De novo HDAC3 variants leading to epigenetic machinery dysfunction are associated with a neurodevelopmental disorder

Histone deacetylase 3 (HDAC3) is a crucial epigenetic modulator essential for brain development. Although its dysfunction is increasingly recognized in various neurodevelopmental disorders, there have been no reports of human diseases related to HDAC3 dysfunction in Online Mendelian Inheritance in Man (OMIM). This study establishes a novel link between heterozygous de novo variants in HDAC3 and a distinct neurodevelopmental syndrome, characterized by intellectual disability, developmental delays, and other variable manifestations such as musculoskeletal anomalies and congenital heart defects. In a cohort of six individuals, we identified de novo missense HDAC3 variants (D93N, A110T, P201S, L266S, G267S, and R359C), all located in evolutionarily conserved sites. Using trio exome sequencing and extensive phenotypic analysis, we correlated these genetic alterations with the observed clinical spectrum. Our investigations using HDAC assays and western blot analyses identified reduced deacetylation activity in the L266S and G267S variants, positioned near the enzymatic pocket. Additionally, proteomic analysis employing co-immunoprecipitation revealed that disrupted interactions with key multi-protein complexes, particularly CoREST and NCoR in the A110T variant, suggesting a critical pathogenic mechanism. Moreover, immunofluorescence analysis revealed diminished fluorescence intensity (nuclear to cytoplasmic ratio) in the A110T, G267S, and R359C variants, indicating impaired nuclear localization. This study highlights that de novo HDAC3 variants are associated with a novel neurodevelopmental syndrome, emphasizing the importance of histone deacetylase activity, multi-protein complex interactions, and nuclear localization for normal cellular function of HDAC3. These insights open new possibilities for understanding the molecular mechanisms of this uncharacterized neurodevelopmental disorder and may inform future therapeutic approaches. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/24301801v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1de196borg.highwire.dtl.DTLVardef@56f40corg.highwire.dtl.DTLVardef@b06d23org.highwire.dtl.DTLVardef@cd2fdb_HPS_FORMAT_FIGEXP M_FIG C_FIG This study identifies de novo HDAC3 variants in patients with neurodevelopmental disorders, characterized by intellectual disability, developmental delays, and other variable manifestations. We demonstrate that these variants result in reduced HDAC activity, compromised interactions with multi-protein complexes, and improper nuclear localization of the HDAC3 protein. This provides a novel gene-disease association and offers insights into the molecular underpinnings of this disorder.