研究者詳細 - 宮　冬樹

論文 - 宮　冬樹

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An organoid library of human esophageal squamous cell carcinomas (ESCCs) uncovers the chemotherapy-resistant ESCC features.

Nakagawa S, Sato T, Ohashi E, Kajita M, Miya F, Yamamoto K, Yotsumata H, Yamaguchi K, Nakajima Y, Miura A, Kinugasa Y, Ohteki T

Communications biology 8 （ 1 ） 507 2025年04月

Esophageal squamous cell carcinoma (ESCC) is a deadly cancer with a poor prognosis and a high recurrence rate after chemotherapy, posing a significant clinical challenge. To elucidate the molecular basis of chemotherapy (chemo)-resistance and to develop methods to effectively eliminate chemo-resistant tumor clones, we established an ESCC organoid (ESCCO) library from 24 ESCC patients of various stages, ages, and treatments. These ESCCOs faithfully recapitulate the oncogenic mutations observed in the original ESCC tissues and manifest tumorigenic properties when xenografted. The ESCCOs respond differently to cisplatin and 5-fluorouracil, chemotherapeutic agents commonly used to treat ESCC patients, with 7 ESCCOs exhibiting potent chemo-resistance. Notably, the chemo-resistant ESCCOs show higher genes involved in antioxidant stress response pathways and more accessible chromatin at their loci than the sensitive ESCCOs. These genes can serve as valuable biomarkers to stratify chemo-resistant ESCCs in histopathological specimens. Through drug screening using the ESCCO library, we reveal that fedratinib effectively induces cell death in chemo-resistant ESCCOs. Collectively, our human ESCCO model offers novel insights into the mechanism of chemo-resistance in ESCCs, which is critical for developing effective therapeutic approaches to eradicate the recurrence of ESCCs.

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Effective calcineurin inhibitor treatment in adult-onset steroid-resistant nephrotic syndrome with a novel splice donor site variant of TRPC6: a case report.

Nagasaka T, Uchiyama K, Hama EY, Kojima D, Kaneko K, Yoshimoto N, Yasuda I, Yamada M, Miya F, Suzuki H, Tajima T, Yamaguchi S, Hayashi K, Kanda T, Hashiguchi A, Kosaki K, Itoh H

CEN case reports 14 （ 2 ） 208 - 216 2025年04月

Transient receptor potential canonical 6 (TRPC6) variants, which were initially detected in adult-onset familial focal segmental glomerulosclerosis (FSGS), were also identified in pediatric-onset one. Here, we present a patient with adult-onset steroid-resistant nephrotic syndrome (SRNS) who harbored a likely pathogenic TRPC6 variant and partially responded to calcineurin inhibitors (CNIs). A 44-year-old woman with stable rheumatoid arthritis, systemic lupus erythematosus, and Sjögren’s syndrome was presented with nephrotic syndrome. Her renal biopsy results showed minor glomerular abnormalities. Upon admission, she was treated with steroids for around 4 weeks, but it was ineffective. After 1–2 weeks of cyclosporine A (CyA) administration, urine output increased, renal function improved without a decrease in proteinuria, and she was discharged. Her renal function was maintained for 2 months, but after a CyA dose reduction, she was again admitted to the hospital due to relapsing edema, decreased urine output, and worsening renal function. CyA was replaced by tacrolimus (TAC). A second renal biopsy showed nearly the same findings as the first except for tubulointerstitial lesions. After 1–2 weeks of TAC administration, urine output increased, and renal function improved. However, urinary protein levels did not decrease as before. After discharge, a whole exome analysis revealed a heterozygous splice donor site variant NM_004621.6;c.2644 + 1G > A in TRPC6. Genetic testing identified a novel splice donor site variant of TRPC6 in a patient with adult-onset SRNS, which prevented unnecessary steroid continuation. The safety and efficacy of CNI in TRPC6 glomerulopathy must be evaluated in future larger studies with longer follow-up.

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BED-Craft for nanopore adaptive sampling: a tool for generating bed files with gene names as input data for enrichment sequencing.

Miya F, Kosaki K

BMC research notes 18 （ 1 ） 79 2025年02月

Objective: Adaptive sampling, a nanopore sequencing method that enriches regions of interest (ROI), is cost-effective and useful. However, the process of defining targeted regions and creating the corresponding definition file (.bed file) are time-consuming and laborious. To simplify this process, we have developed a tool to easily create a.bed file for adaptive sampling directly from gene names. Results: The tool is freely available on GitHub at https://github.com/medicalbioinfo/BED-Craft. The input is a text file containing one or more gene names (symbols), and even with a large number of input genes (e.g., thousands), the resulting.bed file is generated in less than a second. The length of the buffer region added upstream and downstream of the ROI is designed to account for genome strand orientation, ensuring efficient adaptive sampling. The buffer length can also be modified by the user. The tool supports the genomes of human hg19, hg38, T2T-CHM13, and other species. For researchers unfamiliar with command-line input, a GUI version of the tool is also available at https://keio-cmg.jp/BED-Craft/. This easy-to-use.bed file generation tool enables adaptive sampling by easily changing the target genes of interest in nanopore sequencing, and provide great benefits to researchers and diagnostic laboratories.

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Gene-based Hardy-Weinberg equilibrium test using genotype count data: application to six types of cancers.

Nishino J, Miya F, Kato M

BMC genomics 26 （ 1 ） 124 2025年02月

Background: An alternative approach to investigate associations between genetic variants and disease is to examine deviations from the Hardy–Weinberg equilibrium (HWE) in genotype frequencies within a case population, instead of case–control association analysis. The HWE analysis requires disease cases and demonstrates a notable ability in mapping recessive variants. Allelic heterogeneity is a common phenomenon in diseases. While gene-based case–control association analysis successfully incorporates this heterogeneity, there are no such approaches for HWE analysis. Therefore, we proposed a gene-based HWE test (gene-HWT) by aggregating single-nucleotide polymorphism (SNP)-level HWE test statistics in a gene to address allelic heterogeneity. Results: This method used only genotype count data and publicly available linkage disequilibrium information and has a very low computational cost. Extensive simulations demonstrated that gene-HWT effectively controls the type I error at a low significance level and outperforms SNP-level HWE test in power when there are multiple causal variants within a gene. Using gene-HWT, we analyzed genotype count data from a genome-wide association study of six cancer types in Japanese individuals and suggest DGKE and ANO3 as potential germline factors in colorectal cancer. Furthermore, FSTL4 was suggested through a combined analysis across the six cancer types, with particularly notable associations observed in colorectal and prostate cancers. Conclusions: These findings indicate the potential of gene-HWT to elucidate the genetic basis of complex diseases, including cancer.

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Comparative analysis of tongue cancer organoids among patients identifies the heritable nature of minimal residual disease.

Sase M, Sato T, Sato H, Miya F, Zhang S, Haeno H, Kajita M, Noguchi T, Mori Y, Ohteki T

Developmental cell 60 （ 3 ） 396 - 413.e6 2025年02月

ISSN 1534-5807

The relapse of tongue cancer (TC) after chemotherapy is caused by minimal residual disease (MRD), which is a few remaining cancer cells after chemotherapy. To understand the mechanism of MRD in TC, we created a library of TC organoids (TCOs) from 28 untreated TC patients at diverse ages and cancer stages. These TCOs reproduced the primary TC tissues both in vitro and in a xenograft model, and several TCO lines survived after cisplatin treatment (chemo-resistant TCOs). Of note, the chemo-resistant TCOs showed “heritable” embryonic diapause-like features before treatment and activation of the autophagy and cholesterol biosynthetic pathways. Importantly, inhibiting these pathways with specific inhibitors converted the chemo-resistant TCOs into chemo-sensitive TCOs. Conversely, autophagy activation with mTOR inhibitors conferred chemo-resistance on the chemo-sensitive TCOs. This unique model provides insights into the mechanism of MRD formation in TCs, leading to effective therapeutic approaches to reduce the recurrence of TC.

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Brain calcification in congenital heart defects and ectodermal dysplasia (CHDED).

Watanabe D, Hasebe Y, Yagasaki H, Nakato D, Yamada M, Suzuki H, Kono Y, Sunaga Y, Yoshizawa M, Narusawa H, Miya F, Takenouchi T, Inukai T, Kosaki K

European journal of medical genetics 73 104992 2025年02月

ISSN 1769-7212

Congenital Heart Defect and Ectodermal Dysplasia (CHDED) is an autosomal dominant disorder caused by the PRKD1 gene. CHDED is characterized by heart defects and ectodermal dysplasia. To date, eight patients with CHDED have been described. Calcifications were present in three patients with CHDED. (two patients; renal calcifications, one patient; brain calcifications). The organ distribution of calcifications in CHDED has been unclear. We report here another patient with CHDED and brain calcifications. The patient was a 9-month-old Japanese girl. She presented with heart defects and ectodermal dysplasia. At 6 months of age, she had generalized seizures, and a CT scan revealed calcifications in the bilateral deep cerebral white matter. The seizures resolved with the administration of levetiracetam. The patient had a de novo, heterozygous pathogenic variant, c.1808G > A, p.(Arg603His), in the PRKD1 gene. Together with the previously reported patients mentioned above, we demonstrated the role of the PRKD1 variant in brain calcification. We propose that PRKD1 and two genes, ITGB2 and JAM2, which are known to be associated with brain calcification, act through a common signaling pathway abnormality. In support of our hypothesis, there are some experimental results that link PRKD1 and JAM2. PRKD1 functions with the integrin ITGB2 as a partner. JAM2, which is associated with brain calcification and is critical for maintaining of the tight junction of the endothelial cells, interacts with integrins including ITGB2. Therefore, PRKD1 could lead to the pathological phenotype of brain calcification.

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Vigabatrin投与が難治West症候群に有効であった先天性眼球異常を伴うCOL4A1関連疾患の1例

丸金拓蔵, 兵頭勇紀, 柴田敬, 秋山倫之, 高見容子, 宮冬樹, 加藤光広, 小林勝弘

脳と発達（(一社)日本小児神経学会） 57 （ 1 ） 29 - 33 2025年01月

ISSN 0029-0831

COL4A1変異は,IV型コラーゲンの異常により血管などの基底膜を障害し,多臓器に多彩な症状を呈する.てんかんを合併した場合は難治なことが多い.症例は5歳4ヵ月の男児.先天性の眼病変を認め,Peters異常と診断された.発達遅滞を伴い,頭部画像所見に異常を認めた.10ヵ月時にてんかん性スパズムを発症し,West症候群と診断された.ACTH療法を含む初期治療で発作は一時消失したが再発した.1歳9ヵ月時にvigabatrin(VGB)を眼病変の悪化を考慮し慎重に導入し,VGBは適量(100mg/kg/day)で発作は抑制された.眼科的検査を複数回実施し,網膜電図に異常は認めなかった.3歳6ヵ月にVGBを中止後も発作は抑制されている.COL4A1にde novoの既知の病的変異NM_001845.6:c.3620G>A,p.(G1207E)を認めた.COL4A1関連疾患の難治West症候群に対しては先天性眼球異常を伴う例でもVGBを試みる意義があると考えられた.(著者抄録)

Genetic landscape in undiagnosed patients with syndromic hearing loss revealed by whole exome sequencing and phenotype similarity search.

Mutai H, Miya F, Nara K, Yamamoto N, Inoue S, Murakami H, Namba K, Shitara H, Minami S, Nakano A, Arimoto Y, Morimoto N, Kawasaki T, Wasano K, Fujioka M, Uchida Y, Kaga K, Yamazawa K, Kikkawa Y, Kosaki K, Tsunoda T, Matsunaga T

Human genetics 144 （ 1 ） 93 - 112 2025年01月

ISSN 0340-6717

There are hundreds of rare syndromic diseases involving hearing loss, many of which are not targeted for clinical genetic testing. We systematically explored the genetic causes of undiagnosed syndromic hearing loss using a combination of whole exome sequencing (WES) and a phenotype similarity search system called PubCaseFinder. Fifty-five families with syndromic hearing loss of unknown cause were analyzed using WES after prescreening of several deafness genes depending on patient clinical features. Causative genes were identified in 22 families, including both established genes associated with syndromic hearing loss (PTPN11, CHD7, KARS1, OPA1, DLX5, MITF, SOX10, MYO7A, and USH2A) and those associated with nonsyndromic hearing loss (STRC, EYA4, and KCNQ4). Association of a DLX5 variant with incomplete partition type I (IP-I) anomaly of the inner ear was identified in a patient with cleft lip and palate and acetabular dysplasia. The study identified COL1A1, CFAP52, and NSD1 as causative genes through phenotype similarity search or by analogy. ZBTB10 was proposed as a novel candidate gene for syndromic hearing loss with IP-I. A mouse model with homozygous Zbtb10 frameshift variant resulted in embryonic lethality, suggesting the importance of this gene for early embryonic development. Our data highlight a wide spectrum of rare causative genes in patients with syndromic hearing loss, and demonstrate that WES analysis combined with phenotype similarity search is a valuable approach for clinical genetic testing of undiagnosed disease.

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Accumulation of ether phospholipids in induced pluripotent stem cells and oligodendrocyte-lineage cells established from patients with Sjögren-Larsson syndrome.

Yamaguchi Y, Okuno H, Tokuoka S, Kita Y, Sanosaka T, Kohyama J, Kurosawa K, Sakai N, Miya F, Takahashi T, Kosaki K, Okano H

Congenital anomalies 65 （ 1 ） e12587 2025年01月

ISSN 0914-3505

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Effective treatment with vigabatrin for intractable West syndrome in a case of COL4A1-related disorder with congenital ocular anomalies

Marukane T., Hyodo Y., Shibata T., Akiyama T., Takami Y., Miya F., Kato M., Kobayashi K.

No To Hattatsu 57 （ 1 ） 29 - 33 2025年

ISSN 00290831

Aberrations in the COL4A1 gene lead to the faulty secretion of type IV collagen, resulting in damage to vascular basement membrane and various symptoms affecting multiple organs. Epilepsy associated with COL4A1-related disorder is often challenging to treat. We report a 5-year-old boy with developmental delay, congenital ocular abnormalities diagnosed with Peters anomaly, and abnormal neuroimaging findings. The patient had epileptic spasms starting at the age of 10 months and was diagnosed with West syndrome. Initial treatment, including adrenocorticotropic hormone(ACTH), was only transiently effective. At 1 year 9 months of age, vigabatrin(VGB)administration was introduced cautiously considering its potential adverse effects that might worsen ocular lesions. His seizures were suppressed with a modest dose(100 mg/kg/day)of VGB with no signs of electroretinogram abnormalities on repeated ophthalmological examinations. VGB was discontinued successfully at 3 years 6 months of age with no recurrence of seizures. A de novo pathogenic variant NM_001845.6:c.3620G> A(p.G1207E)was found in COL4A1. These findings suggest that VGB may be used effectively and safely in treating refractory West syndrome, even in patients with congenital ocular abnormalities associated with COL4A1-related disorder.

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Clonal Hematopoiesis in Chronic Thromboembolic Pulmonary Hypertension.

Momoi M, Katsumata Y, Kunimoto H, Inami T, Miya F, Anzai A, Goto S, Miura A, Shinya Y, Hiraide T, Shirakawa K, Endo J, Fukuda K, Ieda M, Kosaki K, Nakajima H, Kataoka M

Journal of the American Heart Association 13 （ 23 ） e035498 2024年12月

BACKGROUND: The cause of chronic thromboembolic pulmonary hypertension (CTEPH) remains largely unknown. Recently, clonal hematopoiesis (CH) has been reported to be associated with cardiovascular and thromboembolic diseases. Here, we investigated the prevalence and clinical impact of CH in patients with CTEPH. METHODS AND RESULTS: Whole-exome sequencing and deep-panel sequencing were performed in 214 patients with CTEPH. Clinical data before and after treatment were compared between patients with and without CH. RNA sequencing and serum analysis were performed to explore the pathogenesis that CH contributes to CTEPH. Among the enrolled patients, 20.1%, notably 44.4% who were 80 to 89 years old, had variants in CH-associated genes. In regard to clinical impact, B-type natriuretic peptide levels and home oxygen therapy rate were significantly higher, and 6-minute walk distance was significantly shorter after treatment in patients with CH than in those without CH. Moreover, novel clot reformation in the pulmonary artery despite the use of anticoagulants and additional angioplasty events after treatment completion were more frequent in patients with CH. RNA sequencing analysis revealed that blood coagulation and neutrophil extracellular trap formation pathways were enriched in patients with CH. Additionally, serum citrullinated histone H3 levels were higher in patients with CH than those without CH. These results were consistent in the subgroup of patients who did not have the history of hematological disorders. CONCLUSIONS: The findings in this study raise the possibility that CH will induce a more prothrombotic state through neutrophil activation and neutrophil extracellular trap formation, contributing to pathogenesis and poor treatment response in patients with CTEPH.

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De novo variants in UPF1 associated with intellectual disabilities: Human genetic and functional evidences using Drosophila model.

