Biallelic CC2D2A variants, SNV and LINE-1 insertion simultaneously identified in siblings using long-read whole-genome sequencing and haplotype phasing.

Joubert syndrome (JBTS) is characterized by a magnetic resonance imaging appearance called 'molar tooth sign', neonatal breathing dysregulation and hypotonia, and developmental delay. Whole-exome analysis based on short-read sequencing has often contributed to the identification of causative single-nucleotide variants in patients clinically diagnosed with JBTS. However, ~10% of them are still undiagnosed even though a single possible pathogenic variant has been identified. We report a successful identification of biallelic variants using long-read whole-genome sequencing and haplotype phasing analysis in a family with two Japanese siblings having morphological brain abnormalities. The affected siblings had a novel nonsynonymous variant (CC2D2A:NM_001080522.2:c.4454A>G:p.(Tyr1485Cys)) and an exonic insertion of Long INterspercsed Element-1 (LINE-1). The allelicity of these variants was clearly proven without the data of parents. Finally, our survey of in-house genome sequencing data indicates that there are rare carriers of CC2D2A related diseases, who harbour the exonic LINE-1 insertion in the CC2D2A gene.

MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance.

To date, mutations in 15 actin- or microtubule-associated genes have been associated with the cortical malformation lissencephaly and variable brainstem hypoplasia. During a multicenter review, we recognized a rare lissencephaly variant with a complex brainstem malformation in three unrelated children. We searched our large brain-malformation databases and found another five children with this malformation (as well as one with a less severe variant), analyzed available whole-exome or -genome sequencing data, and tested ciliogenesis in two affected individuals. The brain malformation comprised posterior predominant lissencephaly and midline crossing defects consisting of absent anterior commissure and a striking W-shaped brainstem malformation caused by small or absent pontine crossing fibers. We discovered heterozygous de novo missense variants or an in-frame deletion involving highly conserved zinc-binding residues within the GAR domain of MACF1 in the first eight subjects. We studied cilium formation and found a higher proportion of mutant cells with short cilia than of control cells with short cilia. A ninth child had similar lissencephaly but only subtle brainstem dysplasia associated with a heterozygous de novo missense variant in the spectrin repeat domain of MACF1. Thus, we report variants of the microtubule-binding GAR domain of MACF1 as the cause of a distinctive and most likely pathognomonic brain malformation. A gain-of-function or dominant-negative mechanism appears likely given that many heterozygous mutations leading to protein truncation are included in the ExAC Browser. However, three de novo variants in MACF1 have been observed in large schizophrenia cohorts.

Neurodevelopmental outcome and respiratory management of congenital central hypoventilation syndrome: a retrospective study.

BACKGROUND: Congenital central hypoventilation syndrome (CCHS) is a rare disease characterized by sleep apnea. Anoxia often occurs soon after birth, and it is important to prevent anoxia-mediated central nervous system complications; however, data on the relationship between respiratory management and the prognosis for intellectual development of patients with CCHS is not well yet investigate. METHODS: We performed a retrospective chart review cohort study of patients with CCHS in Japan. We investigated the risk and prognostic factors for developmental outcomes and examined the disease in terms of its symptoms, diagnosis, complications, and treatment. RESULTS: Of the 123 patients with CCHS included in the survey, 88 patients were 6 years old and older. They were divided into two group based on their intelligence quotient. Those treated using positive-pressure ventilation via tracheostomy in the first three months of life had a better developmental prognosis than those managed via tracheostomy after three months of age and those treated by ventilation using mask (OR = 3.80; 95% CI: 1.00-14.37, OR = 4.65; 95% CI: 1.11-19.37). There was no significant difference in physical development (P = 0.64). CONCLUSIONS: The best respiratory treatment for patients with CCHS is ventilation via tracheostomy, initiated ideally before the age of three months.

Unfolded protein response is activated in Krabbe disease in a manner dependent on the mutation type.

Krabbe disease, one of the autosomal-recessive lysosomal storage disorders (LSDs), is caused by a deficiency of galactocerebrosidase (GALC) activity, resulting in the intracellular accumulation of psychosine, which is cytotoxic for neuronal cells. Genetically pathogenic mutations result in conformational changes in GALC and disrupt the lysosmal trafficking of cargos, which subsequently accumulate in the endoplasmic reticulum (ER). Recently, ER stress together with the activation of the unfolded protein response (UPR) has been suggested to play a key role in the pathogenesis of LSDs. In this study, we hence investigated whether the UPR is activated in Krabbe disease using COS-7 cells expressing pathogenic GALC mutants and skin fibroblasts (SFs) from Krabbe disease patients with various phenotypes, using a combination of semiquantitative and quantitative real-time polymerase chain reactions. We found that UPR activation in Krabbe disease depends on the mutations and cell types, and there is the possibility that multiple pathways, involving ER chaperones, inositol-requiring kinase 1, and protein kinase regulated by RNA-like ER kinase are activated by mutations associated with the infantile form. These results indicate that in Krabbe disease, each misfolded/unfolded protein evokes different UPR activation depending on the mutation, and that the activated pathways affect the phenotypes.

Exonic deletions in GALC are frequent in Japanese globoid-cell leukodystrophy patients.

Globoid-cell leukodystrophy is an autosomal-recessive lysosomal storage disorder. Single-base substitutions and small indel mutations in the GALC gene are common in Japanese patients. In this study, we identified three novel deletions, in exons 1, 8, and 11-12, in three patients using Multiplex Ligation-dependent Probe Amplification. We suggest that some patients in whom no or only a single pathogenic mutation is detected by Sanger sequencing may have exon deletions.