The molecular cause of severe congenital neutropenia (SCN) is unknown in 30-50% of patients. SEC61A1 encodes the α subunit of the heterotrimeric Sec61 complex, which governs ER signal peptide-dependent protein transport and passive calcium leakage. Recently autosomal dominant mutations in SEC61A1 were reported to be pathogenic in CVID and glomerulocystic kidney disease with an anecdotical association with neutropenia (p.V67G ) in a single family. However the full spectrum of clinical manifestation in SEC61A1 mutations is yet to be explored. We investigated a SCN patient, only child of healthy non-consanguineous Belgian parents.
WES findings were validated and reported mutations compared in parallel by western blotting, Ca+2 flux assays, differentiation of transduced HL-60 cells using 1% DMSO, in vitro differentiation of primary CD34 cells, qPCR for unfolded protein response genes and 10X Genomics single-cell RNA-sequencing on whole bone marrow.
We identified a de novo private missense mutation in SEC61A1 (c.A275G;p.Q92R; CADD 24.5; msc 6.099) in a patient with SCN. The mutation results in diminished expression in PBMC and fibroblasts and an increase in calcium leakage. In vitro differentiation of CD34+ cells recapitulated the patient’s clinical arrest in granulopoeisis. HL-60 cells stably transduced with p.Q92R-Sec61α1 and p.V67G-Sec61α1 showed reduced differentiation to CD11b+CD16+ cells with decreased CD16 expression compared to both WT-Sec61α1 and p.V85D-Sec61α1, mutation associated with CVID. Analysis of CD34 cells on day 16 of differentiation revealed upregulation of CHOP and BiP indicative of increased unfolded protein response.
Specific autosomal dominant mutations in SEC61A1 cause SCN through upregulation of the unfolded protein response.