SEC31A mutation affects ER homeostasis, causing neurological syndrome

Daniel Halperin ¹ Rotem Kadir ¹ Barak Rotblat ² Max Drabkin ¹ Yuval Yogev ¹ Ohad Wormser ¹ Zamir Shorer ³ Libe Gradstein ⁵ Uri Abdu ² Ilan shelef ⁴ Hagit Flusser ⁶ Ohad Birk ^1,7

¹The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel
²Department of Life Sciences, Ben-Gurion University of the Negev, Israel
³Pediatric Neurology Unit, Division of Pediatrics, Soroka University Medical Center, Israel
⁴Department of Imaging, Soroka University Medical Center, Israel
⁵Department of Ophthalmology, Clalit Health Services, Israel
⁶Zussman Child Development Center, Division of Pediatrics, Soroka University Medical Center, Israel
⁷Genetics Institute, Soroka University Medical Center, Israel

Introduction: Consanguineous kindred presented with an autosomal recessive syndrome of intrauterine growth retardation, marked developmental delay, spastic quadriplegia with profound contractures, pseudobulbar palsy, epilepsy, dysmorphism, neurosensory deafness and optic nerve atrophy with no eye fixation. Affected individuals died by the age of four. Brain MRI demonstrated microcephaly, semilobar holoprosencephally and agenesis of corpus callosum. We aimed at elucidating the molecular basis of this disease.

Methods: Genome-wide linkage analysis combined with whole-exome sequencing were performed to identify disease-causing variants. Functional consequences were investigated in fruit flies null mutant for the Drosophila SEC31A orthologue. SEC31A knockout SH-SY5Y and HEK293T cell-lines were generated using CRISPR/Cas9 and studied through qRT-PCR, immunoblotting and viability assays.

Results: Through genetic studies, we identified a disease-associated homozygous nonsense mutation in SEC31A. We demonstrate that SEC31A is ubiquitously expressed and that the mutation triggers nonsense-mediated decay of its transcript, comprising a practical null mutation. Similar to the human disease phenotype, knockdown SEC31A flies had defective brains and early lethality. Moreover, in line with SEC31A encoding one of the two coating layers comprising the COP-II complex, trafficking newly synthesized proteins from the endoplasmic reticulum to the Golgi, CRISPR/Cas9-mediated SEC31A null mutant cells demonstrated reduced viability through upregulation of ER-stress pathways.

Conclusions: We demonstrate that a severe neurological syndrome is caused by a null mutation in SEC31A, reducing cell viability through enhanced ER-stress response, in line with SEC31A’s role in the COP-II complex.