Background ADAM metallopeptidase with thrombospondin type 1 motif 3 ( ADAMTS3 ) is one of the causative genes for the Hennekam lymphangiectasia-lymphedema syndrome (HKLLS), an autosomal recessive genetic disorder. Here, we reported novel biallelic variants of ADAMTS3 in adult patients affected by HKLLS. Methods The variants were identified via whole-exome sequencing and SNP microarray and confirmed via Sanger sequencing. A minigene-based splicing assay assessed variant effects on splicing. A Pro-vascular endothelial growth factor C (Pro-VEGFC) processing assay evaluated mutant ADAMTS3 function. Results A novel heterozygous deletion of a 308-kb region spanning exons 1–3 of ADAMTS3 was detected in the two affected sisters with HKLLS and their mother. Additionally, a novel heterozygous variant (NM_014243.3:c.1352+5G>T: IVS9+5G>T) located near the splice junction of exon 9 in another allele was found in the two affected sisters. Minigene-based splicing assays revealed splicing abnormalities caused by the variant (IVS9+5G>T). The major splicing variant encoded an in-frame truncated protein. The Pro-VEGFC assay showed this truncated protein failed to mature VEGFC, essential for lymphangiogenesis. Conclusion This is the first report of a pathogenic splicing variant in ADAMTS3 , leading to HKLLS. ADAMTS3 should also be investigated in neonatal oedema. Our findings will broaden the variant spectrum and contribute to the understanding of the pathogenesis of HKLLS.

This study assesses the safety and efficacy of hepatocyte-like cell (HLC) infusion therapy derived from human embryonic stem cells as bridging therapy for neonatal-onset urea cycle disorders (UCD). The research includes both preclinical and clinical evaluations to determine the feasibility of HLC infusion as a therapeutic option for safer pediatric liver transplantation. Preclinical studies were conducted to validate the safety, biodistribution, and ammonia metabolism capabilities of HLCs using SCID mice models of UCD and extensive animal studies. In the clinical trial, five neonates with UCD received HLC infusions, intending to maintain metabolic stability and exceed a target weight of over 6 kg, which is considered necessary for safer liver transplantation. Preclinical studies demonstrated that HLCs successfully engrafted in the liver without adverse migration or tumor formation and effectively elongated survival. Clinically, all five neonates exceeded the target weight of 6 kg while maintaining metabolic stability and successfully bridging to transplantation. Post-transplantation follow-up revealed stable growth, metabolic control, and no neurological complications. The combined preclinical and clinical findings support HLC infusion as a viable bridge therapy for neonates with UCD, providing metabolic support to achieve safer weight thresholds for transplantation. While promising, careful monitoring remains essential, particularly for potential complications such as thrombus formation. jRCT, jRCT1090220412. Registered on 27 February 2019, https://jrct.niph.go.jp/en-latest-detail/jRCT1090220412 (originally registered in JMACCT (JMA-IIA00412)).

ETS2 repressor factor (ERF) is a member of the ETS family of transcriptional repressors downstream of ERK. Although germline truncated variants in ERF have been identified in individuals with Noonan-like syndrome with or without craniosynostosis, the clinical spectrum of ERF variant-positive individuals and the functional characterization of ERF variants are currently not fully understood. In this study, we identified one missense variant (p.G53R) and two truncating variants in ERF using whole exome sequencing (WES) in three individuals and one truncating variant using Sanger sequencing in one of 81 individuals with suspected Noonan syndrome without any pathogenic variants by targeted analysis in the previous study. Four Individuals with pathogenic ERF variants were diagnosed with Noonan-like syndrome, where craniosynostosis was not evident. Our investigation revealed that wild-type ERF undergoes nuclear-cytoplasmic shift, whereas truncated mutant ERF are predominantly localized in the nucleus. Moreover, R183* and G299Rfs variants lost their ability to repress the proliferation of osteoblast-like cells (MC3T3-E1). A luciferase assay examining the transcriptional activity of RUNX2 binding motifs indicated that the truncated variants were defective in their suppressive function. Further experimentation demonstrated that MC3T3-E1 cells expressing the p.G53R and three truncating variants induced ossification compared to the wild-type. These results suggest that loss-of-function mutations in ERF, which result in reduced ossification suppressor activity in MC3T3-E1 cells, can lead to craniofacial abnormalities in individuals with Noonan syndrome-like symptoms.

