Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism

Abstract

From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ~0.1% of individuals with unexplained neurodevelopmental disorders.

Stem cell niche-specific Ebf3 maintains the bone marrow cavity

“…Our data demonstrate that Ebf1 and Ebf3 have roles distinct from those of Ebf2 in regulating bone and HSC niche formation because mice lacking Ebf2 displayed osteopenia with normal CXCL12 expression, indicating that Ebf2 is an osteogenic transcription factor (Kieslinger et al 2005(Kieslinger et al , 2010. Recently, mutations in Ebf3 has been shown to cause neurodevelopmental disorders in humans (Harms et al 2017). Our study raises the possibility of Ebf3 dysfunction in other human diseases, including blood disorders and metabolic bone diseases.…”

Building dialogues between clinical and biomedical research through cross-species collaborations

“…This example illustrates how the efficient diagnosis of a new human neurodevelopmental disorder through functional studies of genetic alterations in the fruit fly occurred through a continual dialogue between clinicians and model organism biologists. In addition, through the use of Genematcher and large-scale research initiatives, two other international collaborations concurrently discovered that EBF3 mutations cause a unique neurodevelopmental syndrome[28, 61, 62]. …”

An ancient role for Collier/Olf/Ebf (COE)-type transcription factors in axial motor neuron development

“…We found, in mice, that mEbf1 and mEbf2 are implicated in axial MN development. In the embryonic mouse spinal cord, mEbf1 is selectively expressed in hypaxial muscle-innervating MNs (HMC), while mEbf2 is expressed in epaxial muscle-innervating MNs [17,[42][43][44][45][46], our findings could help advance our understanding of these conditions.…”