A 22.5 kb deletion in CUL4B causing Cabezas syndrome identified using CNV approach from WES data

Importance of Genetic Diagnosis in Global Developmental Delay: A Case of Cabezas Syndrome Caused by CUL4B Gene Deletion and Not Identified by Array-CHG

Global developmental delay (GDD) and intellectual disability (ID) are common reasons for referral to neurodevelopmental assessment. The etiology of GDD and ID can be genetic, acquired, or multifactorial. We report a case of a 10-year-old boy with ID and GDD who was diagnosed with Cabezas syndrome, a rare genetic disorder caused by a deletion of the CUL4B gene. Despite normal results from previous testing, exome sequencing with copy number variation analysis led to the identification of the deletion. Early diagnosis of GDD and ID is crucial for effective patient management, including planning interventions and providing support, therapy, and genetic counseling for families.

Proteomics and phosphoproteomics profiling in glutamatergic neurons and microglia in an iPSC model of Jansen de Vries Syndrome

Background

Jansen de Vries Syndrome (JdVS) is a rare neurodevelopmental disorder (NDD) caused by gain-of-function (GOF) truncating mutations in PPM1D exons 5 or 6. PPM1D is a serine/threonine phosphatase that plays an important role in the DNA damage response (DDR) by negatively regulating TP53 (P53). JdVS-associated mutations lead to the formation of a truncated PPM1D protein that retains catalytic activity and has a GOF effect because of reduced degradation. Somatic PPM1D exons 5 and 6 truncating mutations are well-established factors in a number of cancers, due to excessive dephosphorylation and reduced function of P53 and other substrates involved in DDR. Children with JdVS have a variety of neurodevelopmental, psychiatric, and physical problems. In addition, a small fraction has acute neuropsychiatric decompensation apparently triggered by infection or severe non-infectious environmental stress factors.

Methods

To understand the molecular basis of JdVS, we developed an induced pluripotent stem cell (iPSC) model system. iPSCs heterozygous for the truncating variant (PPM1D+/tr), were made from a patient, and control lines engineered using CRISPR-Cas9 gene editing. Proteomics and phosphoprotemics analyses were carried out on iPSC-derived glutamatergic neurons and microglia from three control and three PPM1D+/tr iPSC lines. We also analyzed the effect of the TLR4 agonist, lipopolysaccharide, to understand how activation of the innate immune system in microglia could account for acute behavioral decompensation.

Results

One of the major findings was the downregulation of POGZ in unstimulated microglia. Since loss-of-function variants in the POGZ gene are well-known causes of autism spectrum disorder, the decrease in PPM1D+/tr microglia suggests this plays a role in the neurodevelopmental aspects of JdVS. In addition, neurons, baseline, and LPS-stimulated microglia show marked alterations in the expression of several E3 ubiquitin ligases, most notably UBR4, and regulators of innate immunity, chromatin structure, ErbB signaling, and splicing. In addition, pathway analysis points to overlap with neurodegenerative disorders.

Limitations

Owing to the cost and labor-intensive nature of iPSC research, the sample size was small.

Conclusions

Our findings provide insight into the molecular basis of JdVS and can be extrapolated to understand neuropsychiatric decompensation that occurs in subgroups of patients with ASD and other NDDs.