Nakato D, Yasue Y, Matsubara K, Suzuki H, Kosaki R, Takenouchi T, Yamada M, Miya F, Takano-Shimizu T, Kosaki K

European journal of medical genetics 72 104983 2024年12月

ISSN 1769-7212

Nonsense-mediated mRNA decay represents a biologic clearing system against aberrant mRNAs harboring nonsense and frameshift mutations and depends on three factors, UPF1, UPF2, and UPF3 (UPF3A, UPF3B). While germline pathogenic variants of UPF3B and UPF2 are known to be associated with neurodevelopmental disorders, germline variants in UPF1 have not been reported, until date, as being associated with any human disorders. Herein, we report two unrelated patients with de novo UPF1 variants. Patient 1 was a 5-year-old girl with intellectual disabilities, frontal bossing, hypertelorism, high frontal hairline, and thin upper lip. Patient 2 was a 2-year-old female child with intellectual disabilities and similar features. Trio exome analysis revealed a de novo heterozygous variant in UPF1 in both the patients (Patient 1: NM_002911.4): c.949_951del, p.(Asp317del); Patient 2: c.1984G>A, p.(Asp662Asn)). We conducted experiments using Drosophila models to evaluate the functional relevance of these UPF1 variants. Enforced expression of the wild-type Upf1 allele under the control of the pan-neuronal nSyb-GAL4 driver caused mortality, mostly at the pupal stage, but still yielded adult flies. By contrast, expression of the Asp294del (Asp317del in humans) variant caused embryonic or early larval lethality and that of the Asp643Asn (Asp662Asn in humans) caused third instar larval lethality; neither produced pupa nor adult fly. Thus, the developmental defects caused by the variants, especially Asp294del, were more severe than those caused by the wild-type allele. These observations suggest that both variants are deleterious mutations. In conclusion, germline variants in UPF1 are associated with intellectual disabilities in humans.

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Biallelic null variants in PNPLA8 cause microcephaly by reducing the number of basal radial glia.

Nakamura Y, Shimada IS, Maroofian R, Falabella M, Zaki MS, Fujimoto M, Sato E, Takase H, Aoki S, Miyauchi A, Koshimizu E, Miyatake S, Arioka Y, Honda M, Higashi T, Miya F, Okubo Y, Ogawa I, Scardamaglia A, Miryounesi M, Alijanpour S, Ahmadabadi F, Herkenrath P, Dafsari HS, Velmans C, Al Balwi M, Vitobello A, Denommé-Pichon AS, Jeanne M, Civit A, Abdel-Hamid MS, Naderi H, Darvish H, Bakhtiari S, Kruer MC, Carroll CJ, Ghayoor Karimiani E, Khailany RA, Abdulqadir TA, Ozaslan M, Bauer P, Zifarelli G, Seifi T, Zamani M, Al Alam C, Alvi JR, Sultan T, Efthymiou S, Pope SAS, Haginoya K, Matsunaga T, Osaka H, Matsumoto N, Ozaki N, Ohkawa Y, Oki S, Tsunoda T, Pitceathly RDS, Taketomi Y, Houlden H, Murakami M, Kato Y, Saitoh S

Brain : a journal of neurology 147 （ 11 ） 3949 - 3967 2024年11月

ISSN 0006-8950

Patatin-like phospholipase domain-containing lipase 8 (PNPLA8), one of the calcium-independent phospholipase A2 enzymes, is involved in various physiological processes through the maintenance of membrane phospholipids. Biallelic variants in PNPLA8 have been associated with a range of paediatric neurodegenerative disorders. However, the phenotypic spectrum, genotype–phenotype correlations and the underlying mechanisms are poorly understood. Here, we newly identified 14 individuals from 12 unrelated families with biallelic ultra-rare variants in PNPLA8 presenting with a wide phenotypic spectrum of clinical features. Analysis of the clinical features of current and previously reported individuals (25 affected individuals across 20 families) showed that PNPLA8-related neurological diseases manifest as a continuum ranging from variable developmental and/or degenerative epileptic–dyskinetic encephalopathy to childhood-onset neurodegeneration. We found that complete loss of PNPLA8 was associated with the more profound end of the spectrum, with congenital microcephaly. Using cerebral organoids generated from human induced pluripotent stem cells, we found that loss of PNPLA8 led to developmental defects by reducing the number of basal radial glial cells and upper-layer neurons. Spatial transcriptomics revealed that loss of PNPLA8 altered the fate specification of apical radial glial cells, as reflected by the enrichment of gene sets related to the cell cycle, basal radial glial cells and neural differentiation. Neural progenitor cells lacking PNPLA8 showed a reduced amount of lysophosphatidic acid, lysophosphatidylethanolamine and phosphatidic acid. The reduced number of basal radial glial cells in patient-derived cerebral organoids was rescued, in part, by the addition of lysophosphatidic acid. Our data suggest that PNPLA8 is crucial to meet phospholipid synthetic needs and to produce abundant basal radial glial cells in human brain development.

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Novel germline STAT3 gain-of-function mutation causes autoimmune diseases and severe growth failure.

Saito K, Fujimoto M, Funajima E, Serada S, Ohkawara T, Ishihara M, Yamada M, Suzuki H, Miya F, Kosaki K, Fujieda M, Naka T

The journal of allergy and clinical immunology. Global 3 （ 4 ） 100312 2024年11月

Background: In recent years, germline gain-of-function (GOF) mutations in signal transducer and activator of transcription 3 (STAT3) have been identified as a cause of early-onset multiorgan autoimmune diseases with the widespread use of next-generation sequencing, and targeted therapies such as tocilizumab have been reported to be effective. Objective: We sought to assess whether a novel STAT3 mutation detected by whole-exome sequencing is pathogenic and examine the efficacy of targeted therapy. Methods: A pediatric patient with idiopathic pulmonary hemosiderosis, autoimmune thyroiditis, inflammatory bowel disease unclassified, leukocytosis, thrombocytosis, and severe growth failure was examined. Results: This 7-year-old boy had idiopathic pulmonary hemosiderosis at the age of 6 months. Despite high-dose steroid therapy, pulmonary fibrosis progressed. Furthermore, he presented with severe growth failure, autoimmune thyroiditis, leukocytosis, thrombocytosis, and inflammation bowel disease unclassified. Given the presence of multiple autoimmune diseases, whole-exome sequencing was performed, which detected germline de novo heterozygous STAT3 mutation (NM_139276.2; c.2144C>A, p.(P715Q)). Dual-luciferase reporter assay revealed this novel STAT3 mutation as GOF. After starting tocilizumab therapy at the age of 6, hospital stays decreased, and the progression of pulmonary fibrosis was decelerated without increasing the steroid dose. New autoimmune diseases did not develop, and no apparent adverse effects on growth have been observed. Conclusions: Tocilizumab may be effective for patients with STAT3 GOF mutation, including those requiring long-term management of idiopathic pulmonary hemosiderosis. Diagnosis of patients with early-onset multiorgan autoimmune diseases in which STAT3 GOF is suspected should be confirmed by genetic testing and functional analysis to consider the introduction of targeted therapies.

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Japanese Public Health Insurance System's new genomic strategic action to shorten the "diagnostic odyssey" for patients with rare and intractable diseases.

Ezaki J, Takahashi Y, Saijo H, Miya F, Kosaki K

Journal of human genetics 69 （ 11 ） 549 - 552 2024年11月

ISSN 1434-5161

In June 2024, the Japanese government introduced a new genomic strategic action to shorten the “diagnostic odyssey” for patients with rare and intractable diseases: Six groups of rare diseases, (i) Muscle weakness group, (ii) Growth retardation, intellectual disability, and characteristic facial features group, (iii) Intellectual disability/epilepsy group, (iv) Cardiomyopathy group (mainly adult onset) (v) Proteinuria group, (vi) Fever, inflammation, skin rash, osteoarthritis group, have been newly recognized as “difficult-to-differentiate disorders” and comprehensive genomic testing can be reimbursed when patients belong to one of the six groups and certain requirements are met. The introduction of comprehensive genomic testing will improve the diagnosis rate of diseases and have significant potential to enhance Japan’s rare and intractable disease policy. The new strategy in Japan and its rationale will be a reference for insurance reimbursement of comprehensive genomic testing in other countries that have universal health coverage supported by the public health insurance system.

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Café-au-lait Spots and Cleft Palate: Not a Chance Association.

Yamada M, Tanito K, Suzuki H, Nakato D, Miya F, Takenouchi T, Kosaki K

The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association 61 （ 11 ） 1932 - 1936 2024年11月

ISSN 1055-6656

The recognition of syndromic forms of cleft palate is important for condition-specific management. Here, we report a patient with cleft palate, congenital heart disease, intellectual disability, and café-au-lait spots who had a deletion of chromosome 15q14. The identification of the precise breakpoints using a Nanopore-based long-read sequencer showed that the deletion spanned MEIS2 and SPRED1 loci. Cleft palate and café-au-lait spots can be ascribed to MEIS2 and SPRED1, respectively. Patients with cleft palate and café-au-lait spots should be encouraged to undergo a detailed genomic evaluation, including screening for a 15q14 deletion, to enable appropriate anticipatory medico-surgical management and genetic counseling.

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Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response.

Ueda MT, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y

Cell genomics 4 （ 10 ） 100654 2024年10月

Type I interferon (IFN-I) plays an important role in the innate immune response through inducing IFN-I-stimulated genes (ISGs). However, how alternative splicing (AS) events, especially over time, affect their function remains poorly understood. We generated an annotation (113,843 transcripts) for IFN-I-stimulated human B cells called isoISG using high-accuracy long-read sequencing data from PacBio Sequel II/IIe. Transcript isoform profiling using isoISG revealed that isoform switching occurred in the early response to IFN-I so that ISGs would gain functional domains (e.g., C4B) or higher protein production (e.g., IRF3). Conversely, isoforms lacking functional domains increased during the late phase of IFN-I response, mainly due to intron retention events. This suggests that isoform switching both triggers and terminates IFN-I responses at the translation and protein levels. Furthermore, genetic variants influencing the isoform ratio of ISGs were associated with immunological and infectious diseases. AS has essential roles in regulating innate immune response and associated diseases.

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Digital clubbing without hypoxia for lysinuric protein intolerance.

Watanabe D, Tsujioka Y, Nakato D, Yamada M, Suzuki H, Ohnishi T, Tamai N, Kijima T, Takenouchi T, Miya F, Narumi S, Kosaki K

European journal of medical genetics 71 104967 2024年10月

ISSN 1769-7212

Digital clubbing is characterized by bulbous enlargement of the terminal segments of the fingers. Hypotheses including hypoxia have been proposed for the pathogenesis of digital clubbing, but the exact pathogenesis of digital clubbing is still uncertain. Lysinuric protein intolerance (LPI) is caused by pathogenic variants in SLC7A7 and is often associated with interstitial lung disease. Previously two patients of LPI with digital clubbing but without hypoxia have been reported. It is unclear whether digital clubbing in LPI is secondary to hypoxia or directly related to SLC7A7 deficiency. Here we report a 6-year-old Japanese boy presented with digital clubbing without hypoxia. He had episodic vomiting, each episode consisting of a single vomiting event occurring once a month, and his growth had been delayed. He had interstitial lung disease and hepatomegaly. He had compound heterozygous pathogenic variants in the SLC7A7, leading to the diagnosis of LPI. Together with the two previously reported patients mentioned above, we conclude that digital clubbing can occur in the absence of hypoxia. Digital clubbing in the absence of hypoxia has been observed in two genetic disorders related to prostaglandin (PG) E2, HPGD and SLCO2A1. PGE2 synthesis is primarily regulated by the cyclooxygenase 2, which plays a critical role in the control of inflammation. A high urine PGE level in the patient was compatible with the notion that PGE2 production may be increased in LPI. The occurrence of digital clubbing in the absence of hypoxia in LPI patients with SLC7A7 may be attributed to the mechanism of increased PGE2 production.

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Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis.

Watanabe D, Okamoto N, Kobayashi Y, Suzuki H, Kato M, Saitoh S, Kanemura Y, Takenouchi T, Yamada M, Nakato D, Sato M, Tsunoda T, Kosaki K, Miya F

Scientific reports 14 （ 1 ） 19741 2024年08月

Cockayne syndrome (CS) is a rare autosomal recessive disorder caused by mutations in ERCC8 or ERCC6. Most pathogenic variants in ERCC8 are single nucleotide substitutions. Structural variants (SVs) have been reported in patients with ERCC8-related CS. However, comprehensive molecular detection, including SVs of ERCC8, in CS patients remains problematic. Herein, we present three Japanese patients with ERCC8-related CS in whom causative SVs were identified using whole-exome-based copy number variation (CNV) detection tools. One patient showed compound heterozygosity for a 259-kb deletion and a deletion of exon 4 which has previously been reported as an Asia-specific variant. The other two patients were homozygous for the same exon 4 deletion. The exon 4 deletion was detected only by the ExomeDepth software. Intrigued by the discrepancy in the detection capability of various tools for the SVs, we evaluated the analytic performance of four whole-exome-based CNV detection tools using an exome data set from 337 healthy individuals. A total of 1,278,141 exons were predicted as being affected by the 4 CNV tools. Interestingly 95.1% of these affected exons were detected by one tool alone. Thus, we expect that the use of multiple tools may improve the detection rate of SVs from aligned exome data.

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GATA2 deficiency of a novel missense variant with multiorgan inflammation.

Baba H, Kimura N, Kanegane H, Miya F, Kosaki K, Morio T, Koike R

Rheumatology (Oxford, England) 63 （ 8 ） e226 - e228 2024年08月

ISSN 1462-0324

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Biallelic loss-of-function variants in the centriolar protein CCP110 leads to a ciliopathy-like phenotype.

Suzuki H, Muramatsu Y, Miya F, Asada H, Yamada M, Nishimura G, Kosaki K, Takenouchi T

European journal of medical genetics 70 104955 2024年08月

ISSN 1769-7212

CCP110 (centriolar coiled coil protein 110, also known as CP110) is one of the essential proteins localized in the centrosome that plays critical roles in the regulation of the cell cycle and also in the initiation of ciliogenesis. So far, no human congenital disorders have been identified to be associated with pathogenic variants of CCP110. Mice with biallelic loss-of-function variants of Ccp110 (Ccp110−/−) are known to manifest multiple organ defects, including a small body size, polydactyly, omphalocele, congenital heart defects, cleft palate, short ribs, and a small thoracic cage, a pattern of abnormalities closely resembling that in “ciliopathies” in humans. Herein, we report a 7-month-old male infant who presented with growth failure and skeletal abnormalities, including a narrow thorax and severe brachydactyly. Trio exome analysis of the genomic DNA of the patient and his parents showed that the patient was a compound heterozygote for truncating variants of CCP110, including a frameshift variant NM_001323572.2:c.856_857del, p.(Val286Leufs*5) inherited from the father, and a nonsense variant NM_001323572.2:c.1129C>T, p.(Arg377*) inherited from the mother. The strikingly similar pattern of malformations between Ccp110−/− mice and the 7-month-old male infant reported herein carrying unequivocal truncating CCP110 variants strongly supports the contention that CCP110 is a novel disease-causative gene.

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Truncating variants of the sterol recognition region of SHH cause hypertelorism phenotype rather than hypotelorism-holoprosencephaly.

Yamada M, Mizuno S, Inaba M, Uehara T, Inagaki H, Suzuki H, Miya F, Takenouchi T, Kurahashi H, Kosaki K

American journal of medical genetics. Part A 194 （ 8 ） e63614 2024年08月

ISSN 1552-4825

Sonic hedgehog signaling molecule (SHH) is a key molecule in the cilia-mediated signaling pathway and a critical morphogen in embryogenesis. The association between loss-of-function variants of SHH and holoprosencephaly is well established. In mice experiments, reduced or increased signaling of SHH have been shown to be associated with narrowing or excessive expansion of the facial midline, respectively. Herein, we report two unrelated patients with de novo truncating variants of SHH presenting with hypertelorism rather than hypotelorism. The first patient was a 13-year-old girl. Her facial features included hypertelorism, strabismus, telecanthus, malocclusion, frontal bossing, and wide widow's peak. She had borderline developmental delay and agenesis of the corpus callosum. She had a nonsense variant of SHH: Chr7(GRCh38):g.155802987C > T, NM_000193.4:c.1302G > A, p.(Trp434*). The second patient was a 25-year-old girl. Her facial features included hypertelorism and wide widow's peak. She had developmental delay and agenesis of the corpus callosum. She had a frameshift variant of SHH: Chr7(GRCh38):g.155803072_155803074delCGGinsT, NM_000193.4:c.1215_1217delCCGinsA, p.(Asp405Glufs*92). The hypertelorism phenotype contrasts sharply with the prototypical hypotelorism-holoprosencephaly phenotype associated with loss-of-function of SHH. We concluded that a subset of truncating variants of SHH could be associated with hypertelorism rather than hypotelorism.

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SALL4 deletion and kidney and cardiac defects associated with VACTERL association.

