Hydrocephalus is one of the most common pediatric neurological disorders and is associated with monogenic syndromes. Untreated hydrocephalus has a high mortality rate, and current treatment involves surgical implantation of a shunt or third ventriculostomy, both of which have complex follow-up care. Molecular therapies to treat or prevent hydrocephalus might have widespread applications for monogenic syndromes but are currently underinvestigated. To determine whether oligonucleotides are a viable drug class to prevent hydrocephalus, we assessed a monogenic syndrome called Schinzel-Giedion syndrome (SGS). SGS is caused by increased SETBP1 protein due to heterozygous missense mutations in a degron motif of SETBP1. Mice that produce mutant human SETBP1 show hydrocephalus in over 50% of cases and do not live long. Treatment of mice with injections of antisense oligonucleotides targeting SETBP1 prevented or led to a significant reduction of hydrocephalus compared to mock-treated controls and improved long-term survival. These results suggest that hydrocephalus is preventable for a monogenic syndrome with an oligonucleotide intervention.

Schinzel-Giedion syndrome (SGS) is an ultra-rare Mendelian disorder caused by gain-of-function variants in the SETBP1 gene. Although previous studies determined multiple roles for SETBP1 and its associated pathways in disease manifestation, they did not assess whether cell-type-specific alternative splicing (AS) plays a role in SGS. We quantified gene and splice junction expression from single-nuclei RNA-sequencing data from the cerebral cortex and kidney of atypical Setbp1S858R SGS patient variant and wild-type mice. We identified 33 and 62 genes with statistically significant alterations in splice junction usage in the brain and kidney, respectively. We identified significant splice junction usage in a member of the heterogeneous nuclear ribonucleoprotein family, Hnrnpa2b1. These findings were cell-type specific in the cerebral cortex and cell-type agnostic in the kidney, suggesting tissue specificity of AS in Setbp1S858R mice. To broaden the impact of our results for the rare disease community, we developed a point-and-click web application that enables users to explore single-cell-resolution changes at the gene and splice junction levels. Overall, our findings implicate AS in a tissue- and cell-type-specific manner in the cerebral cortex and kidney of Setbp1S858R mice.

Different types of germline de novo SETBP1 variants cause clinically distinct and heterogeneous neurodevelopmental disorders: Schinzel-Giedion syndrome (SGS, via missense variants at a critical degron region) and SETBP1-haploinsufficiency disorder. However, due to the lack of systematic investigation of genotype-phenotype associations of different types of SETBP1 variants, and limited understanding of its roles in neurodevelopment, the extent of clinical heterogeneity and how this relates to underlying pathophysiological mechanisms remains elusive. This imposes challenges for diagnosis. Here, we present a comprehensive investigation of the largest cohort to date of individuals carrying SETBP1 missense variants outside the degron region (n = 18). We performed thorough clinical and speech phenotyping with functional follow-up using cellular assays and transcriptomics. Our findings suggest that such variants cause a clinically and functionally variable developmental syndrome, showing only partial overlaps with classical SGS and SETBP1-haploinsufficiency disorder. We provide evidence of loss-of-function pathophysiological mechanisms impairing ubiquitination, DNA-binding, transcription, and neuronal differentiation capacity and morphologies. In contrast to SGS and SETBP1 haploinsufficiency, these effects are independent of protein abundance. Overall, our study provides important novel insights into diagnosis, patient care, and aetiology of SETBP1-related disorders.

Rare early-onset lower urinary tract (REOLUT) disorders affect the ureter, urinary bladder, or urethra and manifest before birth or in childhood. Monogenic causes have been reported in a subset of such individuals. A possible genetic cause was considered in a child with a megaureter who had syndromic features. Whole-exome sequencing was undertaken in individuals with megaureter. Immunohistochemistry was performed in urinary tract tissues of unaffected human fetuses. The index case presented at 6 months with urosepsis and was found to have a unilateral primary non-refluxing megaureter which required stenting of its distal portion. This, together with dysmorphic features and developmental delay, led to a clinical diagnosis of Schinzel-Giedion syndrome (SGS). She was found to carry a de novo missense variant in SET binding protein 1 (SETBP1), c.2613T>G (GenBank: NM_015559.3) (p.Ile871Met), a gene previously implicated in SGS. She was in good general health at 11 years of age, an unusual outcome given that most individuals with SGS die in the first 2 years of life. SETBP1 was detected in the fetal urinary tract, both in the urothelium and in nerve trunks in the kidney hilum and around the ureter. No SETBP1 gene variants were detected in eight further cases of megaureter. This case indicates the value of genetic testing when a REOLUT disorder is accompanied by syndromic signs outside the urinary tract. SETBP1 may drive the functional differentiation of the human fetal ureter.

Many genes in the human genome encode proteins that are dosage sensitive, meaning they require protein levels within a narrow range to properly execute function. To investigate if clinically relevant variation in protein levels impacts the same downstream pathways in human disease, we generated cell models of two SETBP1 syndromes: Schinzel-Giedion Syndrome (SGS) and SETBP1 haploinsufficiency disease (SHD), where SGS is caused by too much protein, and SHD is caused by not enough SETBP1. Using patient and sex-matched healthy first-degree relatives from both SGS and SHD SETBP1 cases, we assessed how SETBP1 protein dosage affects downstream pathways in human forebrain progenitor cells. We find that extremes of SETBP1 protein dose reciprocally influence important signalling molecules such as AKT, suggesting that the SETBP1 protein operates within a narrow dosage range and that extreme doses are detrimental. We identified SETBP1 nuclear bodies as interacting with the nuclear lamina and suggest that SETBP1 may organize higher order chromatin structure via links to the nuclear envelope. SETBP1 protein doses may exert significant influence on global gene expression patterns via these SETBP1 nuclear bodies. This work provides evidence for the importance of SETBP1 protein dose in human brain development, with implications for two neurodevelopmental disorders.