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% to 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 Our aim was to expand the spectrum of SEC61A1 -mediated disease to include autosomal dominant SCN. Methods Whole exome sequencing findings were validated, and reported mutations were compared by Western blotting, Ca2 + flux assays, differentiation of transduced HL-60 cells, in vitro differentiation of primary CD34 cells, quantitative PCR for unfolded protein response (UPR) 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 who was born to nonconsanguineous Belgian parents. The mutation results in diminished protein expression, disturbed protein translocation, and an increase in calcium leakage from the endoplasmic reticulum. In vitro differentiation of CD34 + cells recapitulated the patient’s clinical arrest in granulopoiesis. The impact of Q92R-Sec61α1 on neutrophil maturation was validated by using HL-60 cells, in which 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 CCAAT/enhancer-binding protein homologous protein and immunoglobulin heavy chain binding protein UPR-response genes. Conclusion Specific mutations in SEC61A1 cause SCN through dysregulation of the UPR.

Severe congenital neutropenia‐associated JAGN1 mutations unleash a calpain‐dependent cell death programme in myeloid cells

“…Recently, mutations in SEC61 translocon subunit alpha 1 (SEC61A1) were identified as a novel cause of autosomal dominant SCN, and this defect was linked to calcium leakage from the ER leading to increased apoptosis. 20 Interestingly, the authors also noted a reduced expression of the B-cell leukaemia/lymphoma 2 apoptosis regulator (BCL2) gene in cells with SEC61A1 mutations. This accords with our observation of defective Bcl-2 expression in the bone marrow of patients with Kostmann disease harbouring HAX1 mutations.…”

“…The ER is also involved in regulation of calcium homeostasis. Recently, mutations in SEC61 translocon subunit alpha 1 ( SEC61A1 ) were identified as a novel cause of autosomal dominant SCN, and this defect was linked to calcium leakage from the ER leading to increased apoptosis 20 . Interestingly, the authors also noted a reduced expression of the B‐cell leukaemia/lymphoma 2 apoptosis regulator ( BCL2 ) gene in cells with SEC61A1 mutations.…”

Complexity and Specificity of Sec61-Channelopathies: Human Diseases Affecting Gating of the Sec61 Complex

“…Mammalian cells, which are highly active in protein secretion, termed professional secretory cells, may be particularly sensitive towards problems in Sec61 channel closure and, therefore, constantly on the verge to apoptosis. This has recently been seen in human patients associated with dominant negative effects in the course of i) autosomal dominant tubulointerstitial kidney disease (ADTKD) and glomerulocystic kidney disease in kidney cells with the Sec61α 1V67G- or Sec61α 1T185A-exchanges [ 256 , 257 ], ii) hypogammaglobulinemia or primary antibody deficiency (PAD) in plasma cells with the Sec61α 1V85D exchange [ 258 ], plus iii) autosomal dominant severe congenital neutropenia (ADSCN) in neutrophils with the Sec61α 1V67G- or Sec61α 1Q92R-exchanges [ 256 , 259 ] and associated with Diabetes mellitus for the β-cells of the mouse with the homozygous Sec61α1Y344H exchange [ 260 ]. The fact that ERj6 (DNAJC3) is involved in Sec61 channel closure and that its absence in human patients, too, causes Diabetes mellitus is in perfect line with this interpretation [ 261 ].…”

“…In three patients suffering from autosomal dominant severe congenital neutropenia (ADSCN) SEC61A1 missense mutations were described for two independent families. The heterozygous SEC61A1 mutations identified included two missense mutations causing the amino acid substitutions V67G (in the plug helix) and Q92R (in the lateral gate TMH 2), respectively [ 256 , 259 ]. The patient with the Sec61α V67G variant also suffered from ADTKD (see above).…”

Neutropenia in Primary Immunodeficiency Diseases

“…Recently, an autosomal dominant mutation in SEC61A1 was reported in a patient with SCN who was born to nonconsanguineous Belgian parents [22]. SEC61A1, encoding the α-subunit of the Sec61 complex controls the endoplasmic reticulum protein transport and passive calcium leakage.…”