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Item does not contain fulltext The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.

Introduction: Glycemic control in patients with type 1 diabetes can be difficult to achieve. One critical aspect of insulin delivery is site rotation, which is necessary to reduce dermatologic complications of repeated insulin infusion. No current application is designed to help patients track sites and instruct on overused sites. Objective: The objectives of this study were to (1) design a smartphone app, Insulin Site Guide, to gather real-time information on continuous subcutaneous insulin infusion (CSII) and continuous glucose monitor (CGM) site location and rotation compliance and instruct subjects on the use of an overused site; (2) conduct a usability study to measure site rotation compliance; and (3) report subject satisfaction with the app. Design: The app is installed on the subject’s smartphone. Subjects use the app to record CSII and CGM placement in real-time. Data are sent to the study team at the end of the study. Subjects complete a questionnaire concerning the app. Results: We report site rotation compliance data for eight subjects and survey responses for 10 subjects. Initial data from eight subjects indicate a high site rotation compliance of 84% for insulin pumps. In general, the majority of users indicate high satisfaction with the app. Conclusions: Insulin Site Guide is a mobile app that uses a novel algorithm to better guide site rotation. Use of the app has the potential to improve site rotation and decrease dermatologic complications of diabetes with long-term use.

Objective A small subset of children with congenital hearing loss have abnormal cochleovestibular nerves (i.e., absent, aplastic, or deficient cochlear nerves), with largely unknown etiology. Our objective was to investigate the underlying pathways and identify novel genetic variants responsible for cochleovestibular malformations and nerve abnormalities. It is our hypothesis that several cochleovestibular nerve abnormalities might share common causative pathways. Design We used a family-based exome sequencing approach to study 12 children with known rare inner ear and/or cochleovestibular nerve malformations. Results Our results highlight a diverse molecular etiology and suggest that genes important in the developing otic vesicle and cranial neural crest, e.g., MASP1, GREB1L, SIX1, TAF1, are likely to underlie inner ear and/or cochleovestibular nerve malformations. Conclusions We show that several cochleovestibular nerve malformations are neurocristopathies, which is consistent with the fact that cochleovestibular nerve development is based on otic placode-derived neurons in close association with neural crest-derived glia cells. In addition, we suggest potential genetic markers for more severely affected phenotypes, which may help prognosticate individual cochlear implantation outcomes. Developing better strategies for identifying which children with abnormal nerves will benefit from a cochlear implantation is crucial, as outcomes are usually far less robust and extremely variable in this population, and current neuroimaging and electrophysiologic parameters cannot accurately predict outcomes. Identification of a suitable treatment early will reduce the use of multiple interventions during the time-sensitive period for language development.

The Okur-Chung Neurodevelopmental Syndrome, or OCNDS, is a newly discovered rare neurodevelopmental disorder. It is characterized by developmental delay, intellectual disability, behavioral problems (hyperactivity, repetitive movements and social interaction deficits), hypotonia, epilepsy and language/verbalization deficits. OCNDS is linked to de novo variants in CSNK2A1, that lead to missense or deletion/truncating mutations in the encoded protein, the protein kinase CK2a. Eighteen different missense CK2a mutants have been identified to date, however no biochemical or cell biological studies have yet been performed to clarify the functional impact of such mutations. Here, we show that 15 different missense CK2a mutations lead to varying degrees of loss of kinase activity as recombinant purified proteins and when mutants are ectopically expressed in mammalian cells. We further detect changes in the phosphoproteome of three patient derived fibroblast lines and show that the subcellular localization of CK2a is altered for some of the OCNDS-linked mutants and in patient derived fibroblasts. Our data argue that reduced kinase activity and abnormal localization of CK2a may underlie the OCNDS phenotype.

Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. Patients with features of classical Rett syndrome, but do not fulfill all the diagnostic criteria (e.g. absence of a MECP2 mutation), are defined as atypical Rett syndrome. Genes encoding for cyclin-dependent kinase-like 5 (CDKL5) and forkhead box G1 (FOXG1) are more commonly found in patients with atypical Rett syndrome. Nevertheless, a subset of patients who are recognized to have an overlapping phenotype with RTT but are lacking a mutation in a gene that causes typical or atypical RTT are described as having Rett syndrome like phenotype (RTT-L). Whole Exome Sequencing (WES) of 8 RTT-L patients from our cohort revealed mutations in the genes GABRG2, GRIN1, ATP1A2, KCNQ2, KCNB1, TCF4, SEMA6B, and GRIN2A, which are seemingly unrelated to Rett syndrome genes. We hypothesized that the phenotypic overlap in RTT and RTT-L is caused by mutations in genes that affect common cellular pathways critical for normal brain development and function. We annotated the list of genes identified causing RTT-L from peer-reviewed articles and performed a protein-protein interaction (PPI) network analysis. We also investigated their interaction with RTT (typical or atypical) genes such as MECP2, CDKL5, NTNG1, and FOXG1. We found that the RTT-L-causing genes were enriched in the biological pathways such as circadian entrainment, the CREB pathway, and RET signaling, and neuronal processes like ion transport, synaptic transmission, and transcription. We conclude that genes that significantly interact with the PPI network established by RTT genes cause RTT-L, explaining the considerable feature overlap between genes that are indicated for RTT-L and RTT.