Watanabe D, Nakato D, Yamada M, Suzuki H, Takenouchi T, Miya F, Kosaki K

Pediatric nephrology (Berlin, Germany) 39 （ 8 ） 2347 - 2349 2024年08月

ISSN 0931-041X

Congenital anomalies of the kidney and urinary tract (CAKUT) can be a part of the VACTERL association, which represents the non-random combination of the following congenital anomalies: vertebral anomalies, anal anomalies, cardiac anomalies, tracheal-esophageal anomalies, kidney anomalies, and limb anomalies. VACTERL association is generally considered to be a non-genetic condition. Exceptions include a patient with a heterozygous nonsense SALL4 variant and anal stenosis, tetralogy of Fallot, sacro-vertebral fusion, and radial and thumb anomalies. SALL4 encodes a transcription factor that plays a critical role in kidney morphogenesis. Here, we report a patient with VACTERL association and a heterozygous 128-kb deletion spanning SALL4 who presented with renal hypoplasia, radial and atrio-septal defects, and patent ductus arteriosus. The present report of SALL4 deletion, in addition to a previously reported patient with VACTERL association phenotype and SALL4 nonsense mutation, further supports the notion that SALL4 haploinsufficiency can lead to VACTERL association.

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SCN8A Encephalopathy with a Significant Long-Term Response to Lacosamide

Yokoyama A., Nakamura T., Ichinose F., Miya F., Kato M., Matsuo M.

Journal of Pediatric Neurology 22 （ 6 ） 470 - 474 2024年06月

ISSN 13042580

Developmental and epileptic encephalopathy associated with SCN8A variants (i.e., SCN8A encephalopathy) causes early-onset epilepsy, involuntary movements, hypotonia, and developmental delay. Sodium channel blockers are effective for treating SCN8A encephalopathy; however, the long-term effects are unknown. Herein, we report the long-term efficacy of lacosamide (LCM) treatment in a patient with SCN8A encephalopathy. Our patient, a 7-year-old girl, presented with a hyperekplexia-like excessive startle response, drug-resistant epilepsy with sinus arrest, and prolonged respiratory failure during the neonatal period. The patient was diagnosed with SCN8A encephalopathy caused by a de novo pathogenic variant of SCN8A: c.3979A > G; p.Ile1327Val. The patient experienced tonic clustered seizures daily, with dramatic responses to high doses of LCM, lasting approximately 3 years.

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West症候群を発症したPTEN病的バリアントの女児例

門田茉莉, 占部良介, 中井まりえ, 星野英紀, 加藤光広, 宮冬樹, 三牧正和

日本小児科学会雑誌（(公社)日本小児科学会） 128 （ 6 ） 828 - 832 2024年06月

ISSN 0001-6543

West症候群(WS)では近年多くの原因遺伝子が知られるようになった。今回、WSの原因遺伝子としては一般的ではないPTEN(Phosphatase and Tensin Homolog)にバリアントをもつWSの女児例を経験した。周産期歴には特に異常なく、生後7ヵ月時にシリーズ形成する癲癇性スパズムを発症した。初診時に筋緊張低下と運動発達遅延および頭囲拡大を認め、発作間欠期脳波検査でヒプサリズミアがみられWSと診断した。頭部MRIでは脳回の構造異常や過誤腫はみられず、ACTH療法とその後の抗発作薬内服治療によって発作は消失し、脳波異常も改善したが、中等度～重度の精神運動発達遅滞がみられた。遺伝子解析でPTENに既知の病的バリアント(NM 000314:exon6:c.517C>T:p.(R173C))が同定された。一般に生殖細胞系列のPTEN病的バリアントを原因とする疾患の表現型としてCowden症候群やBannayan-Riley-Ruvalcaba症候群、Proteus症候群などが知られており、これらはいずれも過誤腫を伴う疾患で、PTEN Hamartoma Tumor Syndromeと総称されている。既報ではPTENバリアントによって脳形成障害をきたした場合でも癲癇を発症する割合は低く、本例のように脳回の構造異常を伴わずにWSをきたした症例の報告はこれまでになかった。

Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration.

Yamada M, Maeta K, Suzuki H, Kurosawa R, Takenouchi T, Awaya T, Ajiro M, Takeuchi A, Nishio H, Hagiwara M, Miya F, Matsuo M, Kosaki K

Scientific reports 14 （ 1 ） 6506 2024年03月

Pathogenic variants in WDR45 on chromosome Xp11 cause neurodegenerative disorder beta-propeller protein-associated neurodegeneration (BPAN). Currently, there is no effective therapy for BPAN. Here we report a 17-year-old female patient with BPAN and show that antisense oligonucleotide (ASO) was effective in vitro. The patient had developmental delay and later showed extrapyramidal signs since the age of 15 years. MRI findings showed iron deposition in the globus pallidus and substantia nigra on T2 MRI. Whole genome sequencing and RNA sequencing revealed generation of pseudoexon due to inclusion of intronic sequences triggered by an intronic variant that is remote from the exon–intron junction: WDR45 (OMIM #300526) chrX(GRCh37):g.48935143G > C, (NM_007075.4:c.235 + 159C > G). We recapitulated the exonization of intron sequences by a mini-gene assay and further sought antisense oligonucleotide that induce pseudoexon skipping using our recently developed, a dual fluorescent splicing reporter system that encodes two fluorescent proteins, mCherry, a transfection marker designed to facilitate evaluation of exon skipping and split eGFP, a splicing reaction marker. The results showed that the 24-base ASO was the strongest inducer of pseudoexon skipping. Our data presented here have provided supportive evidence for in vivo preclinical studies.

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A case of infantile epileptic spasms syndrome and autism spectrum disorder with an RFX3 mutation.

Torio M, Maeda K, Akamine S, Kawakami S, Matsubara Y, Miya F, Kato M, Kira R

Seizure 112 11 - 14 2023年11月

ISSN 1059-1311

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Neurochemistry evaluated by magnetic resonance spectroscopy in a patient with FBXO28-related developmental and epileptic encephalopathy.

Sano K, Miya F, Kato M, Omata T, Takanashi JI

Brain & development 45 （ 10 ） 583 - 587 2023年11月

ISSN 0387-7604

Background: Mutations in the FBXO28 gene, which encodes FBXO28, one of the F-box protein family, may cause developmental and epileptic encephalopathy (DEE). FBXO28-related DEE is radiologically characterized by cerebral atrophy, delayed/abnormal myelination, and brain malformation; however, no neurochemical analyses have been reported. Case report: A female Japanese infant presented with severe psychomotor delay, epileptic spasms, and visual impairment. Whole-exome sequencing revealed a de novo variant of the FBXO28 gene, leading to the diagnosis of FBXO28-related DEE. Magnetic resonance (MR) spectroscopy at 6, 12, and 32 months revealed decreased N-acetylaspartate and choline-containing compounds and increased levels of myoinositol. Conclusion: MR spectroscopy revealed neurochemical derangement in FBXO28-related DEE, that is, disturbed myelination secondary to neuronal damage with astrogliosis.

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Time-dependent cell-state selection identifies transiently expressed genes regulating ILC2 activation.

Tanaka Y, Yamagishi M, Motomura Y, Kamatani T, Oguchi Y, Suzuki N, Kiniwa T, Kabata H, Irie M, Tsunoda T, Miya F, Goda K, Ohara O, Funatsu T, Fukunaga K, Moro K, Uemura S, Shirasaki Y

Communications biology 6 （ 1 ） 915 2023年09月

The decision of whether cells are activated or not is controlled through dynamic intracellular molecular networks. However, the low population of cells during the transition state of activation renders the analysis of the transcriptome of this state technically challenging. To address this issue, we have developed the Time-Dependent Cell-State Selection (TDCSS) technique, which employs live-cell imaging of secretion activity to detect an index of the transition state, followed by the simultaneous recovery of indexed cells for subsequent transcriptome analysis. In this study, we used the TDCSS technique to investigate the transition state of group 2 innate lymphoid cells (ILC2s) activation, which is indexed by the onset of interleukin (IL)-13 secretion. The TDCSS approach allowed us to identify time-dependent genes, including transiently induced genes (TIGs). Our findings of IL4 and MIR155HG as TIGs have shown a regulatory function in ILC2s activation.

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Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences.

Yamada M, Nitta Y, Uehara T, Suzuki H, Miya F, Takenouchi T, Tamura M, Ayabe S, Yoshiki A, Maeno A, Saga Y, Furuse T, Yamada I, Okamoto N, Kosaki K, Sugie A

European journal of medical genetics 66 （ 8 ） 104804 2023年08月

ISSN 1769-7212

DExH-box helicases are involved in unwinding of RNA and DNA. Among the 16 DExH-box genes, monoallelic variants of DHX16, DHX30, DHX34, and DHX37 are known to be associated with neurodevelopmental disorders. In particular, DHX30 is well established as a causative gene for neurodevelopmental disorders. Germline variants of DHX9, the closest homolog of DHX30, have not been reported until now as being associated with congenital disorders in humans, except that one de novo heterozygous variant, p.(Arg1052Gln) of the gene was identified during comprehensive screening in a patient with autism; unfortunately, the phenotypic details of this individual are unknown. Herein, we report a patients with a heterozygous de novo missense variant, p.(Gly414Arg) of DHX9 who presented with a short stature, intellectual disability, and ventricular non-compaction cardiomyopathy. The variant was located in the glycine codon of the ATP-binding site, G-C-G-K-T. To assess the pathogenicity of these variants, we generated transgenic Drosophila lines expressing human wild-type and mutant DHX9 proteins: 1) the mutant proteins showed aberrant localization both in the nucleus and the cytoplasm; 2) ectopic expression of wild-type protein in the visual system led to the rough eye phenotype, whereas expression of the mutant proteins had minimal effect; 3) overexpression of the wild-type protein in the retina led to a reduction in axonal numbers, whereas expression of the mutant proteins had a less pronounced effect. Furthermore, in a gene-editing experiment of Dhx9 G416 to R416, corresponding to p.(Gly414Arg) in humans, heterozygous mice showed a reduced body size, reduced emotionality, and cardiac conduction abnormality. In conclusion, we established that heterozygosity for a loss-of-function variant of DHX9 can lead to a new neurodevelopmental disorder.

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Precise definition of the breakpoints of an apparently balanced translocation between chromosome 3q26 and chromosome 7q36: Role of KMT2C disruption.

Yamada M, Suzuki H, Miya F, Kosugiyama K, Ujiie T, Tonoki H, Kosaki K

Congenital anomalies 63 （ 4 ） 121 - 124 2023年07月

ISSN 0914-3505

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Simple and efficient differentiation of human iPSCs into contractible skeletal muscles for muscular disease modeling.

Rashid MI, Ito T, Miya F, Shimojo D, Arimoto K, Onodera K, Okada R, Nagashima T, Yamamoto K, Khatun Z, Shimul RI, Niwa JI, Katsuno M, Sobue G, Okano H, Sakurai H, Shimizu K, Doyu M, Okada Y

Scientific reports 13 （ 1 ） 8146 2023年05月

Pathophysiological analysis and drug discovery targeting human diseases require disease models that suitably recapitulate patient pathology. Disease-specific human induced pluripotent stem cells (hiPSCs) differentiated into affected cell types can potentially recapitulate disease pathology more accurately than existing disease models. Such successful modeling of muscular diseases requires efficient differentiation of hiPSCs into skeletal muscles. hiPSCs transduced with doxycycline-inducible MYOD1 (MYOD1-hiPSCs) have been widely used; however, they require time- and labor-consuming clonal selection, and clonal variations must be overcome. Moreover, their functionality should be carefully examined. Here, we demonstrated that bulk MYOD1-hiPSCs established with puromycin selection rather than G418 selection showed rapid and highly efficient differentiation. Interestingly, bulk MYOD1-hiPSCs exhibited average differentiation properties of clonally established MYOD1-hiPSCs, suggesting that it is possible to minimize clonal variations. Moreover, disease-specific hiPSCs of spinal bulbar muscular atrophy (SBMA) could be efficiently differentiated via this method into skeletal muscle that showed disease phenotypes, suggesting the applicability of this method for disease analysis. Finally, three-dimensional muscle tissues were fabricated from bulk MYOD1-hiPSCs, which exhibited contractile force upon electrical stimulation, indicating their functionality. Thus, our bulk differentiation requires less time and labor than existing methods, efficiently generates contractible skeletal muscles, and may facilitate the generation of muscular disease models.

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Topologically associating domain underlies tissue specific expression of long intergenic non-coding RNAs.

Hamba Y, Kamatani T, Miya F, Boroevich KA, Tsunoda T

iScience 26 （ 5 ） 106640 2023年05月

Accumulating evidence indicates that long intergenic non-coding RNAs (lincRNAs) show more tissue-specific expression patterns than protein-coding genes (PCGs). However, although lincRNAs are subject to canonical transcriptional regulation like PCGs, the molecular basis for the specificity of their expression patterns remains unclear. Here, using expression data and coordinates of topologically associating domains (TADs) in human tissues, we show that lincRNA loci are significantly enriched in the more internal region of TADs compared to PCGs and that lincRNAs within TADs have higher tissue specificity than those outside TADs. Based on these, we propose an analytical framework to interpret transcriptional status using lincRNA as an indicator. We applied it to hypertrophic cardiomyopathy data and found disease-specific transcriptional regulation: ectopic expression of keratin at the TAD level and derepression of myocyte differentiation-related genes by E2F1 with down-regulation of LINC00881. Our results provide understanding of the function and regulation of lincRNAs according to genomic structure.

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Molecular basis of carotid body tumor and associated clinical features in Japan identified by genomic, immunohistochemical, and clinical analyses.

Yoshihama K, Mutai H, Sekimizu M, Ito F, Saito S, Nakamura S, Mikoshiba T, Nagai R, Takebayashi A, Miya F, Kosaki K, Ozawa H, Matsunaga T

Clinical genetics 103 （ 4 ） 466 - 471 2023年04月

ISSN 0009-9163

Carotid body tumor (CBT) is classified as a paraganglioma (PGL). Here, we report the genetic background, protein expression pattern, and clinical findings of 30 Japanese CBT cases. Germline pathogenic or likely pathogenic (P/LP) variants of genes encoding succinate dehydrogenase subunits (SDHs) were detected in 15 of 30 cases (50%). The SDHB variants were the most frequently detected, followed by SDHA and SDHD variants. One case with SDHAF2 variant was bilateral CBT, and other two multiple PGL cases were not detected P/LP variants. The three cases with germline variants that could be tested did not have somatic P/LP variants of the same genes. Immunohistochemical analysis showed negative SDHB signals in CBT tissues in five cases with germline P/LP variants of SDHB, SDHD, or SDHA. In addition, SDHB signals in CBT tissues were negative in four of nine cases without germline P/LP variants of SDHs. These findings suggest the involvement of unidentified molecular mechanisms affecting SDHs.

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Diagnosis of Prader-Willi syndrome and Angelman syndrome by targeted nanopore long-read sequencing.

Yamada M, Okuno H, Okamoto N, Suzuki H, Miya F, Takenouchi T, Kosaki K

European journal of medical genetics 66 （ 2 ） 104690 2023年02月

ISSN 1769-7212

The CpG island flanking the promoter region of SNRPN on chromosome 15q11.2 contains CpG sites that are completely methylated in the maternally derived allele and unmethylated in the paternally derived allele. Both unmethylated and methylated alleles are observed in normal individuals. Only the methylated allele is observed in patients with Prader-Willi syndrome, whereas only the unmethylated allele is observed in those with Angelman syndrome. Hence, detection of aberrant methylation at the differentially methylated region is fundamental to the molecular diagnosis of Prader-Willi syndrome and Angelman syndromes. Traditionally, bisulfite treatment and methylation-sensitive restriction enzyme treatment or methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) have been used. We here developed a long-read sequencing assay that can distinguish methylated and unmethylated CpG sites at 15q11.2 by the difference in current intensity generated from nanopore reads. We successfully diagnosed 4 Prader-Willi syndrome patients and 3 Angelman syndrome patients by targeting differentially methylated regions. Concurrent copy number analysis, homozygosity analysis, and structural variant analysis also allowed us to precisely delineate the underlying pathogenic mechanisms, including gross deletion, uniparental heterodisomy, uniparental isodisomy, or imprinting defect. Furthermore, we showed allele-specific methylation in imprinting-related differentially methylated regions on chromosomes 6, 7, 11, 14, and 20 in a normal individual together with 4 Prader-Willi patients and 3 Angelman syndrome patients. Hence, presently reported method is likely to be applicable to the diagnosis of imprinting disorders other than Prader-Willi syndrome and Angelman syndrome as well.

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Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci.

Yamaguchi K, Ishigaki K, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Nagafuchi Y, Miya F, Tsunoda T, Shoda H, Fujio K, Yamamoto K, Kochi Y

Nature communications （Nature Communications） 13 （ 1 ） 4659 2022年08月

Splicing quantitative trait loci (sQTLs) are one of the major causal mechanisms in genome-wide association study (GWAS) loci, but their role in disease pathogenesis is poorly understood. One reason is the complexity of alternative splicing events producing many unknown isoforms. Here, we propose two approaches, namely integration and selection, for this complexity by focusing on protein-structure of isoforms. First, we integrate isoforms with the same coding sequence (CDS) and identify 369-601 integrated-isoform ratio QTLs (i2-rQTLs), which altered protein-structure, in six immune subsets. Second, we select CDS incomplete isoforms annotated in GENCODE and identify 175-337 isoform-ratio QTL (i-rQTL). By comprehensive long-read capture RNA-sequencing among these incomplete isoforms, we reveal 29 full-length isoforms with unannotated CDSs associated with GWAS traits. Furthermore, we show that disease-causal sQTL genes can be identified by evaluating their trans-eQTL effects. Our approaches highlight the understudied role of protein-altering sQTLs and are broadly applicable to other tissues and diseases.

