De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder

Eduardo Calpena,Marieke F Van Dooren,Tina Barbaro-Dieber,Theresa A Grebe,Nicola Foulds,Maura R.Z Ruzhnikov,Elise Brimble,Ellen Van Binsbergen,Aida Telegrafi,Eva H Brilstra,Jacqueline A.C Goos,Teresa Kaserer,Irene M.J Mathijssen,Peter J Van Der Spek,Deborah Osio,Kristin G Monaghan,Kai-Ren Ong,Lucy Bownass,Alexia Hervieu,Francis Jeshira Reynoso Santos,Paul A Clarke,Julian Blagg,Andrew O.M Wilkie,María Jesús Ortiz-Ruiz ,Olajumoke Adeniji-Popoola ,Sigrid Swagemakers ,Ruth Newbury‐Ecob ,Melissa Lees ,Stephen R F Twigg ,Aster V E Harder

doi:10.1016/j.ajhg.2019.02.006

Abstract

The Mediator is an evolutionarily conserved, multi-subunit complex that regulates multiple steps of transcription. Mediator activity is regulated by the reversible association of a four-subunit module comprising CDK8 or CDK19 kinases, together with cyclin C, MED12 or MED12L, and MED13 or MED13L. Mutations in MED12, MED13, and MED13L were previously identified in syndromic developmental disorders with overlapping phenotypes. Here, we report CDK8 mutations (located at 13q12.13) that cause a phenotypically related disorder. Using whole-exome or whole-genome sequencing, and by international collaboration, we identified eight different heterozygous missense CDK8 substitutions, including 10 shown to have arisen de novo, in 12 unrelated subjects; a recurrent mutation, c.185C>T (p.Ser62Leu), was present in five individuals. All predicted substitutions localize to the ATP-binding pocket of the kinase domain. Affected individuals have overlapping phenotypes characterized by hypotonia, mild to moderate intellectual disability, behavioral disorders, and variable facial dysmorphism. Congenital heart disease occurred in six subjects; additional features present in multiple individuals included agenesis of the corpus callosum, ano-rectal malformations, seizures, and hearing or visual impairments. To evaluate the functional impact of the mutations, we measured phosphorylation at STAT1-Ser727, a known CDK8 substrate, in a CDK8 and CDK19 CRISPR double-knockout cell line transfected with wild-type (WT) or mutant CDK8 constructs. These experiments demonstrated a reduction in STAT1 phosphorylation by all mutants, in most cases to a similar extent as in a kinase-dead control. We conclude that missense mutations in CDK8 cause a developmental disorder that has phenotypic similarity to syndromes associated with mutations in other subunits of the Mediator kinase module, indicating probable overlap in pathogenic mechanisms.

Highlights

The Mediator is an evolutionarily conserved, multi-subunit complex that regulates multiple steps of transcription
Mediator activity is regulated by the reversible association of a four-subunit module comprising cyclin-dependent kinase 8 (CDK8) or CDK19 kinases, together with cyclin C, MED12 or MED12L, and MED13 or MED13L
Mutations in MED13 (MIM: 603808) have been reported as leading to a neurodevelopmental disorder characterized by intellectual disability (ID) and/or developmental delay, including speech delay; additional features that were present in two or more affected individuals included autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphic features

Summary

REPOR T

De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder. We conclude that missense mutations in CDK8 cause a developmental disorder that has phenotypic similarity to syndromes associated with mutations in other subunits of the Mediator kinase module, indicating probable overlap in pathogenic mechanisms. Parent-child trio-based WGS of a proband with metopic synostosis and ID (subject 3 in Table 1) identified a de novo c.88G>A transition in CDK8; this change leads to the prediction of a heterozygous p.Gly30Ser substitution The position of this substitution, at an almost invariant residue within the highly conserved glycine-rich loop of the kinase domain, and in which pathogenic mutations were previously identified in other protein kinases, led us to seek evidence for additional pathogenic variants in CDK8 through GeneMatcher exchange and from the Deciphering Developmental Disorders (DDD) research study.. MutationTaster predicted all eight substitutions to be disease-causing, and SIFT and PolyPhen-2 predicted all to

Behavioral disorder

Declaration of Interests

Findings

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