Publication – Epub 2020 Jun 17.

Authors

Lisenka E L M Vissers, Sreehari Kalvakuri, Elke de BoerSinje GeuerMachteld OudInge van Outersterp, Michael Kwint, Melde WitmondSimone Kersten, Daniel L Polla, Dilys Weijers, Amber Begtrup, Kirsty McWalter, Anna Ruiz, Elisabeth Gabau, Jenny E V MortonChristopher GriffithKarin WeissCandace GambleJames Bartley, Hilary J VernonKendra Brunet, Claudia Ruivenkamp, Sarina G Kant, Paul Kruszka, Austin LarsonAlexandra AfenjarThierry Billette de Villemeur, Kimberly Nugent, DDD StudyF Lucy Raymond, Hanka Venselaar, Florence DemurgerClaudia Soler-AlfonsoDong LiElizabeth Bhoj, Ian Hayes, Nina Powell Hamilton, Ayesha AhmadRachel Fisher, Myrthe van den Born, Marjolaine WillemsArthur Sorlin, Julian Delanne, Sebastien Moutton, Philippe ChristopheFrederic Tran Mau-Them, Antonio VitobellHimanshu GoelLauren Massingham, Chanika Phornphutkul, Jennifer Schwab, Boris Keren, Perrine Charles, Maaike Vreeburg, Lenika De SimoneGeorge HogansonMaria Iascone, Donatella MilaniLucie Evenepoel, Nicole RevencuD Isum Ward, Kaitlyn Burns, Ian Krantz, Sarah E Raible, Jill R Murrell, Kathleen Wood, Megan T Cho, Hans van Bokhoven, Maximilian Muenke, Tjitske Kleefstra, Rolf Bodmer, Arjan P M de Brouwer

Abstract

CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.

PMID: 32553196   PMCID: PMC7332645   DOI:  10.1016/j.ajhg.2020.05.017