Biallelic Variants in CNPY3, Encoding an Endoplasmic Reticulum Chaperone, Cause Early-Onset Epileptic Encephalopathy

Abstract

Early-onset epileptic encephalopathies, including West syndrome (WS), are a group of neurological disorders characterized by developmental impairments and intractable seizures from early infancy. We have now identified biallelic CNPY3 variants in three individuals with WS; these include compound-heterozygous missense and frameshift variants in a family with two affected siblings (individuals 1 and 2) and a homozygous splicing variant in a consanguineous family (individual 3). All three individuals showed hippocampal malrotation. In individuals 1 and 2, electroencephalography (EEG) revealed characteristic fast waves and diffuse sharp- and slow-wave complexes. The fast waves were clinically associated with seizures. CNPY3 encodes a co-chaperone in the endoplasmic reticulum and regulates the subcellular distribution and responses of multiple Toll-like receptors. The amount of CNPY3 in lymphoblastoid cells derived from individuals 1 and 2 was severely lower than that in control cells. Cnpy3-knockout mice exhibited spastic or dystonic features under resting conditions and hyperactivity and anxiolytic behavior during the open field test. Also, their resting EEG showed enhanced activity in the fast beta frequency band (20-35 Hz), which could mimic the fast waves in individuals 1 and 2. These data suggest that CNPY3 and Cnpy3 perform essential roles in brain function in addition to known Toll-like receptor-dependent immune responses.

Characterization of CNPY5 and its family members

“…CNPY3 protein is widely expressed, with highest levels in neurons, the gastrointestinal (GI) tract, and other glandular epithelia. Biallelic CNPY3 variants have reduced expression of the protein and cause early onset epileptic encephalopathy, a collective term for neurological disorders characterized by developmental impairments and seizures from early infancy. Expression of CNPY3 in lymphoblastoid cells of these patients is severely reduced, and knockout mice show spastic or dystonic features.…”

Genetic Analysis of Children With Unexplained Developmental Delay and/or Intellectual Disability by Whole-Exome Sequencing

“…EIEE is a group of neurological disorders characterized by frequent epileptic seizures and development delay beginning in infancy ( McTague et al, 2016 ). In 2018, biallelic variants in CNPY3 gene (MIM *610774) have been identified to cause EIEE60 (MIM #617929) ( Mutoh et al, 2018 ). CNPY3 gene is located on chromosome 6p21.1, comprises six exons and five introns, and encodes a co-chaperone of 278 amino acid residues in the endoplasmic reticulum.…”

“…In this study, two compound heterozygous variants of CNPY3 gene were identified in patient 5. To date, three individuals with biallelic CNPY3 variants have been reported, and their MRI showed diffuse brain atrophy and hippocampal malrotation ( Mutoh et al, 2018 ). Brain MRI of patient 5 also showed cerebral atrophy, but hippocampal malrotation was not observed.…”

CNPY4 inhibits the Hedgehog pathway by modulating membrane sterol lipids

“…In zebrafish, cnpy1 was reported to regulate the development of Kupffer’s vesicle, which controls left-right asymmetry through HH signaling in zebrafish 36–38 ; however, the interaction of cnpy1 with HH signaling was not explored. In humans and mice, Cnpy1 appears truncated, and Cnpy2 and Cnpy3 knockout mice do not display visible alterations of HH pathway 36,39–41 . We therefore turned to the remaining family member, Cnpy4 , to study whether it may play a role in HH signaling.…”

“…Our data demonstrate that Cnpy4 -dependent alteration of sterol lipid levels in the membrane directly modulate SMO-dependent HH activation. While increasing evidence supports the important role of lipids in signal transduction between PTCH1 and SMO, the molecular mechanisms governing these effects are not fully elucidated 29–35,41–45 . Recent studies have shown that both PTCH1 and SMO have several binding sites for sterols, including cholesterol, and that a subset of these binding events are essential for SMO activation 55,56,63–66 .…”