De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder

Abstract

Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.

Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features

“…The presence of cardiac, renal, genital, and ophthalmological defects and seizures were more commonly seen in individuals with PSMD12 mutations while microcephaly was more commonly associated with a BPTF disruption. Notably, Küry et al 39 also reported that individuals with 17q24.2 deletions involving PSMD12 and BPTF had more prominent microcephaly than those with isolated PSMD12 deficiency, supporting further the causative role of BPTF in microcephaly.…”

“…Recently, we have reported de novo disruption of the proteasome regulatory subunit PSMD12 (MIM: 604450). 39 Reported subjects included four (individuals 1-4) with single-nucleotide variants in PSMD12, three (individuals 5, 7, and 9) with CNV deletions on 17q24.2 affecting PSMD12, BPTF, and other genes, and two (individuals 8 and 10) with deletions on 17q24.2 encompassing PSMD12 and neighboring genes but leaving BPTF intact. 39 We hypothesize that the clinical phenotype of 17q24.2 microdeletion is associated with haploinsufficiency of the affected PSMD12 and/or BPTF, and possibly additional genes.…”

“…39 Reported subjects included four (individuals 1-4) with single-nucleotide variants in PSMD12, three (individuals 5, 7, and 9) with CNV deletions on 17q24.2 affecting PSMD12, BPTF, and other genes, and two (individuals 8 and 10) with deletions on 17q24.2 encompassing PSMD12 and neighboring genes but leaving BPTF intact. 39 We hypothesize that the clinical phenotype of 17q24.2 microdeletion is associated with haploinsufficiency of the affected PSMD12 and/or BPTF, and possibly additional genes. Within the reported deletion region on 17q24.2, five genes have pLI scores greater than 0.95 and are predicted to be highly intolerant of LoF mutations, including PSMD12, BPTF, and three other genes that are currently not implicated in disease: HELZ, PITPNC1, and PRKCA ( Figure 3).…”

“…We and others have shown that zebrafish can serve as robust direct models for craniofacial abnormalities observed in humans. 39,42,[48][49][50][51][52] We assessed the craniofacial patterning by measuring the angle of ceratohyal (CH) cartilage in ventral images acquired from 3 dpf larvae. We observed a significant increase of the CH angle in bptf CRISPR F0 mutants (102 versus 91 for F0 mutants versus controls; p % 0.0001, n ¼ 47-59 larvae/batch, repeated; Figure 2).…”

“…The CRISPR single-guide (sgRNA) target was identified with ChopChop software 38 and synthesized using the GeneArt Precision gRNA Synthesis Kit (Invitrogen) according to manufacturer's instructions as described. 39 To generate F0 mutants, 75 pg of sgRNA and 150 pg of CAS9 protein (PNA bio, CP01) were injected directly into the cell of 1-cell stage zebrafish embryos. The efficiency of the sgRNA was determined by extracting genomic DNA from F0 embryos at 2 dpf by proteinase K digestion (Life technologies, AM2548).…”