PHIP-associated Chung-Jansen syndrome: Report of 23 new individuals

In 2016 and 2018, Chung, Jansen and others described a new syndrome caused by haploinsufficiency of PHIP (pleckstrin homology domain interacting protein, OMIM *612,870) and mainly characterized by developmental delay (DD), learning difficulties/intellectual disability (ID), behavioral abnormalities, facial dysmorphism and obesity (CHUJANS, OMIM #617991). So far, PHIP alterations appear to be a rare cause of DD/ID. "Omics" technologies such as exome sequencing or array analyses have led to the identification of distinct types of alterations of PHIP, including, truncating variants, missense substitutions, splice variants and large deletions encompassing portions of the gene or the entire gene as well as adjacent genomic regions. We collected clinical and genetic data of 23 individuals with PHIP-associated Chung-Jansen syndrome (CHUJANS) from all over Europe. Follow-up investigations (e.g. Sanger sequencing, qPCR or Fluorescence-in-situ-Hybridization) and segregation analysis showed either de novo occurrence or inheritance from an also (mildly) affected parent. In accordance with previously described patients, almost all individuals reported here show developmental delay (22/23), learning disability or ID (22/23), behavioral abnormalities (20/23), weight problems (13/23) and characteristic craniofacial features (i.e. large ears/earlobes, prominent eyebrows, anteverted nares and long philtrum (23/23)). To further investigate the facial gestalt of individuals with CHUJANS, we performed facial analysis using the GestaltMatcher approach. By this, we could establish that PHIP patients are indistinguishable based on the type of PHIP alteration (e.g. missense, loss-of-function, splice site) but show a significant difference to the average face of healthy individuals as well as to individuals with Prader-Willi syndrome (PWS, OMIM #176270) or with a CUL4B-alteration (Intellectual developmental disorder, X-linked, syndromic, Cabezas type, OMIM #300354). Our findings expand the mutational and clinical spectrum of CHUJANS. We discuss the molecular and clinical features in comparison to the published individuals. The fact that some variants were inherited from a mildly affected parent further illustrates the variability of the associated phenotype and outlines the importance of a thorough clinical evaluation combined with genetic analyses for accurate diagnosis and counselling.

CUL4B-associated epilepsy: Report of a novel truncating variant promoting drug-resistant seizures and systematic review of the literature

BACKGROUND

Cabezas syndrome is a rare X-linked disease caused by mutations in CUL4B and characterized by developmental delay/intellectual disability, somatic dysmorphisms, behavioural disorder, ataxia/tremors. Although seizures have been formerly reported, their clinical semiology, EEG features and long-term outcome are largely unknown.

PURPOSE

This study aims to expand knowledge on epilepsy associated with Cabezas syndrome and to understand whether different types of variants in the CUL4B gene or brain MRI abnormalities may influence seizure onset and epilepsy course.

METHODS

With this in mind, we characterised the epileptic phenotype of a 17-year-old adolescent harbouring a CUL4B novel variant and performed a systematic literature review of CUL4B-associated seizures, analysing mutation types and neuroimaging features as epilepsy predictors.

RESULTS

Our case observation indicates that CUL4B-associated epilepsy may also be drug-resistant and persist beyond infancy. Literature analysis shows that 43% of CUL4B patients develop seizures, with no statistically significant differences in epilepsy development according to mutation type and neuroimaging features.

CONCLUSION

Our study extends knowledge of CUL4B-associated epilepsy, offering new insights into disease progression.

SPT16 ubiquitylation by DCAF14-CRL4 regulates FACT binding to histones

The histone chaperone complex FACT comprises SPT16 and SSRP1 and contributes to DNA replication, transcription, and repair, but how it plays such various roles is unclear. Here, we show that human SPT16 is ubiquitylated at lysine-674 (K674) by the DCAF14-CRL4 ubiquitin ligase. K674 is located in the middle domain of SPT16, and the corresponding residue of the yeast ortholog is critical for binding to histone H3.1-H4. We show that the middle domain of human SPT16 binds to histone H3.1-H4 and that this binding is inhibited by K674 ubiquitylation. Cells with heterozygous knockin of a K674R mutant of SPT16 manifest reduction of both SPT16 ubiquitylation and H3.1 in chromatin, a reduced population in mid S phase, impaired proliferation, and increased susceptibility to S phase stress. Our data thus indicate that SPT16 ubiquitylation by DCAF14-CRL4 regulates FACT binding to histones and may thereby control DNA replication-coupled histone incorporation into chromatin.