Nanopore long-read sequencing analysis reveals ZIC1 dysregulation caused by a de novo 3q inversion with a breakpoint located 7 kb downstream of ZIC1.

Zic family member 1 (ZIC1), a gene located on chromosome 3q24, encodes a transcription factor with zinc finger domains that is essential for the normal development of the cerebellum. Heterozygous loss-of-function of ZIC1 causes Dandy-Walker malformation, while heterozygous gain-of-function leads to a multiple congenital anomaly syndrome characterized by craniosynostosis, brain abnormalities, facial features, and learning disability. In this study, we present the results of genetic analysis of a male patient with clinically suspected Gomez-Lopez-Hernandez syndrome. The patient displayed multiple congenital abnormalities, including bicoronal craniosynostosis, characteristic facial features, cerebellar malformation with rhombencephalosynapsis, and temporal alopecia, and a de novo inversion of chromosome 3q. Breakpoint analysis using a Nanopore long-read sequencer revealed a breakpoint in the distal centromere of 3q24 located 7 kb downstream of the 3' untranslated region of ZIC1. On the basis of the clinical similarities, we concluded that the abnormalities in this patient were caused by the transcriptional dysregulation of ZIC1. We hypothesize the underlying molecular mechanisms of transcriptional dysregulation of ZIC1 such as the abnormalities in topologically associated domains encompassing ZIC1. This study highlights the usefulness of long-read sequencing in the analysis of de novo balanced chromosomal abnormalities.

Complex congenital cardiovascular anomaly in a patient with AGO1-associated disorder.

Pathogenic AGO1 variants have been associated with neurodevelopmental disorders, including autism spectrum disorder, developmental delay, intellectual disability, and dysmorphic facial appearance. In mammalian models, defects in microRNA (miRNA) biogenesis are associated with congenital heart disease and dilated cardiomyopathy. We describe the case of a patient with partial anomalous pulmonary venous return, hypoplastic left lung, bilateral pulmonary sequestration, and dilated myocardiopathy. We identified a de novo pathogenic variant of AGO1, which encodes an Argonaute protein forming a gene-silencing complex with microRNAs. The patient was diagnosed with dilated cardiomyopathy with no apparent cause at 3 years of age. She was started on enalapril and carvedilol, and her heart failure was well controlled. We expanded the AGO1-associated phenotype to include complex congenital cardiovascular anomaly and dilated cardiomyopathy in humans.

Different Types of Myocardial Injury due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Variant.

Coronavirus disease 2019 (COVID-19) associated myocardial injury was caused by various mechanisms. We herein describe 2 cases presenting different types of myocardial injury due to Omicron variant. In both patients, diffuse reduced left ventricular (LV) wall motion in transthoracic echocardiography, electrocardiographic abnormality, and elevated myocardial enzymes were demonstrated. In addition, cardiovascular magnetic resonance (CMR) findings fulfilled the 2018 Lake Louise Criteria (LLC) for myocarditis. However, histological findings in 1 patient showed inflammatory cell infiltration with myocyte degeneration, while those in the other showed interstitial edema without inflammatory cell infiltration. Histological findings were crucial for a differential diagnosis of myocardial injury due to Omicron variant.

[Giant Mature Cystic Teratoma Causing Loss of Consciousness before Surgery].

A 30-year-old woman who presented loss of consciousness was diagnosed as having large anterior mediastinal tumor. Computed tomography (CT) showed a 17.0×13.0×7.3 cm cystic mass with internal calcification in the anterior mediastinum that was markedly compressing the heart, great vessels, trachea and bronchi. A mature cystic teratoma was suspected, and the mediastinal tumor was resected through a median sternotomy. At the induction of anesthesia to prevent the development of the respiratory and circulatory collapse, the patient was consciously intubated under the right lateral decubitus position while preparing for percutaneous cardiopulmonary support by cardiac surgeons, and the surgery was safely performed. The tumor was pathologically diagnosed as a mature cystic teratoma, and symptoms such as loss of consciousness have disappeared.

Divergent variant patterns among 19 patients with Rubinstein-Taybi syndrome uncovered by comprehensive genetic analysis including whole genome sequencing.