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Utility of tissue-specific gene expression scores for gene prioritization in Mendelian diseases.

Kato D, Mitsuhashi S, Miya F, Saitoh S, Okamoto N, Tsunoda T, Kochi Y

Journal of human genetics （Journal of Human Genetics） 67 （ 12 ） 739 - 742 2022年08月

ISSN 1434-5161

In genetic testing of Mendelian diseases, it is a bioinformatics challenge to effectively prioritize disease-causing candidate genes listed from massively parallel sequencing. Tissue specificity of the gene expression levels may give a clue because it may reflect tissue-specific disease manifestation. However, considering poor correlations between mRNA and protein expression in some genes, it is not clear whether transcriptomics- or proteomics-based tissue specificity should be used to prioritize candidate genes. Therefore, we compared the efficiency of tissue-specific scores (TS scores) obtained from transcriptome and proteome data in prioritizing candidate genes for whole exome sequencing (WES) analysis of Mendelian disease patients. We show that both Protein and RNA TS scores are useful in prioritizing candidate genes in WES analysis, although diseases like coagulopathies get more benefit from Protein TS score. This study may provide useful evidence in developing new methods to effectively identify novel disease-causing genes.

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First phase 1 clinical study of olaparib in pediatric patients with refractory solid tumors.

Takagi M, Ogawa C, Iehara T, Aoki-Nogami Y, Ishibashi E, Imai M, Kimura T, Nagata M, Yasuhara M, Masutani M, Yoshimura K, Tomizawa D, Ogawa A, Yonemori K, Morishita A, Miyamoto S, Takita J, Kihara T, Nobori K, Hasebe K, Miya F, Ikeda S, Shioda Y, Matsumoto K, Fujimura J, Mizutani S, Morio T, Hosoi H, Koike R

Cancer （Cancer） 128 （ 15 ） 2949 - 2957 2022年08月

ISSN 0008-543X

Background: The survival of patients with high-risk, refractory, relapsed, or metastatic solid tumors remains dismal. A poly(ADP-ribose) polymerase (PARP) inhibitor could be effective for the treatment of pediatric solid tumors with defective homologous recombination. Methods: This open-label, multicenter phase 1 clinical trial evaluated the safety, tolerability, and efficacy of olaparib, a PARP inhibitor, in pediatric patients with refractory solid tumors to recommend a dose for Phase 2 trials. Olaparib (62.5, 125, and 187.5 mg/m2 twice daily) was administered orally every day (1 cycle = 28 days) using a standard 3 + 3 dose-escalation design. Patients aged 3–18 years with recurrent pediatric solid tumors were eligible. Pharmacokinetic and pharmacodynamic analyses were performed. Results: Fifteen patients were enrolled and received olaparib monotherapy, which was well tolerated. The recommended phase 2 dose for daily administration was 187.5 mg/m2 twice daily. Pharmacokinetics were dose proportional. The area under the concentration-time curve from 0 to 12 h and the peak plasma concentration for 187.5 mg/m2 twice daily in children were comparable to previous data obtained in a 200-mg, twice-daily cohort and lower than those in the 300-mg twice-daily cohort in adults. Pharmacodynamic studies demonstrated substantial inhibition of PARP activity. Two partial responses were observed in patients with Wilms tumor and neuroblastoma. Conclusions: This report is the first clinical trial to describe the use of a PARP inhibitor as monotherapy in children. Olaparib was well tolerated, with preliminary antitumor responses observed in DNA damage response-defective pediatric tumors. Lay summary: This Phase 1 trial evaluated the efficacy and safety of olaparib in patients with refractory childhood solid tumors. Olaparib was well tolerated, achieving objective response in 2/15 patients. The DNA damage response was attenuated in nearly one-half of advanced neuroblastoma patients, demonstrating the utility of the PARP inhibitor. The results support further investigation of olaparib as a new treatment for DNA damage-response or repair-defective pediatric cancers.

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Deciphering complex rearrangements at the breakpoint of an apparently balanced reciprocal translocation t(4:18)(q31;q11.2)dn and at a cryptic deletion: Further evidence of TLL1 as a causative gene for atrial septal defect.

Yamada M, Suzuki H, Miya F, Takenouchi T, Kosaki K

American journal of medical genetics. Part A （American Journal of Medical Genetics, Part A） 188 （ 8 ） 2472 - 2478 2022年08月

ISSN 1552-4825

When a de novo balanced reciprocal translocation is identified in patients with multiple congenital abnormalities, attempts are often made to infer the relationship between the phenotype of the patient and genes in the proximity of the breakpoint. Here, we report a patient with intellectual disability, atrial septal defect, syndactyly, and cleft lip and palate who had an “apparently balanced” de novo reciprocal translocation t(4:18)(q31;q11.2) as well as a 7-Mb cryptic deletion spanning the HOXD cluster on chromosome 2q31 that was unrelated to the reciprocal translocation. Further analysis using a nanopore long-read sequencer showed complex rearrangements on both derivative chromosomes 4 and 18 and the deleted chromosome 2. First, the TLL1 locus, which is associated with atrial septal defect, was disrupted by the rearrangement involving chromosome 4. Second, the deleted interval at 2q31 included the entire HOXD cluster, the deletion of which is known to cause toe syndactyly, and the DLX1 and DLX2 loci, which are responsible for cleft lip and palate. Among the haplo-sensitive genes within the deleted interval on 2q31, only the RAPGEF4 gene is known to be associated with an autistic phenotype. Hence, most of the clinical features of the patient could be ascribed to specific genomic rearrangements. We have shown the effectiveness of long-read sequencing in defining, in detail, the likely effects of an apparently balanced translocation and cryptic deletion. The results of the present analysis suggest the possibility of phenotypic prediction through a detailed analysis of structural abnormalities, including balanced translocations and deletions.

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De novo non-synonymous DPYSL2 (CRMP2) variants in two patients with intellectual disabilities and documentation of functional relevance through zebrafish rescue and cellular transfection experiments.

Suzuki H, Li S, Tokutomi T, Takeuchi C, Takahashi M, Yamada M, Okuno H, Miya F, Takenouchi T, Numabe H, Kosaki K, Ohshima T

Human molecular genetics 31 （ 24 ） 4173 - 4182 2022年07月

ISSN 0964-6906

Collapsin response mediator protein 2 (Crmp2) is an evolutionarily well-conserved tubulin-binding cytosolic protein that plays critical roles in the formation of neural circuitry in model organisms including zebrafish and rodents. No clinical evidence that CRMP2 variants are responsible for monogenic neurogenic disorders in humans presently exists. Here, we describe two patients with de novo non-synonymous variants (S14R and R565C) of CRMP2 and intellectual disability associated with hypoplasia of the corpus callosum. We further performed various functional assays of CRMP2 variants using zebrafish and zebrafish Crmp2 (abbreviated as z-CRMP2 hereafter) and an antisense morpholino oligonucleotide [AMO]-based experimental system in which crmp2-morphant zebrafish exhibit the ectopic positioning of caudal primary (CaP) motor neurons. Whereas the co-injection of wild-type z-CRMP2 mRNA suppressed the ectopic positioning of CaP motor neurons in Crmp2-morphant zebrafish, the co-injection of R566C or S15R, z-CRMP2, which corresponds to R565C and S14R of human CRMP2, failed to rescue the ectopic positioning. Transfection experiments of zebrafish or rat Crmp2 using plasmid vectors in HeLa cells, with or without a proteasome inhibitor, demonstrated that the expression levels of mutant Crmp2 protein encoded by R565C and S14R CRMP2 variants were decreased, presumably because of increased degradation by proteasomes. When we compared CRMP2-tubulin interactions using co-immunoprecipitation and cellular localization studies, the R565C and S14R mutations weakened the interactions. These results collectively suggest that the CRMP2 variants detected in the present study consistently led to the loss-of-function of CRMP2 protein and support the notion that pathogenic variants in CRMP2 can cause intellectual disabilities in humans.

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Discordant phenotypes in monozygotic twins with STXBP1 mutation: A case report.

Kobayashi H, Matsushige T, Hoshide M, Hidaka I, Ichiyama T, Kato M, Miya F, Hasegawa S

Seizure （Seizure） 101 8 - 10 2022年07月

ISSN 1059-1311

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Revisiting the definition of glioma recurrence based on a phylogenetic investigation of primary and re-emerging tumor samples: a case report.

Umehara T, Arita H, Miya F, Achiha T, Shofuda T, Yoshioka E, Kanematsu D, Nakagawa T, Kinoshita M, Kagawa N, Fujimoto Y, Hashimoto N, Kiyokawa H, Morii E, Tsunoda T, Kanemura Y, Kishima H

Brain tumor pathology （Brain Tumor Pathology） 39 （ 4 ） 218 - 224 2022年06月

ISSN 1433-7398

A recurrent tumor is defined as a re-emerging subclone originating from an ancestorial clone of the primary neoplasm. Hence, it should be distinguished from de novo tumor emerging from other clones. Herein, we describe an exceptional case in which the locally re-emerging glioma did not share genetic alterations of the primary tumor. While the initial tumor harbored mutations in IDH1 and TERT genes as well as 1p/19q codeletion, the re-emerging tumor did not present any of these genetic abnormalities. Variant calling for tumor samples using whole-genome sequencing revealed that 1696 mutations within the primary tumor faded in the re-emerging tumor, and that 4591 mutations were newly detected in the re-emerging tumor. These results suggested that the initial and re-emerging tumors did not share same clonal origins, although the second tumor appeared adjacent to the old surgical cavity 5 years after the initial surgery. We finally speculated that the re-emerging tumor could be a “de novo glioma” or “radiation-induced glioblastoma following treatment of a diffuse glioma.” This case highlights the importance of molecular re-evaluation of clinically diagnosed “recurrent” glioma lesions.

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Phenotypic overlap between cardioacrofacial dysplasia-2 and oral-facial-digital syndrome.

Yamada M, Suzuki H, Futagawa H, Takenouchi T, Miya F, Yoshihashi H, Kosaki K

European journal of medical genetics （European Journal of Medical Genetics） 65 （ 6 ） 104512 2022年06月

ISSN 1769-7212

Oral-facial digital (OFD) syndrome is characterized by abnormalities of the face (hypertelorism and low set-ears), oral cavity (multiple frenula, lingual hamartoma, or lobulated tongue) and extremities (postaxial polydactyly). At least 19 genes have been implicated in the development of OFD syndrome. Herein, we report the case a 13-year-old patient with atrioventricular septal defect, moderate intellectual disability, epilepsy, and features of OFD, including multiple oral frenula, and postaxial polydactyly of the hands and feet. The patient had a de novo heterozygous variant in PRKACB: chr1(GRCh37):g.84700915T > C, c.1124T > C (NM_182948.4), p.(Phe375Ser). To date, four patients with pathogenic monoallelic variants in PRKACB have been reported, and the condition associated with these variants is referred to as Cardioacrofacial dysplasia-2 (CAFD2, MIM619143). Previously reported features of this condition include congenital heart disease (e.g., atrioventricular septal defect) and postaxial polydactyly, and two of the patients had multiple oral frenula. We suggest that a significant phenotypic overlap exists between CAFD2 and OFD syndrome, in that these patients especially share the features of postaxial polydactyly and multiple oral frenula. The phenotypic similarity between patients with CAFD2 and classic OFD syndrome with an OFD1 variant might be explained by the recent in vitro experimental finding that a protein kinase A subunit encoded by PRKACB directly phosphorylates the OFD1 protein. From the standpoint of genetic counseling, OFD syndrome type1, the prototypic form of OFD, exhibits an X-linked dominant inheritance pattern, whereas other forms of OFD syndrome exhibit an autosomal recessive inheritance pattern. Recognition of CAFD2 as a differential diagnosis or forme fruste of OFD syndrome suggests that an autosomal dominant pattern of inheritance should also be considered during genetic counseling.

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Hemorrhagic shock and encephalopathy syndrome in a patient with a de novo heterozygous variant in KIF1A.

Isobe K, Ieda D, Miya F, Miyachi R, Otsuji S, Asai M, Tsunoda T, Kosaki K, Hattori A, Saitoh S, Mizuno M

Brain & development （Brain and Development） 44 （ 3 ） 249 - 253 2022年03月

ISSN 0387-7604

Introduction: KIF1A, a gene that encodes a neuron-specific motor protein, plays important roles in cargo transport along neurites. Variants in KIF1A have been described in three different disorders, and neurodegeneration and spasticity with or without cerebellar atrophy or cortical visual impairment syndrome (NESCAVS) is the severest phenotype. Case report: A 3-year-old girl was born at term with a birth weight of 2590 g. At five months of age, she visited our hospital due to developmental delay. An EEG showed multiple epileptic discharge, and a nerve conduction study showed severe axonopathy of both motor and sensory nerves. We performed exome sequencing and identified a de novo heterozygous missense variant in KIF1A (NM_001244008.1: c. 757G > A, p.E253K). At six months of age, she developed acute encephalopathy, multiple organ failure and disseminated intravascular coagulation, necessitating intensive care. Her brain CT showed severe brain edema, followed by profound brain atrophy. We diagnosed hemorrhagic shock and encephalopathy syndrome (HSES) according to the clinico-radiological features. Currently, she is bed-ridden, and requires gastrostomy because of dysphagia. Conclusion: The clinical course of our case confirmed that p.E253K is associated with severe neurological features. Severe KIF1A deficiency could cause thermoregulatory dysfunction and may increase the risk of acute encephalopathy including HSES.

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Immune subtypes and neoantigen-related immune evasion in advanced colorectal cancer.

Sugawara T, Miya F, Ishikawa T, Lysenko A, Nishino J, Kamatani T, Takemoto A, Boroevich KA, Kakimi K, Kinugasa Y, Tanabe M, Tsunoda T

iScience （iScience） 25 （ 2 ） 103740 2022年02月

Elimination of cancerous cells by the immune system is an important mechanism of protection from cancer, however, its effectiveness can be reduced owing to development of resistance and evasion. To understand the systemic immune response in advanced untreated primary colorectal cancer, we analyze immune subtypes and immune evasion via neoantigen-related mechanisms. We identify a distinctive cancer subtype characterized by immune evasion and very poor overall survival. This subtype has less clonal highly expressed neoantigens and high chromosomal instability, resulting in adaptive immune resistance mediated by the immune checkpoint molecules and neoantigen presentation disorders. We also observe that neoantigen depletion caused by immunoediting and high clonal neoantigen load are correlated with a good overall survival. Our results indicate that the status of the tumor microenvironment and neoantigen composition are promising new prognostic biomarkers with potential relevance for treatment plan decisions in advanced CRC.

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Diagnosis of SLC25A46-related pontocerebellar hypoplasia in two siblings with fulminant neonatal course: role of postmortem CT and whole genomic analysis: a case report.

Yamada M, Suzuki H, Adachi H, Noguchi A, Miya F, Takahashi T, Kosaki K

BMC neurology （BMC Neurology） 22 （ 1 ） 20 2022年01月

Background: Pontocerebellar hypoplasia (PCH) is increasingly known as a degenerative disease rather than simple “hypoplasia”. At least 21 disease-causing genes have been identified for PCH so far. Because PCH is very heterogenous, prognostic prediction based solely on clinical or radiologic findings is not feasible. Case presentation: Here, we report two siblings who had a fulminant neonatal course. The documentation of pontocerebellar hypoplasia by postmortem brain CT imaging in one of the siblings and a subsequent complex and comprehensive whole genome analysis established that both siblings had bi-allelic compound heterozygous variants (a splicing variant and a deletion) in the SLC25A46 gene which encodes a solute carrier protein essential for mitochondrial function. Long-read whole genome sequencing was required to confirm the presence of the deletion. The fulminant courses suggest that SLC25A46-related PCH is an acutely progressive degenerative condition starting in utero, rather than a simple static hypoplasia. Conclusion: The genomic analysis was instrumental and essential to solving the enigma of the unexplained neonatal deaths of these two siblings and to provide accurate genetic counseling.

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Efficacy of ethosuximide on atonic seizures with KCNB1 mutation.

Hoshino H, Miya F, Kato M, Kanemura H

Pediatrics international : official journal of the Japan Pediatric Society （Pediatrics international : official journal of the Japan Pediatric Society） 64 （ 1 ） e14871 2022年01月

ISSN 1328-8067

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The novel and recurrent variants in exon 31 of CREBBP in Japanese patients with Menke-Hennekam syndrome.

