CNPY3 variants associated with a recessive developmental and epileptic encephalopathy affect inflammasome and TLR function.

Background

Canopy FGF signalling regulator 3 (CNPY3) is an endoplasmic reticulum (ER)-resident chaperone essential for toll-like receptor (TLR) folding, trafficking and inflammasome activation. In rare paediatric cases, biallelic CNPY3 variants have been associated with developmental and epileptic encephalopathy (DEE), but available data remain sparse.

Methods

50 individuals from 38 unrelated families with biallelic CNPY3 variants and DEE were evaluated for exome and genome findings, standardised clinical phenotype descriptions, EEG results, and neuroimaging data. A selection of variants underwent functional analysis focussing on protein stability and localisation, TLR2 function, NLPR3 inflammasome activation, and structural conformation.

Findings

Disease onset occurred in early infancy (median age at onset 68 days), with a clinical phenotype comprising global developmental delay (100%) and intractable epilepsy (86%), accompanied by microcephaly (70%), spasticity (77%), growth faltering (63%), stridor (48%), and early mortality (38%). Epileptic spasms and tonic seizures (46% each) were the most frequent seizure types, and EEG findings included suppression-burst (37%) and hypsarrhythmia (28%). Phenotypic severity varied substantially, with most patients being severely affected (median score 16, range 2-20). Most variants occurred in the homozygous state (95%), including 13 missense changes and 7 truncating alleles. Variants were classified as of uncertain significance (71%), followed by likely pathogenic (23%) and pathogenic (6%) according to ACMG/AMP criteria. Genotype-phenotype correlation showed that individuals with truncating variants were, on average, more severely affected than those with non-truncating variants (median score 18 vs 14.5). Protein modelling predicted conformational effects for most missense variants. In cells, frameshift alleles abolished CNPY3 protein expression, whereas nonsense alleles markedly reduced protein levels. ER localisation of CNPY3 remained preserved across tested genotypes; however, capacity to support TLR2 maturation and processing varied substantially. Remarkably, some missense variants permitted TLR2 surface expression but impaired downstream signalling and inflammasome activation, uncoupling trafficking from signal transduction.

Interpretation

CNPY3-associated DEE is a severe early-onset disorder with genotype-dependent phenotypic severity, accompanied by allele-specific disruption of innate immune pathways. Our findings reveal separable effects on TLR trafficking, downstream signalling and inflammasome activation, identifying CNPY3 as a key regulator of multiple cellular pathways involved in inflammatory responses and neurodevelopment.

Funding

Interdisciplinary Center of Clinical Research and Jena School of Molecular Medicine, Jena University Hospital; Friedrich Schiller University Jena; The Wellcome Trust; The Medical Research Council; The MSA Trust; The National Institute for Health Research University College London Hospitals Biomedical Research Centre; The Michael J Fox Foundation; Biotechnology and Biological Sciences Research Council; The Fidelity Trust; Rosetrees Trust; Ataxia UK; Brain Research UK; Sparks GOSH Charity; Alzheimer's Research UK; CureDRPLA; UK Dementia Research Institute; Parkinson's UK; South-Eastern Norway Regional Health Authority, Norway; France Genomic Medicine Plan 2025; Deutsche Forschungsgemeinschaft; European Commission; Federal Government of Germany; State of Thuringia; Pakistan Science Foundation; King Abdullah International Medical Research Center; Science and Technology Development Fund; King Salman Center for Disability Research.