Rubinstein-Taybi syndrome (RSTS) is characterized by dysmorphic facial features, broad thumbs, and intellectual disability. CREB-binding protein (CREBBP) or E1A-binding protein P300 (EP300) are causative genes. To elucidate the underlying genetic and genomic architecture related to the RSTS phenotype, we performed comprehensive genetic analysis targeting CREBBP and/or EP300 in 22 clinically diagnosed patients. During the 11-year study period, we used several analysis methods including high-resolution melting, array-based comparative genomic hybridization, panel-based exome sequencing, whole exome sequencing, and whole genome sequencing (WGS). We identified the causative variants in 19 patients (86.3%), but they were variable and complex, so we must combine multiple analysis methods. Notably, we found genetic alterations in the non-coding regions of two patients (10.5%, 2/19): scattered deletions including a partial 5'-untranslated region of CREBBP in one patient (all coding exons were intact), and a deep 229-bp intronic deletion in another patient, resulting in a splicing error. Furthermore, we identified rare clinical findings: two patients with an EP300 variant showed abnormal development of the neural tube, and one patient with a CREBBP variant had anorectal atresia with a cloaca. Our findings expand the allelic heterogeneity of RSTS, underscore the utility of comprehensive genetic analysis, and suggest that WGS may be a practical diagnostic strategy.

Analysis of the Persistence and Particle Size Distributional Shift of Sperm-Derived Environmental DNA to Monitor Jack Mackerel Spawning Activity.

Environmental DNA (eDNA) analysis holds great promise as an efficient and noninvasive method to monitor not only the distribution of organisms but also their spawning activity. In eDNA analysis-based monitoring of spawning activity, the detection of sperm-derived eDNA is a key point; however, its characteristics and dynamics are completely unknown. The present study focuses on the persistence and particle size distribution (PSD) of eDNA derived from the sperm of Japanese jack mackerel. First, we investigated the time-dependent degradation and the PSD of sperm-derived eDNA by artificially adding sperm to seawater. Next, we kept fish in tanks and examined the changes in eDNA concentration and PSD before and after spawning. The results of two experiments showed that the degradation of sperm-derived eDNA proceeded rapidly, with PSD shifting to a smaller size regardless of the DNA region (Cyt b or ITS1). Additionally, it was shown that the nuclei and mitochondria released from sperm through degradation had a size distribution that was not simply dependent on each organelle size. These results will contribute to elucidating the characteristics and dynamics of eDNA specifically during the spawning season and to further developing eDNA analysis as a powerful tool for the monitoring of spawning activity.

Rothmund-Thomson syndrome investigated by two nationwide surveys in Japan.

BACKGROUND: Rothmund-Thomson syndrome (RTS) is an autosomal recessive genetic disorder characterized by poikiloderma of the face, small stature, sparse scalp hair, juvenile cataract, radial aplasia, and predisposition to cancers. Due to the rarity of RTS, the situation of patients with RTS in Japan has not been elucidated. METHODS: In 2010 and 2020, following the results of a primary questionnaire survey, a secondary questionnaire survey on RTS was conducted nationwide to investigate the number of RTS cases and their associated skin lesions, bone lesions, other clinical features, and quality of life in Japan. RESULTS: In 2010 and 2020, 10 and eight patients with RTS were recruited, respectively. Skin lesions such as poikiloderma, erythema, pigmentation, and abnormal scalp hair were observed in almost all cases. Bone lesions were observed in four cases in the 2010 and 2020 surveys, respectively. Two cases had mutations in the RECQL4 gene in the 2020 survey. CONCLUSIONS: Two nationwide surveys have shown the actual situation of patients with RTS in Japan. Cutaneous and bone manifestations are important for the diagnosis of RTS. However, many patients have no RECQL4 mutations. The novel causative gene of RTS should be further elucidated.

Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling.

Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.

Update of the genotype and phenotype of KMT2D and KDM6A by genetic screening of 100 patients with clinically suspected Kabuki syndrome.

Kabuki syndrome is characterized by a variable degree of intellectual disability, characteristic facial features, and complications in various organs. Many variants have been identified in two causative genes, that is, lysine methyltransferase 2D (KMT2D) and lysine demethylase 6A (KDM6A). In this study, we present the results of genetic screening of 100 patients with a suspected diagnosis of Kabuki syndrome in our center from July 2010 to June 2018. We identified 76 variants (43 novel) in KMT2D and 4 variants (3 novel) in KDM6A as pathogenic or likely pathogenic. Rare variants included a deep splicing variant (c.14000-8C>G) confirmed by RNA sequencing and an 18% mosaicism level for a KMT2D mutation. We also characterized a case with a blended phenotype consisting of Kabuki syndrome, osteogenesis imperfecta, and 16p13.11 microdeletion. We summarized the clinical phenotypes of 44 patients including a patient who developed cervical cancer of unknown origin at 16 years of age. This study presents important details of patients with Kabuki syndrome including rare clinical cases and expands our genetic understanding of this syndrome, which will help clinicians and researchers better manage and understand patients with Kabuki syndrome they may encounter.