Nishi E, Takenouchi T, Miya F, Uehara T, Yanagi K, Hasegawa Y, Ueda K, Mizuno S, Kaname T, Kosaki K, Okamoto N

American journal of medical genetics. Part A （American Journal of Medical Genetics, Part A） 2021年10月

ISSN 1552-4825

Menke–Hennekam syndrome-1 (MKHK1) is a congenital disorder caused by the heterozygous variants in exon 30 or 31 of CREBBP (CREB binding protein) gene mapped on 16p13.3. It is characterized by psychomotor delay, variable impairment of intellectual disability (ID), feeding difficulty, autistic behavior, hearing impairment, short stature, microcephaly, and facial dysmorphisms. The CREBBP loss-of-function variants cause Rubinstein–Taybi syndrome-1 (RSTS1). The function of CREBBP leading to MKHK1 has not been clarified so far, and the phenotype of MKHK1 significantly differs from that of RSTS1. We examined six patients with de novo pathogenic variants affecting the last exon of CREBBP, and they shared the clinical features of MKHK1. This study revealed that one frameshift and three nonsense variants of CREBBP cause MKHK1, and inferred that the nonsense variants of the last exon could further help in the elucidation of the etiology of MKHK1.

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Landscape of prognostic signatures and immunogenomics of the AXL/GAS6 axis in renal cell carcinoma.

Hakozaki K, Tanaka N, Takamatsu K, Takahashi R, Yasumizu Y, Mikami S, Shinojima T, Kakimi K, Kamatani T, Miya F, Tsunoda T, Aimono E, Nishihara H, Mizuno R, Oya M

British journal of cancer （British Journal of Cancer） 2021年10月

ISSN 0007-0920

Background: Cabozantinib is an oral tyrosine kinase inhibitor in renal cell carcinoma (RCC), whose targets include oncogenic AXL and unique ligand GAS6. Critical gaps in basic knowledge need to be addressed to devise an exclusive biomarker and candidate when targeting the AXL/GAS6 axis. Methods: To clarify the effects of the AXL/GAS6 axis on RCC, we herein performed a large-scale immunogenomic analysis and single-cell counts including various metastatic organs and histological subtypes of RCC. We further applied genome-wide mutation analyses and methylation arrays. Results: Varying patterns of AXL and GAS6 expression were observed throughout primary RCC tumours and metastases. Scoring individual AXL/GAS6 levels in the tumour centre and invasive margin, namely, the AXL/GAS6 score, showed a good ability to predict the prognosis of clear cell RCC. Metastasis- and histological subtype-specific differences in the AXL/GAS6 score existed since lung metastasis and the papillary subtype were weakly related to the AXL/GAS6 axis. Cell-by-cell immunohistological assessments clarified an immunosuppressive environment in tumours with high AXL/GAS6 scores. Genomic alterations in the PI3K-mTOR pathway and DNA methylation profiling revealed distinct differences with the AXL/GAS6 score in ccRCC. Conclusion: The AXL/GAS6 scoring system could predict the outcome of prognosis and work as a robust biomarker for the immunogenomic state in RCC.

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Four pedigrees with aminoacyl-tRNA synthetase abnormalities.

Okamoto N, Miya F, Tsunoda T, Kanemura Y, Saitoh S, Kato M, Yanagi K, Kaname T, Kosaki K

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology （Neurological Sciences） 2021年09月

ISSN 1590-1874

Aminoacyl tRNA synthetases (ARSs) are highly conserved enzymes that link amino acids to their cognate tRNAs. Thirty-seven ARSs are known and their deficiencies cause various genetic disorders. Variants in some ARSs are associated with the autosomal dominant inherited form of axonal neuropathy, including Charcot-Marie-Tooth (CMT) disease. Variants of genes encoding ARSs often cause disorders in an autosomal recessive fashion. The clinical features of cytosolic ARS deficiencies are more variable, including systemic features. Deficiencies of ARSs localized in the mitochondria are often associated with neurological disorders including Leigh and early-onset epileptic syndromes. Whole exome sequencing (WES) is an efficient way to identify the genes causing various symptoms in patients. We identified 4 pedigrees with novel compound heterozygous variants in ARS genes (WARS1, MARS1, AARS2, and PARS2) by WES. Some unique manifestations were noted. The number of patients with ARSs has been increasing since the application of WES. Our findings broaden the known genetic and clinical spectrum associated with ARS variants.

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Profiling the inhibitory receptors LAG-3, TIM-3, and TIGIT in renal cell carcinoma reveals malignancy.

Takamatsu K, Tanaka N, Hakozaki K, Takahashi R, Teranishi Y, Murakami T, Kufukihara R, Niwa N, Mikami S, Shinojima T, Sasaki T, Sato Y, Kume H, Ogawa S, Kakimi K, Kamatani T, Miya F, Tsunoda T, Aimono E, Nishihara H, Sawada K, Imamura T, Mizuno R, Oya M

Nature communications （Nature Communications） 12 （ 1 ） 5547 2021年09月

A cutting edge therapy for future immuno-oncology is targeting a new series of inhibitory receptors (IRs): LAG-3, TIM-3, and TIGIT. Both immunogenomic analyses and diagnostic platforms to distinguish candidates and predict good responders to these IR-related agents are vital in clinical pathology. By applying an automated single-cell count for immunolabelled LAG-3, TIM-3, and TIGIT, we reveal that individual IR levels with exclusive domination in each tumour can serve as valid biomarkers for profiling human renal cell carcinoma (RCC). We uncover the immunogenomic landscape associated with individual IR levels in human RCC tumours with metastases in various organs and histological subtypes. We then externally validate our results and devise a workflow with optimal biomarker cut-offs for discriminating the LAG-3, TIM-3, and TIGIT tumour profiles. The discrimination of LAG-3, TIM-3, and TIGIT profiles in tumours may have a broad impact on investigations of immunotherapy responses after targeting a new series of IRs.

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Two cases of DYNC1H1 mutations with intractable epilepsy.

Matsumoto A, Kojima K, Miya F, Miyauchi A, Watanabe K, Iwamoto S, Kawai K, Kato M, Takahashi Y, Yamagata T

Brain & development （Brain and Development） 43 （ 8 ） 857 - 862 2021年09月

ISSN 0387-7604

Background: The DYNC1H1 gene encodes the heavy chain of cytoplasmic dynein 1, a core structure of the cytoplasmic dynein complex. Dominant DYNC1H1 mutations are implicated in Charcot–Marie–Tooth disease, axonal, type 20, spinal muscular atrophy, lower extremity-predominant 1, and autosomal dominant mental retardation 13 with neuronal migration defects. We report two patients with DYNC1H1 mutations who had intractable epilepsy and intellectual disability (ID), one with and one without pachygyria. Case reports: Patient 1 had severe ID. At the age of 2 months, she presented myoclonic seizures and tonic seizures, and later experienced atonic seizures and focal impaired-awareness seizures (FIAS). EEG showed slow waves in right central areas during myoclonic seizures. Brain MRI revealed pachygyria, predominantly in the occipital lobe. After callosal transection her atonic seizures disappeared, but FIAS remained. Patient 2 was diagnosed with autism spectrum disorder (ASD) and severe ID. At the age of 7 years, he presented generalized tonic–clonic seizures, myoclonic seizures, and FIAS. Interictal EEG showed generalized spike-and-wave complexes, predominantly in the left frontal area. Brain MRI was unremarkable. Exome sequencing revealed novel de novo mutations in DYNC1H1: c.4691A > T, p.(Glu1564Val) in Patient 1 and c.12536 T > C, p.(Leu4179Ser) in Patient 2. Conclusions: DYNC1H1 comprises a stem, stalk, and six AAA domains. Patient 2 is the second report of an AAA6 domain mutation without malformations of cortical development. The p.(Gly4072Ser) mutation in the AAA6 domain was also reported in a patient with ASD. It may be that the AAA6 domain has little effect on neuronal movement of DYNC1H1 along microtubules.

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Genotype-Structure-Phenotype Correlations of Disease-Associated IGF1R Variants and Similarities to Those of INSR Variants.

Hosoe J, Kawashima-Sonoyama Y, Miya F, Kadowaki H, Suzuki K, Kato T, Matsuzawa F, Aikawa SI, Okada Y, Tsunoda T, Hanaki K, Kanzaki S, Shojima N, Yamauchi T, Kadowaki T

Diabetes （Diabetes） 70 （ 8 ） 1874 - 1884 2021年08月

ISSN 0012-1797

We previously reported genotype-phenotype correlations in 12 missense variants causing severe insulin resistance, located in the second and third fibronectin type III (FnIII) domains of the insulin receptor (INSR), containing the α-β cleavage and part of insulin-binding sites. This study aimed to identify genotype-phenotype correlations in FnIII domain variants of IGF1R, a structurally related homolog of INSR, which may be associated with growth retardation, using the recently reported crystal structures of IGF1R. A structural bioinformatics analysis of five previously reported disease-associated heterozygous missense variants and a likely benign variant in the FnIII domains of IGF1R predicted that the disease-associated variants would severely impair the hydrophobic core formation and stability of the FnIII domains or affect the α-β cleavage site, while the likely benign variant would not affect the folding of the domains. A functional analysis of these variants in CHO cells showed impaired receptor processing and autophosphorylation in cells expressing the disease-associated variants but not in those expressing the wild-type form or the likely benign variant. These results demonstrated genotype-phenotype correlations in the FnIII domain variants of IGF1R, which are presumably consistent with those of INSR and would help in the early diagnosis of patients with disease-associated IGF1R variants.

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Structural basis of ethnic-specific variants of PAX4 associated with type 2 diabetes.

Hosoe J, Suzuki K, Miya F, Kato T, Tsunoda T, Okada Y, Horikoshi M, Shojima N, Yamauchi T, Kadowaki T

Human genome variation （Human Genome Variation） 8 （ 1 ） 25 2021年07月

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Homozygous ADCY5 mutation causes early-onset movement disorder with severe intellectual disability.

Okamoto N, Miya F, Kitai Y, Tsunoda T, Kato M, Saitoh S, Kanemura Y, Kosaki K

Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology （Neurological Sciences） 42 （ 7 ） 2975 - 2978 2021年07月

ISSN 1590-1874

Background: Mutations of theADCY5 have been identified in patients with familial dyskinesia, early-onsetautosomal dominant chorea and dystonia, and benign hereditary chorea. Most ofthe ADCY5 mutations are de novo or transmitted in an autosomal dominantfashion. Only two pedigrees are known to show autosomal recessive inheritance. Objectives: We report twosiblings with severe ID, dystonic movement, and growth failure with unknownetiology. Methods: We planned a proband-parentapproach using whole exome sequencing. Results: Homozygous mutationin exon 21 of the ADCY5 (p.R1238W) was identified in the siblings. Althoughtheir parents were heterozygous for the mutation, they were free from clinicalmanifestations. Conclusions: Our results furtherexpand the phenotype/genotype correlations of the ADCY5-related disorders.Mutations of ADCY5 should be considered in pediatric patients with ID andinvoluntary movement.

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A novel missense variant in CUL3 shows altered binding ability to BTB-adaptor proteins leading to diverse phenotypes of CUL3-related disorders.

Kato K, Miya F, Oka Y, Mizuno S, Saitoh S

Journal of human genetics （Journal of Human Genetics） 66 （ 5 ） 491 - 498 2021年05月

ISSN 1434-5161

CUL3 forms Cullin-Ring ubiquitin ligases (CRL) with Ring-box protein and BTB-adaptor proteins. A variety of BTB-adaptor proteins have been reported to interact with the N-terminus of CUL3, which makes it possible to recognize various substrates for degradation. Regarding the association of CUL3 with neurodevelopmental disorders, a recent study reported three patients with global developmental delay, who carried de novo variants in CUL3. Here, we describe a novel de novo CUL3 variant (c.158G > A, p.Ser53Asn) identified in a patient with global developmental delay, who presented some novel dysmorphic features, including macrocephaly, characteristic facial features, and cutis marmorata. Immunoprecipitation and immunoblot analyses identified significantly weaker binding ability to some BTB proteins in CUL3-S53N compared to wild-type. Interestingly, label-free quantification proteomics analysis of samples immunoprecipitated by CUL3-S53N showed a significantly decreased interaction with some BTB proteins, while almost equal interaction or significantly increased interaction was observed with other BTB proteins. The binding between CUL3 and BTB proteins is essential for CRL substrate recognition, and alteration of their interaction is thought to result in the quantitative alteration in substrate proteins. It is possible that the difference of dysmorphic features between the present case and previously reported cases is caused by the distinctive effect of each CUL3 variant on substrate proteins. The clinical information of the present case will expand the picture of CUL3-related global developmental disorders, and subsequent cell biological analysis of the novel mutation will provide insight into the underlying molecular mechanism of how CUL3 pathogenic variants cause neurological disorders.

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Decoding Activation of ILC2 using Time-Dependent Cell-State Selection

Tanaka Y and Yamagishi M and Motomura Y and Kamatani T and Oguchi Y and Suzuki N and Kiniwa T and Kabata H and Tsunoda T and Miya F and Goda K and Ohara O and Fukunaga K and Moro K and Shirasaki Y

2021年04月

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De novo ATP1A3 variants cause polymicrogyria.

Miyatake S, Kato M, Kumamoto T, Hirose T, Koshimizu E, Matsui T, Takeuchi H, Doi H, Hamada K, Nakashima M, Sasaki K, Yamashita A, Takata A, Hamanaka K, Satoh M, Miyama T, Sonoda Y, Sasazuki M, Torisu H, Hara T, Sakai Y, Noguchi Y, Miura M, Nishimura Y, Nakamura K, Asai H, Hinokuma N, Miya F, Tsunoda T, Togawa M, Ikeda Y, Kimura N, Amemiya K, Horino A, Fukuoka M, Ikeda H, Merhav G, Ekhilevitch N, Miura M, Mizuguchi T, Miyake N, Suzuki A, Ohga S, Saitsu H, Takahashi H, Tanaka F, Ogata K, Ohtaka-Maruyama C, Matsumoto N

Science advances （Science Advances） 7 （ 13 ） 2021年03月

Polymicrogyria is a common malformation of cortical development whose etiology remains elusive. We conducted whole-exome sequencing for 124 patients with polymicrogyria and identified de novo ATP1A3 variants in eight patients. Mutated ATP1A3 causes functional brain diseases, including alternating hemiplegia of childhood (AHC), rapid-onset dystonia parkinsonism (RDP), and cerebellar ataxia, areflexia, pes cavus, optic nerve atrophy, and sensorineural deafness (CAPOS). However, our patients showed no clinical features of AHC, RDP, or CAPOS and had a completely different phenotype: a severe form of polymicrogyria with epilepsy and developmental delay. Detected variants had different locations in ATP1A3 and different functional properties compared with AHC-, RDP-, or CAPOS-associated variants. In the developing cerebral cortex of mice, radial neuronal migration was impaired in neurons overexpressing the ATP1A3 variant of the most severe patients, suggesting that this variant is involved in cortical malformation pathogenesis. We propose a previously unidentified category of polymicrogyria associated with ATP1A3 abnormalities.

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A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa.

Nishiguchi KM, Miya F, Mori Y, Fujita K, Akiyama M, Kamatani T, Koyanagi Y, Sato K, Takigawa T, Ueno S, Tsugita M, Kunikata H, Cisarova K, Nishino J, Murakami A, Abe T, Momozawa Y, Terasaki H, Wada Y, Sonoda KH, Rivolta C, Tsunoda T, Tsujikawa M, Ikeda Y, Nakazawa T

Communications biology （Communications Biology） 4 （ 1 ） 140 2021年01月

The genetic basis of Japanese autosomal recessive retinitis pigmentosa (ARRP) remains largely unknown. Herein, we applied a 2-step genome-wide association study (GWAS) in 640 Japanese patients. Meta-GWAS identified three independent peaks at P < 5.0 × 10−8, all within the major ARRP gene EYS. Two of the three were each in linkage disequilibrium with a different low frequency variant (allele frequency < 0.05); a known founder Mendelian mutation (c.4957dupA, p.S1653Kfs*2) and a non-synonymous variant (c.2528 G > A, p.G843E) of unknown significance. mRNA harboring c.2528 G > A failed to restore rhodopsin mislocalization induced by morpholino-mediated knockdown of eys in zebrafish, consistent with the variant being pathogenic. c.2528 G > A solved an additional 7.0% of Japanese ARRP cases. The third peak was in linkage disequilibrium with a common non-synonymous variant (c.7666 A > T, p.S2556C), possibly representing an unreported disease-susceptibility signal. GWAS successfully unraveled genetic causes of a rare monogenic disorder and identified a high frequency variant potentially linked to development of local genome therapeutics.

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ELF3 Overexpression as Prognostic Biomarker for Recurrence of Stage II Colorectal Cancer.

Takaoka A, Ishikawa T, Okazaki S, Watanabe S, Miya F, Tsunoda T, Kikuchi A, Yamauchi S, Matsuyama T, Tokunaga M, Uetake H, Kinugasa Y

In vivo (Athens, Greece) （In Vivo） 35 （ 1 ） 191 - 201 2021年01月

ISSN 0258-851X

Background/Aim: Adjuvant chemotherapy for highrisk Stage II colorectal cancer (CRC) is weakly recommended; however, no consensus exists on "high-risk" definition. Prognostic biomarker identification is important for selecting patients with poor prognosis who may benefit from adjuvant chemotherapy. Materials and Methods: Using Microarray data analyses, ELF3 was identified as a candidate gene highly expressed in Stage II CRC with distant recurrences. ELF3 mRNA expression in 168 Stage II CRC patients was subjected to quantitative RT-PCR analysis and ELF3 protein expression in 185 patients was quantified by immunohistochemical analysis. The relationship between mRNA and protein expression levels and patient characteristics were also investigated. Results: The overall recurrence rate and relapsefree survival were significantly poorer in the ELF3 highexpression than the low-expression group at the mRNA and protein levels. High ELF3 mRNA and protein expression levels were independent poor prognostic factors. Conclusion: High ELF3 expression was associated with recurrence of Stage II.

