New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome

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Chater-Diehl, Eric | Ejaz, Resham | Cytrynbaum, Cheryl | Siu, Michelle | Turinsky, Andrei | Choufani, Sanaa | Goodman, Sarah | Abdul-Rahman, Omar | Bedford, Melanie | Dorrani, Naghmeh | Engleman, Kendra | Flores-Daboub, Josue | Geneviève, David | Mendoza-Londono, Roberto | Meschino, Wendy | Perrin, Laurence | Safina, Nicole | Townshend, Sharron | Scherer, Stephen, W. | Anagnostou, Evdokia | Piton, Amélie | Deardorff, Matthew, A. | Brudno, Michael | Chitayat, David | Weksberg, Rosanna

Edité par CCSD ; BioMed Central -

International audience. BACKGROUND:Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes in DNA methylation (DNAm) in affected individuals termed DNAm signatures.METHODS:Genome-wide DNAm was assessed in whole-blood samples from the individuals with pathogenic SMARCA2 variants and NCBRS diagnosis (n = 8) compared to neurotypical controls (n = 23) using the Illumina MethylationEPIC array. Differential methylated CpGs between groups (DNAm signature) were identified and used to generate a model enabling classification variants of uncertain significance (VUS; n = 9) in SMARCA2 as "pathogenic" or "benign". A validation cohort of NCBRS cases (n = 8) and controls (n = 96) demonstrated 100% model sensitivity and specificity.RESULTS:We identified a DNAm signature of 429 differentially methylated CpG sites in individuals with NCBRS. The genes to which these CpG sites map are involved in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. DNAm model classifications of VUS were concordant with the clinical phenotype; those within the SMARCA2 ATPase/helicase domain classified as "pathogenic". A patient with a mild neurodevelopmental NCBRS phenotype and a VUS distal to the ATPase/helicase domain did not score as pathogenic, clustering away from cases and controls. She demonstrated an intermediate DNAm profile consisting of one subset of signature CpGs with methylation levels characteristic of controls and another characteristic of NCBRS cases; each mapped to genes with ontologies consistent with the patient's unique clinical presentation.

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