Rad50-interacting protein (RINT1) interacts with the endoplasmic reticulum (ER) tethering and SNARE complex, playing a central role in membrane trafficking and lipid metabolism. Loss-of-function variants of RINT1 have been related to episodic severe transaminitis with skeletal dysplasia or spastic paraplegia. We report two unrelated patients with recurrent markedly elevated aminotransferase triggered by fever, accompanied by coagulopathy and hyperammonemia. Liver biopsy revealed liver steatosis and bridging fibrosis in one patient, while the other displayed mild hepatocyte enlargement. Trio-whole-exome sequencing identified biallelic pathogenic RINT1 variants in the two patients. A novel missense variant [c.662 A > C, p.(His221Pro)] and a recurrent splice-site variant (c.1333+1 G > A) were identified in the first case. In the second case, a recurrent pathogenic RINT1 homozygous missense variant [c.1102 G > A, p.(Ala368Thr)] was identified. We investigated the pathogenicity of these variants through immunoprecipitation. Recombinant proteins produced from the mutant RINT1 transcript (p.His221Pro or p.Ala368Thr) displayed disrupted ER tether and SNARE interactions. Since the inhibition of ER-Golgi transport is associated with ER-stress activation, unfolded protein response (UPR)-related gene expression was investigated by qPCR. TIP20, a RINT1 homolog in Saccharomyces cerevisiae, is needed for autophagosome formation; therefore, an LC3-II turnover assay was performed and revealed disrupted autophagic flux. In addition, we created a fat-body-specific Rint1 knockdown in Drosophila. In the mutant larva, tissue atrophy and decreased lipid droplets in the fat body were observed. These results indicated that a loss of RINT1 function activated the UPR, impairs autophagy, and led to lipid storage abnormalities, contributing to the pathogenesis of liver disease.

Targeted genome editing has made significant advancements; however, safety and ethical issues have not been fully elucidated, resulting in strict control of the technique. We tested genome editing tools on gametes from a genetically humanized mouse model using a phenylketonuria (PKU) mouse model to gain insights into genome editing in human embryos. The human PKU mouse model PahhR111X mice was generated. The junctional region between exon 3 and intron 3 of Pah was replaced with a 120 bp corresponding human PAH sequence, including the pathogenic common variant c.331C > T in PahhR111X mice. PahhR111X mice successfully recapitulated the PKU phenotype and showed cognitive dysfunction and depressive-like behavior, which are observed in human patients with PKU. Genome editing was applied to fertilized eggs of PahhR111X mice utilizing sgRNA that targets the human sequence. Mice with the corrected allele exhibited normal serum phenylalanine levels. Through genome editing, we validated the utility of sgRNA. The genetically humanized mouse model suggested that germ-line genome editing of the pathogenic variant may be feasible for monogenic disorders by revealing the recovery of the phenotype; however, there are remaining issues with the tool, including its efficiency and accuracy. This genome editing protocol using a genetically humanized mouse model will provide insights for improving current issues and contribute to the establishment of heritable human genome editing protocols.

PURPOSE:To explore the frequency and positions of genetic mutations in CYP1B1 and FOXC1 in a Japanese population. STUDY DESIGN:Molecular genetic analysis. METHODS:Genomic DNA was extracted from 31 Japanese patients with childhood glaucoma (CG) from 29 families. We examined the CYP1B, FOXC1, and MYOC genes using Sanger sequencing and whole-exome sequencing (WES). RESULTS:For CYP1B1, we identified 9 families that harbored novel mutations, p.A202T, p.D274E, p.Q340*, and p.V420G; the remaining mutations had been previously reported. When mapped to the CYP1B1 protein structure, all mutations appeared to influence the enzymatic activity of CYP1B1 by provoking structural deformity. Five patients were homozygotes or compound heterozygotes, supporting the recessive inheritance of the CYP1B1 mutations in CG. In contrast, four patients were heterozygous for the CYP1B1 mutation, suggesting the presence of regulatory region mutations or strong modifiers. For the FOXC1 gene, we identified 3 novel mutations, p.Q23fs, p.Q70R, and p.E163*, all of which were identified in a heterozygous state. No mutation was found in the MYOC gene in these CG patients. All individuals with CYP1B1 and FOXC1 mutations were severely affected by early-onset CG. In the CYP1B1-, FOXC1-, and MYOC-negative families, we also searched for variants in the other candidate genes reported for CG through WES, but could not find any mutations in these genes. CONCLUSIONS:Our analyses of 29 CG families revealed 9 families with point mutations in the CYP1B1 gene, and four of those patients appeared to be heterozygotes, suggesting the presence of complex pathogenic mechanisms. FOXC1 appears to be another major causal gene of CG, indicating that panel sequencing of CYP1B1 and FOXC1 will be useful for diagnosis of CG in Japanese individuals.