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Clinical usefulness of multigene screening with phenotype-driven bioinformatics analysis for the diagnosis of patients with monogenic diabetes or severe insulin resistance.

Hosoe J, Miya F, Kadowaki H, Fujiwara T, Suzuki K, Kato T, Waki H, Sasako T, Aizu K, Yamamura N, Sasaki F, Kurano M, Hara K, Tanaka M, Ishiura H, Tsuji S, Honda K, Yoshimura J, Morishita S, Matsuzawa F, Aikawa SI, Boroevich KA, Nangaku M, Okada Y, Tsunoda T, Shojima N, Yamauchi T, Kadowaki T

Diabetes research and clinical practice （Diabetes Research and Clinical Practice） 169 108461 2020年11月

ISSN 0168-8227

Aims: Monogenic diabetes is clinically heterogeneous and differs from common forms of diabetes (type 1 and 2). We aimed to investigate the clinical usefulness of a comprehensive genetic testing system, comprised of targeted next-generation sequencing (NGS) with phenotype-driven bioinformatics analysis in patients with monogenic diabetes, which uses patient genotypic and phenotypic data to prioritize potentially causal variants. Methods: We performed targeted NGS of 383 genes associated with monogenic diabetes or common forms of diabetes in 13 Japanese patients with suspected (n = 10) or previously diagnosed (n = 3) monogenic diabetes or severe insulin resistance. We performed in silico structural analysis and phenotype-driven bioinformatics analysis of candidate variants from NGS data. Results: Among the patients suspected having monogenic diabetes or insulin resistance, we diagnosed 3 patients as subtypes of monogenic diabetes due to disease-associated variants of INSR, LMNA, and HNF1B. Additionally, in 3 other patients, we detected rare variants with potential phenotypic effects. Notably, we identified a novel missense variant in TBC1D4 and an MC4R variant, which together may cause a mixed phenotype of severe insulin resistance. Conclusions: This comprehensive approach could assist in the early diagnosis of patients with monogenic diabetes and facilitate the provision of tailored therapy.

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Serum anti-recoverin antibodies is found in elderly patients with retinitis pigmentosa and cancer.

Sato T, Nishiguchi KM, Fujita K, Miya F, Inoue T, Sasaki E, Asano T, Tsuda S, Shiga Y, Kunikata H, Nakazawa M, Nakazawa T

Acta ophthalmologica （Acta Ophthalmologica） 98 （ 6 ） e722 - e729 2020年09月

ISSN 1755-375X

Purpose: To screen for anti-recoverin antibodies in elderly patients with retinitis pigmentosa (RP) with or without cancer and cross-sectionally characterize the seropositive patients clinically. Methods: Serum from 75 RP patients who had been tested for mutations in a panel of 83 RP genes and 73 normal controls, all aged 50–80 years, were screened for anti-recoverin antibodies by Western blot using recombinant recoverin, retinal lysate from a marmoset and commercial anti-recoverin antibodies as a control. Results: Three RP patients with typical pigmentary degeneration of the 75 (4.0%) were seropositive for anti-recoverin antibody. Pathogenic mutations were identified in two seropositive RP patients. All three patients had visual impairment since childhood and were diagnosed as RP by the age of 30. The severity of the retinopathy varied greatly among these three patients, ranging in visual acuity from light perception OU to 20/30 OU. Retinitis pigmentosa (RP) patients with a history of cancer were more likely to have anti-recoverin antibodies (3/14; 21.4%) than those without (0/61; 0%; p = 0.005, Fischer exact test). All 73 healthy controls with no history of cancer were also seronegative. Conclusion: Our results show that serum anti-recoverin antibodies can be detected in typical RP patients with identified pathogenic mutations and that a history of cancer may increase the risk of developing anti-recoverin antibodies.

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Quantification of multicellular colonization in tumor metastasis using exome-sequencing data.

Nishino J, Watanabe S, Miya F, Kamatani T, Sugawara T, Boroevich KA, Tsunoda T

International journal of cancer （International Journal of Cancer） 146 （ 9 ） 2488 - 2497 2020年05月

ISSN 0020-7136

Metastasis is a major cause of cancer-related mortality, and it is essential to understand how metastasis occurs in order to overcome it. One relevant question is the origin of a metastatic tumor cell population. Although the hypothesis of a single-cell origin for metastasis from a primary tumor has long been prevalent, several recent studies using mouse models have supported a multicellular origin of metastasis. Human bulk whole-exome sequencing (WES) studies also have demonstrated a multiple “clonal” origin of metastasis, with different mutational compositions. Specifically, there has not yet been strong research to determine how many founder cells colonize a metastatic tumor. To address this question, under the metastatic model of “single bottleneck followed by rapid growth,” we developed a method to quantify the “founder cell population size” in a metastasis using paired WES data from primary and metachronous metastatic tumors. Simulation studies demonstrated the proposed method gives unbiased results with sufficient accuracy in the range of realistic settings. Applying the proposed method to real WES data from four colorectal cancer patients, all samples supported a multicellular origin of metastasis and the founder size was quantified, ranging from 3 to 17 cells. Such a wide-range of founder sizes estimated by the proposed method suggests that there are large variations in genetic similarity between primary and metastatic tumors in the same subjects, which may explain the observed (dis)similarity of drug responses between tumors.

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Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans.

Mutai H, Wasano K, Momozawa Y, Kamatani Y, Miya F, Masuda S, Morimoto N, Nara K, Takahashi S, Tsunoda T, Homma K, Kubo M, Matsunaga T

PLoS genetics （PLoS Genetics） 16 （ 4 ） e1008643 2020年04月

ISSN 1553-7390

Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss. Furthermore, we detected another de novo missense variant of SLC12A2 in a sporadic case. SLC12A2 encodes Na+, K+, 2Cl− cotransporter (NKCC) 1 and plays critical roles in the homeostasis of K+-enriched endolymph. Slc12a2-deficient mice have congenital, profound deafness; however, no human variant of SLC12A2 has been reported as associated with hearing loss. All identified SLC12A2 variants mapped to exon 21 or its 3’-splice site. In vitro analysis indicated that the splice-site variant generates an exon 21-skipped SLC12A2 mRNA transcript expressed at much lower levels than the exon 21-included transcript in the cochlea, suggesting a tissue-specific role for the exon 21-encoded region in the carboy-terminal domain. In vitro functional analysis demonstrated that Cl− influx was significantly decreased in all SLC12A2 variants studied. Immunohistochemistry revealed that SLC12A2 is located on the plasma membrane of several types of cells in the cochlea, including the strial marginal cells, which are critical for endolymph homeostasis. Overall, this study suggests that variants affecting exon 21 of the SLC12A2 transcript are responsible for hereditary hearing loss in humans.

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Unveiling synapse pathology in spinal bulbar muscular atrophy by genome-wide transcriptome analysis of purified motor neurons derived from disease specific iPSCs.

Onodera K, Shimojo D, Ishihara Y, Yano M, Miya F, Banno H, Kuzumaki N, Ito T, Okada R, de Araújo Herculano B, Ohyama M, Yoshida M, Tsunoda T, Katsuno M, Doyu M, Sobue G, Okano H, Okada Y

Molecular brain （Molecular Brain） 13 （ 1 ） 18 2020年02月

Spinal bulbar muscular atrophy (SBMA) is an adult-onset, slowly progressive motor neuron disease caused by abnormal CAG repeat expansion in the androgen receptor (AR) gene. Although ligand (testosterone)-dependent mutant AR aggregation has been shown to play important roles in motor neuronal degeneration by the analyses of transgenic mice models and in vitro cell culture models, the underlying disease mechanisms remain to be fully elucidated because of the discrepancy between model mice and SBMA patients. Thus, novel human disease models that recapitulate SBMA patients' pathology more accurately are required for more precise pathophysiological analysis and the development of novel therapeutics. Here, we established disease specific iPSCs from four SBMA patients, and differentiated them into spinal motor neurons. To investigate motor neuron specific pathology, we purified iPSC-derived motor neurons using flow cytometry and cell sorting based on the motor neuron specific reporter, HB9 e438 ::Venus, and proceeded to the genome-wide transcriptome analysis by RNA sequences. The results revealed the involvement of the pathology associated with synapses, epigenetics, and endoplasmic reticulum (ER) in SBMA. Notably, we demonstrated the involvement of the neuromuscular synapse via significant upregulation of Synaptotagmin, R-Spondin2 (RSPO2), and WNT ligands in motor neurons derived from SBMA patients, which are known to be associated with neuromuscular junction (NMJ) formation and acetylcholine receptor (AChR) clustering. These aberrant gene expression in neuromuscular synapses might represent a novel therapeutic target for SBMA.

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Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice.

Nishiguchi KM, Fujita K, Miya F, Katayama S, Nakazawa T

Nature communications （Nature Communications） 11 （ 1 ） 482 2020年01月

Supplementing wildtype copies of functionally defective genes with adeno-associated virus (AAV) is a strategy being explored clinically for various retinal dystrophies. However, the low cargo limit of this vector allows its use in only a fraction of patients with mutations in relatively small pathogenic genes. To overcome this issue, we developed a single AAV platform that allows local replacement of a mutated sequence with its wildtype counterpart, based on combined CRISPR-Cas9 and micro-homology-mediated end-joining (MMEJ). In blind mice, the mutation replacement rescued approximately 10% of photoreceptors, resulting in an improvement in light sensitivity and an increase in visual acuity. These effects were comparable to restoration mediated by gene supplementation, which targets a greater number of photoreceptors. This strategy may be applied for the treatment of inherited disorders caused by mutations in larger genes, for which conventional gene supplementation therapy is not currently feasible.

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Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor-infiltrating cells.

Sato Y, Wada I, Odaira K, Hosoi A, Kobayashi Y, Nagaoka K, Karasaki T, Matsushita H, Yagi K, Yamashita H, Fujita M, Watanabe S, Kamatani T, Miya F, Mineno J, Nakagawa H, Tsunoda T, Takahashi S, Seto Y, Kakimi K

Clinical & translational immunology （Clinical and Translational Immunology） 9 （ 10 ） e1194 2020年

Objectives: A better understanding of antitumor immunity will help predict the prognosis of gastric cancer patients and tailor the appropriate therapies in each patient. Therefore, we propose a novel immunological classification of gastric cancer. Methods: We performed whole-exome sequencing (WES), RNA-Seq and flow cytometry in 29 gastric cancer patients who received surgery. The TCGA data set of 323 gastric cancer patients and RNA-Seq data of 45 patients who received pembrolizumab (Kim et al. Nat Med 2018; 24: 1449–1458) were also analysed. Results: Immunogram analysis of cancer–immunity interaction of gastric cancer revealed immune signatures of four main types, designated Hot1, Hot2, Intermediate and Cold. Immunologically hot tumors displayed a dysfunctional T-cell signature, while cold tumors had an exclusion signature. Ex vivo tumor-infiltrating lymphocyte analysis documented T-cell dysfunction with the expression of checkpoint molecules and impaired cytokine production. The T-cell function was more profoundly damaged in Hot1 than Hot2 tumors. Patients in Hot2 subtypes had better survival in our cohort and TCGA cohort. Although these immunological subtypes overlapped to some degree with the molecular subtypes in the TCGA, intratumoral immune responses cannot be predicted solely based on histological or molecular subtyping of gastric cancer. Molecular and immunological classifications complement each other to predict the responses to anti-PD-1 therapy and have the potential to be a biomarker for the treatment of gastric cancer. Conclusion: The immunological classification of gastric cancer resulted in four subtypes. Hot tumors were further divided into two subtypes, between which the functional status of T cells was different.

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Systematic detection of Mendelian and non-Mendelian variants associated with retinitis pigmentosa by genome-wide association study

Nishiguchi KM and Miya F and Mori Y and Fujita K and Akiyama M and Kamatani T and Koyanagi Y and Kota S and Takigawa T and Ueno S and Tsugita M and Kunikata H and Cisarova K and Nishino J and Nakazawa T

2019年12月

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Author Correction: A missense mutation in the HECT domain of NEDD4L identified in a girl with periventricular nodular heterotopia, polymicrogyria, and cleft palate.

Kato K, Miya F, Hori I, Ieda D, Ohashi K, Negishi Y, Hattori A, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S

Journal of human genetics （Journal of Human Genetics） 64 （ 7 ） 701 - 702 2019年07月

ISSN 1434-5161

Since the publication of this article, it has been brought to our attention, that the identified mutation (NM_015277: c.2617 G > A; p.Glu873Lys) is identical with the mutation (NM_001144967: c.2677 G > A; p.Glu893Lys) reported by Broix et al (Nature Genetics 48, 1349–1358, 2016 https://doi.org/10.1038/ng.3676). Therefore the mutation is not novel but recurrent. Accordingly, the word “novel” should be deleted throughout the article including the title. Thus, the title should read “A missense mutation in the HECT domain of NEDD4L identified in a girl with periventricular nodular heterotopia, polymicrogyria, and cleft palate”.

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A frequent variant in the Japanese population determines quasi-Mendelian inheritance of rare retinal ciliopathy.

Nikopoulos K, Cisarova K, Quinodoz M, Koskiniemi-Kuendig H, Miyake N, Farinelli P, Rehman AU, Khan MI, Prunotto A, Akiyama M, Kamatani Y, Terao C, Miya F, Ikeda Y, Ueno S, Fuse N, Murakami A, Wada Y, Terasaki H, Sonoda KH, Ishibashi T, Kubo M, Cremers FPM, Kutalik Z, Matsumoto N, Nishiguchi KM, Nakazawa T, Rivolta C

Nature communications （Nature Communications） 10 （ 1 ） 2884 2019年06月

Hereditary retinal degenerations (HRDs) are Mendelian diseases characterized by progressive blindness and caused by ultra-rare mutations. In a genomic screen of 331 unrelated Japanese patients, we identify a disruptive Alu insertion and a nonsense variant (p.Arg1933*) in the ciliary gene RP1, neither of which are rare alleles in Japan. p.Arg1933* is almost polymorphic (frequency = 0.6%, amongst 12,000 individuals), does not cause disease in homozygosis or heterozygosis, and yet is significantly enriched in HRD patients (frequency = 2.1%, i.e., a 3.5-fold enrichment; p-value = 9.2 × 10−5). Familial co-segregation and association analyses show that p.Arg1933* can act as a Mendelian mutation in trans with the Alu insertion, but might also associate with disease in combination with two alleles in the EYS gene in a non-Mendelian pattern of heredity. Our results suggest that rare conditions such as HRDs can be paradoxically determined by relatively common variants, following a quasi-Mendelian model linking monogenic and complex inheritance.

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<i>MYCN</i> de novo gain-of-function mutation in a patient with a novel megalencephaly syndrome.

Kato K, Miya F, Hamada N, Negishi Y, Narumi-Kishimoto Y, Ozawa H, Ito H, Hori I, Hattori A, Okamoto N, Kato M, Tsunoda T, Kanemura Y, Kosaki K, Takahashi Y, Nagata KI, Saitoh S

Journal of medical genetics （Journal of Medical Genetics） 56 （ 6 ） 388 - 395 2019年06月

ISSN 0022-2593

background in this study, we aimed to identify the gene abnormality responsible for pathogenicity in an individual with an undiagnosed neurodevelopmental disorder with megalencephaly, ventriculomegaly, hypoplastic corpus callosum, intellectual disability, polydactyly and neuroblastoma. We then explored the underlying molecular mechanism. Methods trio-based, whole-exome sequencing was performed to identify disease-causing gene mutation. Biochemical and cell biological analyses were carried out to elucidate the pathophysiological significance of the identified gene mutation. results We identified a heterozygous missense mutation (c.173c>t; p.thr58Met) in the MYCN gene, at the thr58 phosphorylation site essential for ubiquitination and subsequent MYcn degradation. the mutant MYcn (MYcn-t58M) was non-phosphorylatable at thr58 and subsequently accumulated in cells and appeared to induce ccnD1 and ccnD2 expression in neuronal progenitor and stem cells in vitro. Overexpression of Mycn mimicking the p.thr58Met mutation also promoted neuronal cell proliferation, and affected neuronal cell migration during corticogenesis in mouse embryos. Conclusions We identified a de novo c.173c>t mutation in MYCN which leads to stabilisation and accumulation of the MYcn protein, leading to prolonged ccnD1 and ccnD2 expression. this may promote neurogenesis in the developing cerebral cortex, leading to megalencephaly. While loss-of-function mutations in MYCN are known to cause Feingold syndrome, this is the first report of a germline gain-of-function mutation in MYCN identified in a patient with a novel megalencephaly syndrome similar to, but distinct from, ccnD2-related megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome. the data obtained here provide new insight into the critical role of MYcn in brain development, as well as the consequences of MYcn defects.

