Gain and loss of function variants in EZH1 disrupt neurogenesis and cause dominant and recessive neurodevelopmental disorders

Abstract

Autism spectrum disorders

Trastorns de l'espectre autista

Trastornos del espectro autista

Genetic variants in chromatin regulators are frequently found in neurodevelopmental disorders, but their effect in disease etiology is rarely determined. Here, we uncover and functionally define pathogenic variants in the chromatin modifier EZH1 as the cause of dominant and recessive neurodevelopmental disorders in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 methyltransferases of the PRC2 complex. Unlike the other PRC2 subunits, which are involved in cancers and developmental syndromes, the implication of EZH1 in human development and disease is largely unknown. Using cellular and biochemical studies, we demonstrate that recessive variants impair EZH1 expression causing loss of function effects, while dominant variants are missense mutations that affect evolutionarily conserved aminoacids, likely impacting EZH1 structure or function. Accordingly, we found increased methyltransferase activity leading to gain of function of two EZH1 missense variants. Furthermore, we show that EZH1 is necessary and sufficient for differentiation of neural progenitor cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell-derived neural cultures and forebrain organoids, we demonstrate that EZH1 variants perturb cortical neuron differentiation. Overall, our work reveals a critical role of EZH1 in neurogenesis regulation and provides molecular diagnosis for previously undefined neurodevelopmental disorders.

This work was supported by the CHOP/UPENN IDDRC-New Program Development award, CHOP-Junior Faculty Pilot Program award, Margaret Q Landerbergen Foundation Award and NIH/NINDS R01NS119699, NIH/NICHD R21HD107592 (to N.A.), NIH/NINDS R35NS116843 (to H.S.), NIH/NINDS R35NS097370 and NIH/NIMH RF1MH123979 (to G.-l.M.)., BFU2015-69248-P and PGC2018-096082-B-I00 from the Spanish Ministry of Economy (to M.A.M.B.), Alabama Genomic Health Initiative F170303004 through University of Alabama at Birmingham (to A.C.H., M.T.), PID2019-111217RB-I00 Spanish Ministerio de Ciencia e Innovación (to X.D.L.C.), ID2019-110157RA-I00 (to M.S.), FPU Spanish Ministry of Education and Science predoctoral fellowship (to R.F.) and 2021 FISDU 00400 (to P.E-B.), NIHR Manchester Biomedical Research Centre NIHR203308 and Solve-RD which is supported by the European Union’s Horizon 2020 research and innovation program grant agreement No 779257 (to S.B.). This research was made possible through access to the data and findings generated by the 100KGP and the DDD. The 100KGP is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100KGP is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100KGP uses data provided by patients and collected by the National Health Service as part of their care and support. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network.