Defective SEC61α1 underlies a novel cause of autosomal dominant severe congenital neutropenia

Abstract Background The molecular cause of severe congenital neutropenia (SCN) is unknown in 30-50% of patients. SEC61A1 encodes the α subunit of the SEC61 complex, which governs endoplasmic reticulum protein transport and passive calcium leakage. Recently, mutations in SEC61A1 were reported to be pathogenic in common variable immunodeficiency and glomerulocystic kidney disease. Objective To expand the spectrum of SEC61A1- mediated disease to include autosomal dominant SCN. Methods WES findings were validated and reported mutations compared by western blotting, Ca+2 flux assays, differentiation of transduced HL-60 cells, in vitro differentiation of primary CD34 cells, qPCR for unfolded protein response genes and single-cell RNA-sequencing on whole bone marrow. Results We identified a novel de novo missense mutation in SEC61A1 (c.A275G;p.Q92R) in a patient with SCN born to non-consanguineous Belgian parents. The mutation results in diminished protein expression, disturbed protein translocation and an increase in calcium leakage from the ER. In vitro differentiation of CD34+ cells recapitulated the patient's clinical arrest in granulopoiesis. The impact of Q92R-SEC61α1 on neutrophil maturation was validated using HL-60 cells, where transduction reduced differentiation into CD11b+CD16+ cells. A potential mechanism for this defect is the uncontrolled initiation of the unfolded protein stress response, with single-cell analysis of primary bone-marrow revealing perturbed UPR in myeloid precursors, and in vitro differentiation of primary CD34+ cells revealing upregulation of CHOP and BiP UPR-response genes. Conclusion Specific mutations in SEC61A1 cause SCN through dysregulation of the UPR.