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難治性てんかんと退行を示したPOGZ変異症の1例

山形誠也, 服部文子, 宮冬樹, 久保田裕子, 遠藤剛, 根岸豊, 中村勇治, 角田達彦, 小崎健次郎, 齋藤伸治

脳と発達（(一社)日本小児神経学会） 51 （ 1 ） 29 - 32 2019年01月

ISSN 0029-0831

Pogo transposable element with zinc finger domain(POGZ)遺伝子は近年、本遺伝子の変異と自閉症スペクトラム障害および知的障害の関連性が指摘されている。これまでに40例の報告があり、言語発達遅滞、視力障害、小頭症、肥満傾向といった表現型が指摘されている。脳波異常は20%に報告されているが、てんかんとして治療を要した症例の報告はない。今回、これまでに報告のなかった難治性のてんかんと退行を有する症例にde novoのPOGZ遺伝子短縮型変異(c.2102del;p.Pro701Leufs*18)をヘテロ接合性に同定した。POGZ変異が原因となる表現型は自閉症スペクトラム障害に止まらず、多彩な神経症状を示し、進行性のてんかん症候群の原因となる可能性が示唆された。(著者抄録)

Refractory epilepsy and regression in a patient with a de novo heterozygous POGZ mutation

Yamagata S., Hattori A., Miya F., Kubota Y., Endo T., Negishi Y., Nakamura Y., Tsunoda T., Kosaki K., Saitoh S.

No To Hattatsu （No To Hattatsu） 51 （ 1 ） 29 - 32 2019年

ISSN 00290831

Mutations in the pogo transposable element with zinc finger domain（POGZ）gene are associated with autism spectrum disorder （ASD）and intellectual disability. A total of 40 cases have been reported, and their clinical features include severe phenotypes such as severe speech and language delay, vision problems, microcephaly, and a predisposition towards obesity. Although 20% of these cases showed EEG abnormalities, epilepsy has not been reported. We present the case of a patient with refractory epilepsy and regression in which whole exome sequencing identified a de novo heterozygous POGZ mutation（c.2102del;p.Pro701Leufs ＊ 18）. He was diagnosed with autism spectrum disorder at 6 years of age. From 7 years and 8 months of age, he experienced epileptic seizures that involved falling backwards, head nodding and ocular deviation. An EEG showed a spike-and-slow-wave at F3 and F4. He was diagnosed with frontal lobe epilepsy, and treated with various anti-epileptic drugs （e.g. CZP, VPA, CLB, PHT, LTG, PB, CBZ and LEV）, which eventually reduced his epileptic seizures from over 10 to 2-3 times per day. Moreover, this patient had repetitive aspiration pneumonia from 14 years of age, necessitating a tracheotomy and laryngo-tracheal separation. Phenotypes associated with a POGZ mutation might, therefore, have a wider spectrum than previously recognized, and include not only ASD, but various neurological problems such as progressive epilepsy syndrome.

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Gene expression dataset for whole cochlea of Macaca fascicularis.

Mutai H, Miya F, Shibata H, Yasutomi Y, Tsunoda T, Matsunaga T

Scientific reports （Scientific Reports） 8 （ 1 ） 15554 2018年10月

Macaca fascicularis is a highly advantageous model in which to study human cochlea with regard to both evolutionary proximity and physiological similarity of the auditory system. To better understand the properties of primate cochlear function, we analyzed the genes predominantly expressed in M. fascicularis cochlea. We compared the cochlear transcripts obtained from an adult male M. fascicularis by macaque and human GeneChip microarrays with those in multiple macaque and human tissues or cells and identified 344 genes with expression levels more than 2-fold greater than in the other tissues. These “cochlear signature genes” included 35 genes responsible for syndromic or nonsyndromic hereditary hearing loss. Gene set enrichment analysis revealed groups of genes categorized as “ear development” and “ear morphogenesis” in the top 20 gene ontology categories in the macaque and human arrays, respectively. This dataset will facilitate both the study of genes that contribute to primate cochlear function and provide insight to discover novel genes associated with hereditary hearing loss that have yet to be established using animal models.

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Genome-wide association study suggests four variants influencing outcomes with ranibizumab therapy in exudative age-related macular degeneration.

Akiyama M, Takahashi A, Momozawa Y, Arakawa S, Miya F, Tsunoda T, Ashikawa K, Oshima Y, Yasuda M, Yoshida S, Enaida H, Tan X, Yanagi Y, Yasukawa T, Ogura Y, Nagai Y, Takahashi K, Fujisawa K, Inoue M, Arakawa A, Tanaka K, Yuzawa M, Kadonosono K, Sonoda KH, Ishibashi T, Kubo M

Journal of human genetics （Journal of Human Genetics） 63 （ 10 ） 1083 - 1091 2018年10月

ISSN 1434-5161

To identify factors associated with ranibizumab responses in patients with exudative age-related macular degeneration (AMD), we performed a genome-wide association study (GWAS) and a replication study using a total of 919 exudative AMD patients treated with intravitreal ranibizumab in a Japanese population. In the combined analysis of GWAS and the replication study, no loci reached genome-wide significant level; however, we found four variants showed suggestive level of associations with visual loss at month three (rs17822656, rs76150532, rs17296444, and rs75165563: Pcombined < 1.0 × 10−5). Of the candidate genes within these loci, three were relevant to VEGF-related pathway (KCNMA1, SOCS2, and OTX2). The proportions of patients who worsened visual acuity were 13.7%, 38.8%, 58.0%, and 80.0% in patients with 0, 1, 2, and 3 or more identified risk variants, respectively. Changes in visual acuity decreased linearly as the number of risk variants increased (P = 1.67 × 10–12). The area under the curve using age, baseline visual acuity, and history of previous treatment was 0.607, and improved significantly to 0.713 in combination with identified variants (P < 0.0001). Although further study is needed to confirm their associations, our results offer candidate variants influencing response to ranibizumab therapy.

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A novel homozygous missense mutation in the SH3-binding motif of STAMBP causing microcephaly-capillary malformation syndrome.

Hori I, Miya F, Negishi Y, Hattori A, Ando N, Boroevich KA, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S

Journal of human genetics （Journal of Human Genetics） 63 （ 9 ） 957 - 963 2018年09月

ISSN 1434-5161

Microcephaly-capillary malformation syndrome is a congenital and neurodevelopmental disorder caused by biallelic mutations in the STAMBP gene. Here we identify the novel homozygous mutation located in the SH3 binding motif of STAMBP (NM_006463.4) (c.707C>T: p.Ser236Phe) through whole-exome sequencing. The case patient was a 2-year-old boy showing severe global developmental delay, progressive microcephaly, refractory seizures, dysmorphic facial features, and multiple capillary malformations. Immunoblot analysis of patient-derived lymphoblastoid cell lines (LCLs) revealed a severe reduction in STAMBP expression, indicating that Ser236Phe induces protein instability. STAMBP interacts with the SH3 domain of STAM and transduces downstream signals from the Jaks-STAM complex. The substitution of Ser236Phe found in the case patient was located in the SH3-binding motif, and we propose the mutation may block STAM binding and subsequently induce STAMBP degradation. Contrary to previously reported STAMBP mutations, the Ser236Phe mutation did not lead to constitutive activation of the PI3K-AKT-mTOR pathway in patient-derived LCLs, as indicated by the expression of phosphorylated S6 ribosomal protein, suggesting that it is not the major pathomechanism underlying the disorder in this patient.

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A case report of reversible generalized seizures in a patient with Waardenburg syndrome associated with a novel nonsense mutation in the penultimate exon of SOX10.

Suzuki N, Mutai H, Miya F, Tsunoda T, Terashima H, Morimoto N, Matsunaga T

BMC pediatrics （BMC Pediatrics） 18 （ 1 ） 171 2018年05月

Background: Waardenburg syndrome type 1 (WS1) can be distinguished from Waardenburg syndrome type 2 (WS2) by the presence of dystopia canthorum. About 96% of WS1 are due to PAX3 mutations, and SOX10 mutations have been reported in 15% of WS2. Case presentation: This report describes a patient with WS1 who harbored a novel SOX10 nonsense mutation (c.652G>T, p.G218*) in exon 3 which is the penultimate exon. The patient had mild prodromal neurological symptoms that were followed by severe attacks of generalized seizures associated with delayed myelination of the brain. The immature myelination recovered later and the neurological symptoms could be improved. This is the first truncating mutation in exon 3 of SOX10 that is associated with neurological symptoms in Waardenburg syndrome. Previous studies reported that the neurological symptoms that associate with WS are congenital and irreversible. These findings suggest that the reversible neurological phenotype may be associated with the nonsense mutation in exon 3 of SOX10. Conclusions: When patients of WS show mild prodromal neurological symptoms, the clinician should be aware of the possibility that severe attacks of generalized seizures may follow, which may be associated with the truncating mutation in exon 3 of SOX10.

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IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.

Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T

Scientific reports （Scientific Reports） 8 （ 1 ） 5608 2018年04月

Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads. We report the performance comparison of our method, GATK, PINDEL and ScanIndel, using whole exome sequencing data from the same samples. False positive and false negative counts were determined through Sanger sequencing of all predicted indels across these four methods. The harmonic mean of the recall and precision, F-measure, was used to measure the performance of each method. Our method achieved the highest F-measure of 0.84 in one sample, compared to 0.56 for GATK, 0.52 for PINDEL and 0.46 for ScanIndel. Similar results were obtained in additional samples, demonstrating that our method was superior to the other methods for detecting intermediate-size indels. We believe that this methodology will contribute to the discovery of intermediate-size indels associated with human disease.

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Fetal ultrasonographic findings including cerebral hyperechogenicity in a patient with non-lethal form of Raine syndrome.

Tamai K, Tada K, Takeuchi A, Nakamura M, Marunaka H, Washio Y, Tanaka H, Miya F, Okamoto N, Kageyama M

American journal of medical genetics. Part A （American Journal of Medical Genetics, Part A） 176 （ 3 ） 682 - 686 2018年03月

ISSN 1552-4825

Raine syndrome is a rare osteosclerotic bone dysplasia characterized by craniofacial anomalies and intracranial calcification. Most patients with Raine syndrome are of Arab ancestry and die during the neonatal period. We herein report a Japanese patient with non-lethal Raine syndrome who presented with characteristic cerebral hyperechogenicity and a hypoplastic nose by fetal ultrasonography. She was admitted to the NICU due to pyriform aperture stenosis. Craniofacial abnormalities, intracranial calcification, osteosclerosis, chondrodysplasia punctata, and a mutation of FAM20C was identified. She was subsequently discharged without surgical intervention and is now 2 years old with mild neurodevelopmental delays. Images of cerebral hyperechogenicity by fetal ultrasonography in a non-lethal case were described herein for the first time. This patient represents a rare occurrence of a child with Raine syndrome born to Japanese parents and confirms that this syndrome is not always lethal. Even if Raine syndrome is suspected in a fetus due to cerebral hyperechogenicity and a hypoplastic nose, cerebral hyperechogenicity without pulmonary hypoplasia does not always predict lethality or severe neurodevelopmental delays. The information provided herein will be useful for prenatal counseling.

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Discovery of a Cynomolgus Monkey Family With Retinitis Pigmentosa.

Ikeda Y, Nishiguchi KM, Miya F, Shimozawa N, Funatsu J, Nakatake S, Fujiwara K, Tachibana T, Murakami Y, Hisatomi T, Yoshida S, Yasutomi Y, Tsunoda T, Nakazawa T, Ishibashi T, Sonoda KH

Investigative ophthalmology & visual science （Investigative Ophthalmology and Visual Science） 59 （ 2 ） 826 - 830 2018年02月

ISSN 0146-0404

PURPOSE. To accelerate the development of new therapies, an inherited retinal degeneration model in a nonhuman primate would be useful to confirm the efficacy in preclinical studies. In this study, we describe the discovery of retinitis pigmentosa in a cynomolgus monkey (Macaca fascicularis) pedigree. METHODS. First, screening with fundus photography was performed on 1443 monkeys at the Tsukuba Primate Research Center. Ophthalmic examinations, such as indirect ophthalmoscopy, ERGs using RETeval, and optic coherent tomography (OCT) measurement, were then performed to confirm diagnosis. RESULTS. Retinal degeneration with cystoid macular edema was observed in both eyes of one 14-year-old female monkey. In her examinations, the full-field ERGs were nonrecordable and the outer layer of the retina in the parafoveal area was not visible on OCT imaging. Moreover, less frequent pigmentary retinal anomalies also were observed in her 3-year-old nephew. His full-field ERGs were almost nonrecordable and the outer layer was not visible in the peripheral retina. His father was her cousin (the son of her mother’s older brother) and his mother was her younger half-sibling sister with a different father. CONCLUSIONS. The hereditary nature is highly probable (autosomal recessive inheritance suspected). However, whole-exome analysis performed identified no pathogenic mutations in these monkeys.

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A novel genetic syndrome with STARD9 mutation and abnormal spindle morphology.

Okamoto N, Tsuchiya Y, Miya F, Tsunoda T, Yamashita K, Boroevich KA, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K, Kitagawa D

American journal of medical genetics. Part A （American Journal of Medical Genetics, Part A） 173 （ 10 ） 2690 - 2696 2017年10月

ISSN 1552-4825

Intellectual disability (ID) is one of neurodevelopmental disorders characterized by serious defects in both intelligence and adaptive behavior. Although it has been suggested that genetic aberrations associated with the process of cell division underlie ID, the cytological evidence for mitotic defects in actual patient's cells is rarely reported. Here, we report a novel mutation in the STARD9 (also known as KIF16A) gene found in a patient with severe ID, characteristic features, epilepsy, acquired microcephaly, and blindness. Using whole-exome sequence analysis, we sequenced potential candidate genes in the patient. We identified a homozygous single-nucleotide deletion creating a premature stop codon in the STARD9 gene. STARD9 encodes a 4,700 amino acid protein belonging to the kinesin superfamily. Depletion of STARD9 or overexpression of C-terminally truncated STARD9 mutants were known to induce spindle assembly defects in human culture cells. To determine cytological features in the patient cells, we isolated lymphoblast cells from the patient, and performed immunofluorescence analysis. Remarkably, mitotic defects, including multipolar spindle formation, fragmentation of pericentriolar materials and centrosome amplification, were observed in the cells. Taken together, our findings raise the possibility that controlled expression of full-length STARD9 is necessary for proper spindle assembly in cell division during human development. We propose that mutations in STARD9 result in abnormal spindle morphology and cause a novel genetic syndrome with ID.

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Structural Basis and Genotype-Phenotype Correlations of INSR Mutations Causing Severe Insulin Resistance.

Hosoe J, Kadowaki H, Miya F, Aizu K, Kawamura T, Miyata I, Satomura K, Ito T, Hara K, Tanaka M, Ishiura H, Tsuji S, Suzuki K, Takakura M, Boroevich KA, Tsunoda T, Yamauchi T, Shojima N, Kadowaki T

Diabetes （Diabetes） 66 （ 10 ） 2713 - 2723 2017年10月

ISSN 0012-1797

The insulin receptor (INSR) gene was analyzed in four patients with severe insulin resistance, revealing five novel mutations and a deletion that removed exon 2. A patient with Donohue syndrome (DS) had a novel p.V657F mutation in the second fibronectin type III domain (FnIII-2), which contains the a-b cleavage site and part of the insulin-binding site. The mutant INSR was expressed in Chinese hamster ovary cells, revealing that it reduced insulin proreceptor processing and impaired activation of downstream signaling cascades. Using online databases, we analyzed 82 INSR missense mutations and demonstrated that mutations causing DS were more frequently located in the FnIII domains than those causing the milder type A insulin resistance (P = 0.016). In silico structural analysis revealed that missense mutations predicted to severely impair hydrophobic core formation and stability of the FnIII domains all caused DS, whereas those predicted to produce localized destabilization and to not affect folding of the FnIII domains all caused the less severe Rabson-Mendenhall syndrome. These results suggest the importance of the FnIII domains, provide insight into the molecular mechanism of severe insulin resistance, will aid early diagnosis, and will provide potential novel targets for treating extreme insulin resistance.

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Siblings with optic neuropathy and RTN4IP1 mutation.

Okamoto N, Miya F, Hatsukawa Y, Suzuki Y, Kawato K, Yamamoto Y, Tsunoda T, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K

Journal of human genetics （Journal of Human Genetics） 62 （ 10 ） 927 - 929 2017年10月

ISSN 1434-5161

Inherited optic neuropathies (IONs) are neurodegenerative disorders affecting the optic nerve and the nervous system. Dominant and recessive IONs are known. Many of the dominant IONs are caused by mutations of OPA1. Autosomal-recessive IONs are rare. OPA10 is an autosomal-recessive ION due to mutations in RTN4IP1. Patients with RTN4IP1 mutations show extraocular manifestations. We report brothers with optic neuropathy who had novel mutations in the RTN4IP1 gene. This is the first report of Japanese patients with OPA10. They showed extraocular manifestations resembling mitochondrial encephalopathy.

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A novel missense mutation in the HECT domain of NEDD4L identified in a girl with periventricular nodular heterotopia, polymicrogyria and cleft palate.