Introduction: RRAS2, a member of the R-Ras subfamily of Ras-like low-molecular-weight GTPases, is considered to regulate cell proliferation and differentiation via the RAS/MAPK signaling pathway. Seven RRAS2 pathogenic variants have been reported in patients with Noonan syndrome; however, few functional analyses have been conducted. Herein, we report two patients who presented with a Noonan-like phenotype with recurrent and novel RRAS2 pathogenic variants (p.Gly23Val and p.Gly24Glu, respectively) and the results of their functional analysis.Materials and methods: Wild-type (WT) and mutant RRAS2 genes were transiently expressed in Human Embryonic Kidney293 cells. Expression of RRAS2 and phosphorylation of ERK1/2 were confirmed by Western blotting, and the RAS signaling pathway activity was measured using a reporter assay system with the serum response element-luciferase construct. WT and p.Gly23Val RRAS2 were expressed in Drosophila eye using the glass multiple reporter-Gal4 driver. Mutant mRNA microinjection into zebrafish embryos was performed, and the embryo jaws were observed.Results: No obvious differences in the expression of proteins WT, p.Gly23Val, and p.Gly24Glu were observed. The luciferase reporter assay showed that the activity of p.Gly23Val was 2.45 ± 0.95-fold higher than WT, and p.Gly24Glu was 3.06 ± 1.35-fold higher than WT. For transgenic flies, the p.Gly23Val expression resulted in no adults flies emerging, indicating lethality. For mutant mRNA-injected zebrafish embryos, an oval shape and delayed jaw development were observed compared with WT mRNA-injected embryos. These indicated hyperactivity of the RAS signaling pathway.Discussion: Recurrent and novel RRAS2 variants that we reported showed increased in vitro or in vivo RAS signaling pathway activity because of gain-of-function RRAS2 variants. Clinical features are similar to those previously reported, suggesting that RRAS2 gain-of-function variants cause this disease in patients.

Glycosylphosphatidylinositol (GPI)-anchored proteins are located at the cell surface by a covalent attachment between protein and GPI embedded in the plasma membrane. This attachment is catalyzed by GPI transamidase comprising five subunits (PIGK, PIGS, PIGT, PIGU, and GPAA1) in the endoplasmic reticulum. Loss of either subunit of GPI transamidase eliminates cell surface localization of GPI-anchored proteins. In humans, pathogenic variants in either subunit of GPI transamidase cause neurodevelopmental disorders. However, how the loss of GPI-anchored proteins triggers neurodevelopmental defects remains largely unclear. Here, we identified a novel homozygous variant of PIGK, NM_005482:c.481A > G,p. (Met161Val), in a Japanese female patient with neurodevelopmental delay, hypotonia, cerebellar atrophy, febrile seizures, hearing loss, growth impairment, dysmorphic facial features, and brachydactyly. The missense variant was found heterozygous in her father, but not in her mother. Zygosity analysis revealed that the homozygous PIGK variant in the patient was caused by paternal isodisomy. Rescue experiments using PIGK-deficient CHO cells revealed that the p.Met161Val variant of PIGK reduced GPI transamidase activity. Rescue experiments using pigk mutant zebrafish confirmed that the p.Met161Val variant compromised PIGK function in tactile-evoked motor response. We also demonstrated that axonal localization of voltage-gated sodium channels and concomitant generation of action potentials were impaired in pigk-deficient neurons in zebrafish, suggesting a link between GPI-anchored proteins and neuronal defects. Taken together, the missense p.Met161Val variant of PIGK is a novel pathogenic variant that causes the neurodevelopmental disorder.

The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. We analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective from the genomic data of 9,287 samples obtained by high-coverage whole-genome sequencing (WGS) by the National Center Biobank Network. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Haplotype analysis suggested increased allele frequencies for genes related to alcohol and fatty acid metabolism, which were reported as loci that had experienced positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to increase in the allele frequency; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production.

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.

