Autosomal Recessive COPZ1 Mutations Cause Isolated Severe Neutropenia or Complex Syndrome with Severe Neutropenia

We have identified new autosomal recessive mutations in the COPZ1 gene in three severe congenital neutropenia (CN) patients from two unrelated families. In one family, two siblings with a stop-codon COPZ1 mutation (NP_057141:p.Gln141Ter) suffered from CN, lymphopenia, anemia, thrombocytopenia, and syndromic organ involvement, including hepatosplenomegaly, atypical autism with mental retardation, varying degrees of bone defects, and dermatitis. An unrelated patient with a missense COPZ1 mutation (NP_057141:p.Gly132Arg) exhibited isolated CN and chilblains.

The COPZ1 gene encodes the zeta 1 subunit of the coatomer protein complex I (COPI), which is phylogenetically highly conserved, with two identified mutation positions in the conserved region. The protein structure of human COPZ1 is still unknown, and computational analysis using bovine COPZ1 and COPG1 proteins predicted that truncated COPZ1 exhibits substantial structural instability and reduced interaction with COPG1, whereas missense COPZ1 retains interaction with COPG1. Consistent with structural defects, truncated COPZ1 blocked retrograde protein transport from the Golgi to the ER in human fibroblasts, suggesting a detrimental effect on COPI complex functions.

We also found that truncated or missense COPZ1 mutations caused impaired granulocytic differentiation of human CD34⁺ cells in vitro with a more pronounced phenotype in COPZ1 truncated cells. In zebrafish embryos, truncated Copz1 also resulted in defective myelopoiesis. Intracellularly, truncated COPZ1 downregulated JAK-STAT-C/EBPE-G-CSFR signaling and hypoxia-responsive pathways while inducing interferon-stimulated genes (ISGs) and STING, stimulating oxidative phosphorylation activity, and increasing reactive oxygen species (ROS) levels in CD34+ cells. Missense COPZ1 protein also deregulated interferon signaling.

Therapeutically, by applying connectivity map analysis, we discovered that treatment with the HIF1α activator IOX2 successfully restored granulopoiesis in truncated Copz1 zebrafish embryos and human CD34⁺ cells. Furthermore, transduction with COPZ2 cDNA effectively corrected granulocytic differentiation defects in COPZ1-mutated CD34⁺ cells.

In summary, our findings elucidate the distinct pathogenic mechanisms and clinical presentations associated with truncated versus missense COPZ1 mutations and underscore the potential of HIF1α activation as a promising therapeutic approach for CN.