Pontocerebellar Hypoplasia 1B (PCH1B) patients exhibit profound underdevelopment of the neocerebellum and its adjacent structures, leading to severe developmental delays as well as poor survival. Here, we report a new case of PCH1B with a known mutation in EXOSC3, a component of the RNA exosome. We reprogrammed blood from the PCH1B patient and the healthy carrier parents into human induced pluripotent stem cells and differentiated these cells into neural stem cells (NSCs). Proteomic content was analyzed by mass spectrometry to reveal a slight underexpression of mutated EXOSC3 in the PCH1B patient. We discovered that several processes implicated in cell differentiation were impaired. NSCs from the mother were incubated with ERD03, a small molecule rationally developed to model PCH1B in zebrafish and analyzed by high-throughput mass spectrometry-based proteomics. In addition to affecting individual protein expression, we demonstrated the ability of the compound ERD03 to mimic PCH1B-induced protein pathways.

KIF26B is a member of the kinesin superfamily with evolutionarily conserved functions in controlling aspects of embryogenesis, including the development of the nervous system, though its function is incompletely understood. We describe an infant with progressive microcephaly, pontocerebellar hypoplasia, and arthrogryposis secondary to the involvement of anterior horn cells and ventral (motor) nerves. We performed whole exome sequencing on the trio and identified a de novo KIF26B missense variant, p.Gly546Ser, in the proband. This variant alters a highly conserved amino acid residue that is part of the phosphate-binding loop motif and motor-like domain and is deemed pathogenic by several in silico methods. Functional analysis of the variant protein in cultured cells revealed a reduction in the KIF26B protein's ability to promote cell adhesion, a defect that potentially contributes to its pathogenicity. Overall, KIF26B may play a critical role in the brain development and, when mutated, cause pontocerebellar hypoplasia with arthrogryposis.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that demonstrates variable severity, such that affected family members may have mild or severe disease. We performed exome and RNA sequencing of blood leukocytes from mild and severe cases across four families to identify mTOR pathway aberrations that may underlie phenotypic variability. In each family, we identified TSC1/TSC2 aberrations along with different mTOR pathway gene alterations, including base substitutions, deletions, and skewed allelic frequencies. Here, we describe the first reported DNA and RNA analysis of TSC families demonstrating mTOR pathway aberrations in mild and severe forms of the disease.

Background Childhood hearing impairment affects language and cognitive development. Profound congenital sensorineural hearing impairment can be due to an abnormal cochleovestibular nerve (CVN) and cochleovestibular malformations, however, the etiology of these conditions remains unclear. Methods We used a trio‐based exome sequencing approach to unravel the underlying molecular etiology of a child with a rare nonsyndromic CVN abnormality and cochlear hypoplasia. Clinical and imaging data were also reviewed. Results We identified a de novo missense variant [p(Asn174Tyr)] in the DNA‐binding Homeodomain of SIX1, a gene which previously has been associated with autosomal dominant hearing loss (ADHL) and branchio‐oto‐renal or Branchio‐otic syndrome, a condition not seen in this patient. Conclusions SIX1 has an important function in otic vesicle patterning during embryogenesis, and mice show several abnormalities to their inner ear including loss of inner ear innervation. Previous reports on patients with SIX1 variants lack imaging data and nonsyndromic AD cases were reported to have no inner ear malformations. In conclusion, we show that a de novo variant in SIX1 in a patient with sensorineural hearing loss leads to cochleovestibular malformations and abnormalities of the CVN, without any other abnormalities. Without proper interventions, severe to profound hearing loss is devastating to both education and social integration. Choosing the correct intervention can be challenging and a molecular diagnosis may adjust intervention and improve outcomes, especially for rare cases., Our work describes a novel variant of SIX1 identified to likely be associated with congenital abnormality of the cochleovestibular nerve and congenital pediatric hearing loss.

Mutations in CASK cause X-linked intellectual disability, microcephaly with pontine and cerebellar hypoplasia, optic atrophy, nystagmus, feeding difficulties, GI hypomotility, and seizures. Here we present a patient with a de novo carboxyl-terminus splice site mutation in CASK (c.2521-2A>G) and clinical features of the rare FG syndrome-4 (FGS4). We provide further characterization of genotype-phenotype correlations in CASK mutations and the presentation of nystagmus and the FGS4 phenotype. There is considerable variability in clinical phenotype among patients with a CASK mutation, even among variants predicted to have similar functionality. Our patient presented with developmental delay, nystagmus, and severe gastrointestinal and gastroesophageal complications. From a cognitive and neuropsychological perspective, language skills and IQ are within normal range, although visual-motor, motor development, behavior, and working memory were impaired. The c.2521-2A>G splice mutation leads to skipping of exon 26 and a 9 base-pair deletion associated with a cryptic splice site, leading to a 28-AA and a 3-AA in-frame deletion, respectively (p.Ala841_Lys843del and p.Ala841_Glu868del). The predominant mutant transcripts contain an aberrant guanylate kinase domain and thus are predicted to degrade CASK's ability to interact with important neuronal and ocular development proteins, including FRMD7. Upregulation of CASK as well as dysregulation among a number of interactors is also evident by RNA-seq. This is the second CASK mutation known to us as cause of FGS4. © 2017 Wiley Periodicals, Inc.