Background: Allergic diseases were long considered to be complex multifactorial disorders. However, recent findings indicate that severe allergic inflammation can be caused by monogenic immune defects. Objectives: We sought to clarify the molecular pathogenesis of a patient with early-onset multiple allergic diseases, a high serum IgE level, hypereosinophilia, treatment-resistant severe atopic dermatitis with increased dermal collagen fiber deposition, and eosinophilic gastrointestinal disorder with numerous polypoid nodules. Methods: A missense variant in STAT6 was identified, and its function was examined using peripheral blood, transfected HEK293 cells, lymphoblastoid cell lines, and knock-in mice with the corresponding mutation. Results: Whole-exome sequencing identified a de novo heterozygous missense variant in signal transducer and activator of transcription 6 (STAT6) (p.Asp419Asn). Luciferase reporter assay revealed that the transcriptional activity of this STAT6 mutant was upregulated even without IL-4 stimulation. Phosphorylation of STAT6 was not observed in either the patient's TH2 cells or lymphoblastoid cell lines without stimulation, whereas it was induced more strongly in both by IL-4 stimulation compared with healthy controls. STAT6 protein was present in the nuclear fraction of the lymphoblastoid cell lines of the patient even in the absence of IL-4 stimulation. The patient's gastric mucosa showed upregulation of STAT6-, fibrosis-, and germinal center formation-related molecules. Some of the knock-in mice with the corresponding mutation spontaneously developed dermatitis with skin thickening and eosinophil infiltration. Moreover, serum IgE levels and mRNA expression of type 2 cytokines were increased in the knock-in mice-with or without development of spontaneous dermatitis-compared with the wild-type mice. Conclusions: A novel STAT6 gain-of-function variant is a potential cause of primary atopic disorders. (J Allergy Clin Immunol 2023;151:1402-9.)

Abstract Childhood glaucoma is a group of heterogeneous genetic disorders. The purpose of this study was to explore the genetic background in the Japanese population. Genomic DNA was extracted from 31 patients with childhood glaucoma from 29 families in the Japanese population. We screened the CYP1B1, FOXC1 and candidate genes using Sanger sequencing and whole-exome sequencing (WES). In the CYP1B1 gene, we identified nine mutations, of which four were novel. Almost all affected individuals had severe early-onset childhood glaucoma. In the FOXC1 gene, three novel mutations were identified in a heterozygous state. We next attempted to extract the candidate genes from the subjects showing negative results for two genes. The iterative filtering process by WES revealed 4 single-nucleotide variations (SNVs) in the PTPRF, SMPD4, VPS13B, and DHRS1 genes on autosomal chromosomes and 4 SNVs in the NHS, KCND1, BRWD3, and ENOX2 genes on the X chromosome. The CYP1B1 and FOXC1 genes are major causal genes of childhood glaucoma in Japanese families (30% and 10%, respectively), and WES results reveal the heterogeneity of the genetic background. Screening the CYP1B1 and FOXC1 genes is useful to ensure the proper diagnosis and adequate treatment of childhood glaucoma.

The identification of causative genetic variants for hereditary diseases has revolutionized clinical medicine and an extensive collaborative framework with international cooperation has become a global trend to understand rare disorders. The Initiative on Rare and Undiagnosed Diseases (IRUD) was established in Japan to provide accurate diagnosis, discover causes, and ultimately provide cures for rare and undiagnosed diseases. The fundamental IRUD system consists of three pillars: IRUD diagnostic coordination, analysis centers (IRUD-ACs), and a data center (IRUD-DC). IRUD diagnostic coordination consists of clinical centers (IRUD-CLs) and clinical specialty subgroups (IRUD-CSSs). In addition, the IRUD coordinating center (IRUD-CC) manages the entire IRUD system and temporarily operates the IRUD resource center (IRUD-RC). By the end of March 2021, 6301 pedigrees consisting of 18,136 individuals were registered in the IRUD. The whole-exome sequencing method was completed in 5136 pedigrees, and a final diagnosis was established in 2247 pedigrees (43.8%). The total number of aberrated genes and pathogenic variants was 657 and 1718, among which 1113 (64.8%) were novel. In addition, 39 novel disease entities or phenotypes with 41 aberrated genes were identified. The 6-year endeavor of IRUD has been an overwhelming success, establishing an all-Japan comprehensive diagnostic and research system covering all geographic areas and clinical specialties/subspecialties. IRUD has accurately diagnosed diseases, identified novel aberrated genes or disease entities, discovered many candidate genes, and enriched phenotypic and pathogenic variant databases. Further promotion of the IRUD is essential for determining causes and developing cures for rare and undiagnosed diseases.