A novel gene (FAM20B encoding glycosaminoglycan xylosylkinase) for neonatal short limb dysplasia resembling Desbuquois dysplasia.

Desbuquois dysplasia (DBQD) is an autosomal recessive heterogeneous disorder characterized by joint laxity and skeletal changes, including a distinctive monkey-wrench appearance of the femora, advanced carpal ossification, and abnormal patterning of the preaxial digits. Two genes for DBQD (CANT1 encoding calcium-activated nucleotidase-1 and XYLT1 encoding xylosyltransferase-1) have been reported. We propose a novel gene for neonatal short limb dysplasia resembling DBQD, based on the phenotype and genotype of two affected siblings. The affected boy and girl died in early infancy and shortly after birth, respectively. The clinical hallmarks included mid-face hypoplasia, thoracic hypoplasia with respiratory failure, very short stature (approximately -7 SD of birth length) with mesomelic shortening of the limbs, and multiple dislocations of the large joints. Radiological examinations showed prominent lesser trochanter, flared metaphyses of the long bones, and joint dislocations. The affected boy had preaxial digital hypoplasia, and the affected girl showed overlapping and syndactyly of the preaxial digits. Molecular analyses of the girl showed compound heterozygous variants in FAM20B (NM_014864: c.174_178delTACCT p.T59Afs*19/c.1038delG p.N347Mfs*4). FAM20B encodes glycosaminoglycan xylosylkinase, which acts downstream of xylosyltransferase-1. Given the fact that FAM20B deficiency causes skeletal phenotypes in mice and zebrafish, these variants are highly probable to be pathogenic.

Particle Size Distribution of Environmental DNA from the Nuclei of Marine Fish.

Environmental DNA (eDNA) analyses have enabled a more efficient surveillance of species distribution and composition than conventional methods. However, the characteristics and dynamics of eDNA (e.g., origin, state, transport, and fate) remain unknown. This is especially limited for the eDNA derived from nuclei (nu-eDNA), which has recently been used in eDNA analyses. Here, we compared the particle size distribution (PSD) of nu-eDNA from Japanese Jack Mackerel (Trachurus japonicus) with that of mt-eDNA (eDNA derived from mitochondria) reported in previous studies. We repeatedly sampled rearing water from the tanks under multiple temperatures and fish biomass levels, and quantified the copy numbers of size-fractioned nu-eDNA. We found that the concentration of nu-eDNA was higher than that of mt-eDNA at 3-10 µm size fraction. Moreover, at the 0.8-3 µm and 0.4-0.8 µm size fractions, eDNA concentrations of both types increased with higher temperature and their degradation tended to be suppressed. These results imply that the production of eDNA from large to small size fractions could buffer the degradation of small-sized eDNA, which could improve its persistence in water. Our findings will contribute to refine the difference between nu- and mt-eDNA properties, and assist eDNA analyses as an efficient tool for the conservation of aquatic species.

Biomass-dependent emission of environmental DNA in jack mackerel Trachurus japonicus juveniles.

Environmental DNA (eDNA) from juvenile jack mackerel Trachurus japonicus was detected in tanks with 1, 3, 10, or 30 individuals per tank. Quantitative PCR using a set of species-specific primers and a probe revealed that the concentration of eDNA increased almost linearly with the density of fish. The coefficient of determination (R2 ) in the linear regression was lower than values previously reported for freshwater fishes in similar settings.

[Metastatic Lung Tumor from Papillary Thyroid Carcinoma Suspected of Primary Lung Cancer;Report of Two Cases].

Radiological finding of pulmonary metastasis of thyroid cancer is generally known to be multiple small nodular shadow. We experienced 2 cases of lung solitary tumor, which were suspected of primary lung cancer as differential diagnosis. Patient 1:A 67-year-old man;the tumor obstructed subsegmental bronchus (B10) of the right lobe, and pathological diagnosis by transbronchial biopsy was adeno-squamous carcinoma. Fluoro-2-deoxy-D-glucose (FDG) positron emission tomography (PET) showed abnormal uptake in the tumor and also in the left lobe of his thyroid gland, but no malignant findings were found by the fine-needle aspiration cytology from the thyroid gland. Patient 2:A 51-year-old woman;she had a lobulated nodule in the left lower lobe, which was diagnosed as adenocarcinoma. She had undergone an operation for thyroid cancer about 30 years earlier, but after the operation, there has been no recurrence. In both cases, primary lung cancer were suspected and the tumors were resected surgically. By immunohistochemistry, both tumors were diagnosed as pulmonary metastases from papillary thyroid carcinoma.

A newly developed surgeon-controlled suction device in robotic-assisted thoracoscopic surgery.

INTRODUCTION: Assistant surgeons usually clean the surgical field with a suction cannula in robotic-assisted surgery. This manipulation requires skill and experience to avoid interfering with the operation of the console surgeon. Recently, we created a new suction device that a console surgeon can manipulate with the robotic arms. MATERIALS AND SURGICAL TECHNIQUE: A small metal suction tip with as a lumen and small side pores for suction and can be connected to a silicone tube connected to wall suction. The tip of the silicone tube can be grasped with robotic forceps and used for organ retraction as well as suction. The suction device has been used in eight lung lobectomy cases and four lung segmentectomy cases to date. There were no major difficulties related to the new suction device except for metal tip disconnection and blood clots clogging. DISCUSSION: Our newly developed surgeon-controlled suction device is inexpensive, easy to handle, and useful for suction, blunt dissection, and organ retraction in robotic-assisted thoracoscopic surgery, especially when performing lymph node dissection.

Cdc48 and its co-factor Ufd1 extract CENP-A from centromeric chromatin and can induce chromosome elimination in the fission yeast Schizosaccharomyces pombe.

CENP-A determines the identity of the centromere. Because the position and size of the centromere and its number per chromosome must be maintained, the distribution of CENP-A is strictly regulated. In this study, we have aimed to understand mechanisms to regulate the distribution of CENP-A (Cnp1SP) in fission yeast. A mutant of the ufd1+ gene (ufd1-73) encoding a cofactor of Cdc48 ATPase is sensitive to Cnp1 expressed at a high level and allows mislocalization of Cnp1. The level of Cnp1 in centromeric chromatin is increased in the ufd1-73 mutant even when Cnp1 is expressed at a normal level. A preexisting mutant of the cdc48+ gene (cdc48-353) phenocopies the ufd1-73 mutant. We have also shown that Cdc48 and Ufd1 proteins interact physically with centromeric chromatin. Finally, Cdc48 ATPase with Ufd1 artificially recruited to the centromere of a mini-chromosome (Ch16) induce a loss of Cnp1 from Ch16, leading to an increased rate of chromosome loss. It appears that Cdc48 ATPase, together with its cofactor Ufd1 remove excess Cnp1 from chromatin, likely in a direct manner. This mechanism may play a role in centromere disassembly, a process to eliminate Cnp1 to inactivate the kinetochore function during development, differentiation, and stress response.

Development of a Manufacturing Process toward the Convergent Synthesis of the COVID-19 Antiviral Ensitrelvir.

We describe the development of the practical manufacturing of Ensitrelvir, which was discovered as a SARS-CoV-2 antiviral candidate. Scalable synthetic methods of indazole, 1,2,4-triazole and 1,3,5-triazinone structures were established, and convergent couplings of these fragments enabled the development of a concise and efficient scale-up process to Ensitrelvir. In this process, introducing a meta-cresolyl moiety successfully enhanced the stability of intermediates. Compared to the initial route at the early research and development stage, the overall yield of the longest linear sequence (6 steps) was improved by approximately 7-fold. Furthermore, 9 out of the 12 isolated intermediates were crystallized directly from each reaction mixture without any extractive workup (direct isolation). This led to an efficient and environmentally friendly manufacturing process that minimizes waste of organic solvents, reagents, and processing time. This practical process for manufacturing Ensitrelvir should contribute to protection against COVID-19.

Delineation of a Phenotype Caused by a KAT6B Missense Variant Not Resembling Say-Barber-Biesecker-Young-Simpson and Genitopatellar Syndromes.

Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS) and genitopatellar syndrome (GPS) are caused by variants of lysine acetyltransferase 6B (KAT6B). These variants tend to occur in the terminal exons of KAT6B. Here, we report a patient with global developmental delay, intellectual disability, autistic behavior, muscular hypotonia, facial dysmorphism, and seizures caused by a novel missense variant in exon 7 of KAT6B. The patient showed a phenotype differing from those of SBBYSS and GPS. We also report patients with missense variants in the proximal exons of KAT6B showing dysmorphic features and autistic behavior not resembling the characteristics of SBBYSS and GPS. Missense variants in the proximal exons of KAT6B may have a dominant negative effect or cause gain of function, leading to unique phenotypes not resembling those of SBBYSS and GPS.

