and Hi-C identify ETV6 binding at inflammatory gene loci, including those within the TNF pathway in Etv6+/+ HSPCs, the mouse BM-progenitor derived HPC5 cell line, and G-CSF-mobilized human CD34+ cells. Further, single-cell RNA sequencing of mouse LSK cells isolated six-weeks post-competitive transplantation reveals upregulation of inflammatory gene pathways. Corroborating these findings, we observe significantly increased production of TNF by Etv6R355X/+ versus Etv6+/+ HSPCs post-transplantation. From these studies, we conclude that ETV6 represses inflammatory response genes within HSPCs under conditions of hematopoietic stress, and that this mechanism may be critical to sustain HSPC function. Functionally, Etv6R355X/+ bone marrow (BM) cells exhibited reduced colony formation in later rounds of serial replating, while Etv6R355X/+ LSKs exhibited significantly impaired engraftment in serial competitive transplantation. RNA-seq of Etv6R355X/+ LSKs and/or sort-purified HSPCs revealed upregulation of genes associated with an active stem cell phenotype and pro-inflammatory signaling, including increased expression of the cytokine Tnf. CUT&RUN of Etv6+/+ LSKs and HPC5 hematopoietic progenitors showed that ETV6 binds to the Tnf locus at regions of open chromatin, while CUT&RUN of human CD34+ cells identified ETV6 targets enriched in TNF signaling. In line with these findings, Etv6R355X/+ HSPCs exhibited increased cell-cycling and TNF expression post-transplantation. Finally, genetic deletion of Tnf restored the serial replating capacity of Etv6R355X/+ BM cells.

Dataset Information

Heterozygous NFKB1 variant causes inflammatory dysregulation shaped by broader genetic context in common variable immunodeficiency

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets