Butyrate modifies epigenetic and immune pathways in peripheral mononuclear cells from children with neurodevelopmental disorders associated with chromatin dysregulation

Pathogenic DNA variants in chromatin-related genes constitute an important minority of neurodevelopmental disorders (NDDs). Epigenetic mechanisms, including chromatin regulation driven by genetic or environmental factors, are increasingly recognised as key contributors to pathogenesis of diverse NDDs. We hypothesise that therapeutic strategies targeting chromatin dysregulation, such as histone deacetylase inhibition with butyrate, may be a potential disease modifying therapy for NDDs. We first performed peripheral blood bulk RNA sequencing (RNA-seq) to explore baseline gene regulation in children with chromatin-related NDDs (Kabuki syndrome (KMT2D, n ​= ​4), CHARGE syndrome (CHD7, n ​= ​2), and Rett syndrome (MECP2, n ​= ​5), and children with NDDs but without a monogenic diagnosis (non-monogenic, n ​= ​8), compared with sex-matched healthy controls (total n ​= ​21). Next, to explore the effects of butyrate, single-cell RNA sequencing (scRNA-seq) was performed on 101,539 peripheral immune cells from four selected patients (one per condition) and two controls, before and after butyrate treatment. At baseline, dysregulation of ribosomal and immune pathways was seen in all four NDD cohorts (KMT2D, CHD7, MECP2, non-monogenic) compared to controls. Butyrate largely reversed these pathways, normalising ribosomal and immune pathways in patient and control cells. Butyrate induced up-regulation of ribosome, GTPase, cytoskeletal, mitochondrial pathways, and down-regulation of epigenetic and immune pathways. In conclusion, we identified a common ribosomal-immune RNA signature in chromatin-related NDDs, and a similar signature in non-monogenic NDDs. We showed that butyrate modulates epigenetic and immune gene networks in monogenic and non-monogenic NDDs, positioning butyrate as a promising therapeutic modulator across diverse NDDs.