A Case of NAA10-related Syndrome With Prolonged QTc Treated With a Subcutaneous Implantable Cardioverter Defibrillator After Ventricular Fibrillation.

NAA10 is an enzyme involved in the N-terminal acetylation of proteins. NAA10-related syndrome is caused by a pathogenic variant of NAA10 on X chromosome, resulting in several phenotypes, including mental retardation, hypotonia, growth retardation, and various external malformations, with varying degrees of severity. With regard to cardiac diseases, hypertrophic cardiomyopathy is a possible complication. Some mutations are also associated with long QT syndrome. Herein, we describe the case of a 7-year-old boy with a novel NAA10 mutation who experienced cardiopulmonary arrest possibly due to long QT syndrome and was implanted with a subcutaneous implantable cardioverter defibrillator.

La NAA10 est une enzyme qui intervient dans l'acétylation N-terminale des protéines. Le syndrome lié au gène NAA10 est causé par un variant pathogène du NAA10 sur le chromosome X qui entraîne plusieurs phénotypes, comme une déficience intellectuelle, une hypotonie, un retard de croissance ou différentes malformations externes, et ce, à divers degrés de sévérité. En ce qui concerne les maladies cardiaques, une cardiomyopathie hypertrophique est une complication possible. Certaines mutations sont également associées au syndrome du QT long. Nous décrivons ici le cas d'un garçon âgé de sept ans qui présente une nouvelle mutation du gène NAA10 et qui a fait un arrêt cardiorespiratoire, possiblement en raison d'un syndrome du QT long. L'enfant a reçu un défibrillateur cardiaque implantable sous-cutané.

Persistent Hyperplastic Primary Vitreous with Microphthalmia and Coloboma in a Patient with Okur-Chung Neurodevelopmental Syndrome.

Okur-Chung neurodevelopmental syndrome is a rare autosomal dominant disorder caused by pathogenic variants in CSNK2A1, which encodes the alpha 1 catalytic subunit of -casein kinase II. This syndrome is characterized by intellectual disability, developmental delay, and multisystemic -abnormalities including those of the brain, extremities, and skin as well as cardiovascular, gastrointestinal, and immune systems. In this study, we describe a 5-year-old boy with a de novo novel nonsense variant in CSNK2A1, NM_001895.3:c.319C>T (p.Arg107*). He showed bilateral persistent hyperplastic primary vitreous with microphthalmia, lens dysplasia, and coloboma. Ocular manifestations are very rare in this syndrome, and this study expands the spectrum of the clinical presentations of this syndrome.

A solitary pulmonary nodule caused by Mycobacterium avium with pleural effusion and pleuritis after transbronchial biopsy: a case report.

BACKGROUND: Pleural effusion and pleuritis are uncommon manifestations of Mycobacterium avium complex pulmonary disease. Pleuritis caused by Mycobacterium avium complex pulmonary disease presenting as a solitary pulmonary nodule is extremely rare. The pathogenesis of Mycobacterium avium complex pleuritis has not been elucidated. However, it has been suggested that secondary spontaneous pneumothorax from Mycobacterium avium complex pulmonary disease is one of the causes of Mycobacterium avium complex pleuritis. CASE PRESENTATION: A 67-year-old Japanese woman who presented with a solitary pulmonary nodule developed a transient pneumothorax after transbronchial biopsy. A definitive diagnosis of solitary pulmonary nodule could not be made on bronchoscopy, so video-assisted thoracoscopic surgery was performed 1 month after bronchoscopy. On the day of hospitalization for the procedure, a left-sided pleural effusion appeared on a chest radiograph. Thickening of the parietal and visceral pleura and numerous scattered white small granules were seen on thoracoscopy. Histologic examination of the resected left lower lobe and a biopsy of the parietal pleura showed Mycobacterium avium complex solitary pulmonary nodule and Mycobacterium avium complex pleuritis. CONCLUSION: Iatrogenic pneumothorax can be a cause of pleuritis in a patient with Mycobacterium avium complex pulmonary disease. Clinicians should watch for the appearance of secondary pleuritis after transbronchial biopsy even in a patient with localized disease such as Mycobacterium avium complex solitary pulmonary nodule.