Kato K, Miya F, Hori I, Ieda D, Ohashi K, Negishi Y, Hattori A, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S

Journal of human genetics （Journal of Human Genetics） 62 （ 9 ） 861 - 863 2017年09月

ISSN 1434-5161

We identified a novel de novo heterozygous missense mutation in the NEDD4L gene (NM-015277: c.2617G>A; p.Glu873Lys) through whole-exome sequencing in a 3-year-old girl showing severe global developmental delay, infantile spasms, cleft palate, periventricular nodular heterotopia and polymicrogyria. Mutations in the HECT domain of NEDD4L have been reported in patients with a neurodevelopmental disorder along with similar brain malformations. All patients reported with NEDD4L HECT domain mutations showed periventricular nodular heterotopia, and most had seizures, cortex anomalies, cleft palate and syndactyly. The unique constellation of clinical features in patients with NEDD4L mutations might help clinically distinguish them from patients with other genetic mutations including FLNA, which is a well-known causative gene of periventricular nodular heterotopia. Although mutations in the HECT domain of NEDD4L that lead to AKT-mTOR pathway deregulation in forced expression system were reported, our western blot analysis did not show an increased level of AKT-mTOR activity in lymphoblastoid cell lines (LCLs) derived from the patient. In contrast to the forced overexpression system, AKT-mTOR pathway deregulation in LCLs derived from our patient seems to be subtle.

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Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis.

Ishigaki K, Kochi Y, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Yamaguchi K, Nagafuchi Y, Nakachi S, Kato R, Sakurai K, Shoda H, Ikari K, Taniguchi A, Yamanaka H, Miya F, Tsunoda T, Okada Y, Momozawa Y, Kamatani Y, Yamada R, Kubo M, Fujio K, Yamamoto K

Nature genetics （Nature Genetics） 49 （ 7 ） 1120 - 1125 2017年07月

ISSN 1061-4036

Recent evidence suggests that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner. To identify candidate causal genes and biological pathways of immune-related complex diseases, we conducted expression quantitative trait loci (eQTL) analysis on five subsets of immune cells (CD4 + T cells, CD8 + T cells, B cells, natural killer (NK) cells and monocytes) and unfractionated peripheral blood from 105 healthy Japanese volunteers. We developed a three-step analytical pipeline comprising (i) prediction of individual gene expression using our eQTL database and public epigenomic data, (ii) gene-level association analysis and (iii) prediction of cell-specific pathway activity by integrating the direction of eQTL effects. By applying this pipeline to rheumatoid arthritis data sets, we identified candidate causal genes and a cytokine pathway (upregulation of tumor necrosis factor (TNF) in CD4 + T cells). Our approach is an efficient way to characterize the polygenic contributions and potential biological mechanisms of complex diseases.

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The prediction models for postoperative overall survival and disease-free survival in patients with breast cancer.

Shigemizu D, Iwase T, Yoshimoto M, Suzuki Y, Miya F, Boroevich KA, Katagiri T, Zembutsu H, Tsunoda T

Cancer medicine （Cancer Medicine） 6 （ 7 ） 1627 - 1638 2017年07月

The goal of this study is to establish a method for predicting overall survival (OS) and disease-free survival (DFS) in breast cancer patients after surgical operation. The gene expression profiles of cancer tissues from the patients, who underwent complete surgical resection of breast cancer and were subsequently monitored for postoperative survival, were analyzed using cDNA microarrays. We detected seven and three probes/genes associated with the postoperative OS and DFS, respectively, from our discovery cohort data. By incorporating these genes associated with the postoperative survival into MammaPrint genes, often used to predict prognosis of patients with early-stage breast cancer, we constructed postoperative OS and DFS prediction models from the discovery cohort data using a Cox proportional hazard model. The predictive ability of the models was evaluated in another independent cohort using Kaplan–Meier (KM) curves and the area under the receiver operating characteristic curve (AUC). The KM curves showed a statistically significant difference between the predicted high- and low-risk groups in both OS (log-rank trend test P = 0.0033) and DFS (log-rank trend test P = 0.00030). The models also achieved high AUC scores of 0.71 in OS and of 0.60 in DFS. Furthermore, our models had improved KM curves when compared to the models using MammaPrint genes (OS: P = 0.0058, DFS: P = 0.00054). Similar results were observed when our model was tested in publicly available datasets. These observations indicate that there is still room for improvement in the current methods of predicting postoperative OS and DFS in breast cancer.

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Defects in autophagosome-lysosome fusion underlie Vici syndrome, a neurodevelopmental disorder with multisystem involvement.

Hori I, Otomo T, Nakashima M, Miya F, Negishi Y, Shiraishi H, Nonoda Y, Magara S, Tohyama J, Okamoto N, Kumagai T, Shimoda K, Yukitake Y, Kajikawa D, Morio T, Hattori A, Nakagawa M, Ando N, Nishino I, Kato M, Tsunoda T, Saitsu H, Kanemura Y, Yamasaki M, Kosaki K, Matsumoto N, Yoshimori T, Saitoh S

Scientific reports （Scientific Reports） 7 （ 1 ） 3552 2017年06月

Vici syndrome (VICIS) is a rare, autosomal recessive neurodevelopmental disorder with multisystem involvement characterized by agenesis of the corpus callosum, cataracts, cardiomyopathy, combined immunodeficiency, developmental delay, and hypopigmentation. Mutations in EPG5, a gene that encodes a key autophagy regulator, have been shown to cause VICIS, however, the precise pathomechanism underlying VICIS is yet to be clarified. Here, we describe detailed clinical (including brain MRI and muscle biopsy) and genetic features of nine Japanese patients with VICIS. Genetic dissection of these nine patients from seven families identified 14 causative mutations in EPG5. These included five nonsense, two frameshift, three splicing, one missense, and one multi-exon deletion mutations, and two initiation codon variants. Furthermore, cultured skin fibroblasts (SFs) from two affected patients demonstrated partial autophagic dysfunction. To investigate the function of EPG5, siRNA based EPG5 knock-down, and CRISPR/Cas9 mediated EPG5 knock-out HeLa cells were generated. EPG5-depleted cells exhibited a complete block of autophagic flux caused by defective autophagosome-lysosome fusion. Unexpectedly, endocytic degradation was normal in both VICIS SFs and EPG5 depleted cells, suggesting that EPG5 function is limited to the regulation of autophagosome-lysosome fusion.

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Novel MCA/ID syndrome with ASH1L mutation.

Okamoto N, Miya F, Tsunoda T, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K

American journal of medical genetics. Part A （American Journal of Medical Genetics, Part A） 173 （ 6 ） 1644 - 1648 2017年06月

ISSN 1552-4825

We identified a novel mutation in ASH1L in a patient with severe intellectual disability, growth failure, microcephaly, facial dysmorphism, myelination delay, and skeletal abnormalities. ASH1L is a histone methyltransferase that associates with the transcribed region of all active genes examined, including Hox genes. It catalyzes H3K36 methylation and plays important roles in development. There has been increasing evidence that heterozygous mutation of ASH1L is associated with ID and autism spectrum disorders. We suggest that ASH1L abnormalities may cause a novel MCA/ID syndrome.

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Identification of a Human Clonogenic Progenitor with Strict Monocyte Differentiation Potential: A Counterpart of Mouse cMoPs.

Kawamura S, Onai N, Miya F, Sato T, Tsunoda T, Kurabayashi K, Yotsumoto S, Kuroda S, Takenaka K, Akashi K, Ohteki T

Immunity （Immunity） 46 （ 5 ） 835 - 848.e4 2017年05月

ISSN 1074-7613

Monocytes give rise to macrophages and dendritic cells (DCs) under steady-state and inflammatory conditions, thereby contributing to host defense and tissue pathology. A common monocyte progenitor (cMoP) that is strictly committed to the monocyte lineage has been recently identified in mice. Here, we identified human cMoPs as a CLEC12AhiCD64hi subpopulation of conventional granulocyte-monocyte progenitors (cGMPs) in umbilical cord blood and in bone marrow. Human cMoPs gave rise to monocyte subsets without showing any potential for differentiating into myeloid or lymphoid cells. Within the cGMP population, we also identified revised GMPs that completely lacked DC and lymphoid potential. Collectively, our findings expand and revise the current understanding of human myeloid cell differentiation pathways.

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A combination of genetic and biochemical analyses for the diagnosis of PI3K-AKT-mTOR pathway-associated megalencephaly.

Negishi Y, Miya F, Hattori A, Johmura Y, Nakagawa M, Ando N, Hori I, Togawa T, Aoyama K, Ohashi K, Fukumura S, Mizuno S, Umemura A, Kishimoto Y, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Nakanishi M, Saitoh S

BMC medical genetics （BMC Medical Genetics） 18 （ 1 ） 4 2017年01月

Background: Constitutive activation of the PI3K-AKT-mTOR pathway (mTOR pathway) underlies megalencephaly in many patients. Yet, prevalence of the involvement of the PI3K-AKT-mTOR pathway in patients with megalencephaly remains to be elucidated, and molecular diagnosis is challenging. Here, we have successfully established a combination of genetic and biochemical methods for diagnosis of mTOR pathway-associated megalencephaly, and have attempted to delineate the clinical characteristics of the disorder. Methods: Thirteen patients with an increased head circumference and neurological symptoms participated in the study. To evaluate the activation of the mTOR pathway, we performed western blot analysis to determine the expression levels of phosphorylated S6 ribosomal protein (phospho-S6 protein) in lymphoblastoid cell lines from 12 patients. Multiplex targeted sequencing analysis for 15 genes involved in the mTOR pathway was performed on 12 patients, and whole-exome sequencing was performed on one additional patient. Clinical features and MRI findings were also investigated. Results: We identified pathogenic mutations in six (AKT3, 1 patient; PIK3R2, 2 patients; PTEN, 3 patients) of the 13 patients. Increased expression of phospho-S6 protein was demonstrated in all five mutation-positive patients in whom western blotting was performed, as well as in three mutation-negative patients. Developmental delay, dysmorphic facial features were observed in almost all patients. Syndactyly/polydactyly and capillary malformations were not observed, even in patients with AKT3 or PIK3R2 mutations. There were no common phenotypes or MRI findings among these patients. Conclusions: A combination of genetic and biochemical methods successfully identified mTOR pathway involvement in nine of 13 (approximately 70%) patients with megalencephaly, indicating a major contribution of the pathway to the pathogenesis of megalencephaly. Our combined approach could be useful to identify patients who are suitable for future clinical trials using an mTOR inhibitor.

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Role of a heterotrimeric G-protein, Gi2, in the corticogenesis: possible involvement in periventricular nodular heterotopia and intellectual disability.

Hamada N, Negishi Y, Mizuno M, Miya F, Hattori A, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Tabata H, Saitoh S, Nagata KI

Journal of neurochemistry （Journal of Neurochemistry） 140 （ 1 ） 82 - 95 2017年01月

ISSN 0022-3042

We analyzed the role of a heterotrimeric G-protein, Gi2, in the development of the cerebral cortex. Acute knockdown of the α-subunit (Gαi2) with in utero electroporation caused delayed radial migration of excitatory neurons during corticogenesis, perhaps because of impaired morphology. The migration phenotype was rescued by an RNAi-resistant version of Gαi2. On the other hand, silencing of Gαi2 did not affect axon elongation, dendritic arbor formation or neurogenesis at ventricular zone in vivo. When behavior analyses were conducted with acute Gαi2-knockdown mice, they showed defects in social interaction, novelty recognition and active avoidance learning as well as increased anxiety. Subsequently, using whole-exome sequencing analysis, we identified a de novo heterozygous missense mutation (c.680C>T; p.Ala227Val) in the GNAI2 gene encoding Gαi2 in an individual with periventricular nodular heterotopia and intellectual disability. Collectively, the phenotypes in the knockdown experiments suggest a role of Gαi2 in the brain development, and impairment of its function might cause defects in neuronal functions which lead to neurodevelopmental disorders. (Figure presented.).

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Novel compound heterozygous variants in PLK4 identified in a patient with autosomal recessive microcephaly and chorioretinopathy.

Tsutsumi M, Yokoi S, Miya F, Miyata M, Kato M, Okamoto N, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S, Kurahashi H

European journal of human genetics : EJHG （European Journal of Human Genetics） 24 （ 12 ） 1702 - 1706 2016年12月

ISSN 1018-4813

It has been well documented that variants in genes encoding centrosomal proteins cause primary autosomal recessive microcephaly, although the association between centrosomal defects and the etiology of microcephaly syndromes is not fully understood. Polo-like kinase 4 (PLK4) is one of the centrosomal proteins required for centriole duplication. We here describe a patient with microcephaly and chorioretinopathy that harbors compound heterozygous missense variants, c.[442A>G]; [2336G>A], in the PLK4 gene. One of these variants, c.442A>G (p.(M148V)), resides in the kinase domain, and the other, c.2336G>A (p.(C779Y)), in the polo-box domain. Aberrant spindle formation was observed in a LCL derived from this patient. Overexpression experiments of the variant PLK4 proteins demonstrated that the p.(C779Y) but not the p.(M148V) had lost centriole overduplication ability. The altered mobility pattern of both variant proteins on a western blot further suggested alterations in post-translation modification. Our data lend support to the hypothesis that impaired centriole duplication caused by PLK4 variants may be involved in the etiology of microcephaly disorder.

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Nozaki F, Kusunoki T, Okamoto N, Yamamoto Y, Miya F, Tsunoda T, Kosaki K, Kumada T, Shibata M, Fujii T

Brain & development （Brain and Development） 38 （ 7 ） 678 - 84 2016年08月

ISSN 0387-7604

Cutis laxa (CL) syndromes are connective tissue disorders characterized by redundant, sagging, inelastic and wrinkled skin, with organ involvement. Here, we describe a patient with ALDH18A1-related CL who developed cyclic vomiting. The patient was a 12-year-old boy who presented with poor postnatal growth, hypotonia, short stature, joint hyperlaxity, microcephaly, strabismus, bilateral cataracts, facial dysmorphism and severe mental retardation. Bone radiographs showed osteopenia and osteoporosis, and magnetic resonance angiography showed marked kinking and tortuosity of the brain vessels. These findings were clinically compatible with ALDH18A1-related CL. Molecular analysis revealed a de novo heterozygous mutation (p.R138Q) in ALDH18A1. No mutations were found in PYCR1 gene. The patient developed cyclic vomiting with decreased blood levels of ornithine, citrulline, arginine and proline without hyperammonemia and other hypoaminoacidemias were also found. ALDH18A1 encodes δ1-pyrroline-5-carboxylate synthase, which is related to the biosynthesis of ornithine, citrulline, arginine, and proline. Cyclic vomiting has never been reported in other ALDH18A1-related CL patients. This is the first case report of ALDH18A1-related CL with cyclic vomiting associated with amino acid abnormalities.

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Novel splicing mutation in the ASXL3 gene causing Bainbridge-Ropers syndrome.

Hori I, Miya F, Ohashi K, Negishi Y, Hattori A, Ando N, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S

American journal of medical genetics. Part A （American Journal of Medical Genetics, Part A） 170 （ 7 ） 1863 - 7 2016年07月

ISSN 1552-4825

Bainbridge–Ropers syndrome (BRPS) is characterized by severe developmental delay, feeding problems, short stature, characteristic facal appearance including arched eyebrows and anteverted nares, and ulnar deviation of the hands. BRPS is caused by a heterozygous mutation in the additional sex combs-like 3 (ASXL3) gene. We describe a patient with severe developmental delay, feeding problems, short stature, autism, and sleep disturbance with a heterozygous de novo splicing mutation in the ASXL3 gene. Reported disease-causing mutations in ASXL3 are located mostly in the first half of exon 11, analogous to ASXL1 mutations of which result in Bohring–Opitz syndrome (BOS). Our findings suggest that the expression of the truncated ASXL3 protein, including ASXN and ASXH domains, give rise to BRPS, which is distinct from but overlaps with BOS. © 2016 Wiley Periodicals, Inc.

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TUBA1A mutation can cause a hydranencephaly-like severe form of cortical dysgenesis.

Yokoi S, Ishihara N, Miya F, Tsutsumi M, Yanagihara I, Fujita N, Yamamoto H, Kato M, Okamoto N, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Kojima S, Saitoh S, Kurahashi H, Natsume J

Scientific reports （Scientific Reports） 5 15165 2015年10月

TUBA1A mutations cause a wide spectrum of lissencephaly and brain malformations. Here, we report two patients with severe cortical dysgeneses, one with an extremely thin cerebral parenchyma apparently looking like hydranencephaly and the other with lissencephaly accompanied by marked hydrocephalus, both harbouring novel de novo missense mutations of TUBA1A. To elucidate how the various TUBA1A mutations affect the severity of the phenotype, we examined the capacity of the mutant protein to incorporate into the endogenous microtubule network in transfected COS7 cells by measuring line density using line extraction in an immunofluorescence study. The mutants responsible for severe phenotypes were found to incorporate extensively into the network. To determine how each mutant alters the microtubule stability, we examined cold-induced microtubule depolymerisation in fibroblasts. The depolymerisation of patients' fibroblasts occurred earlier than that of control fibroblasts, suggesting that microtubules bearing mutated tubulins are unstable. Both mutations are predicted to participate in lateral interactions of microtubules. Our data suggest that the TUBA1A mutations disrupting lateral interactions have pronounced dominant-negative effects on microtubule dynamics that are associated with the severe end of the lissencephaly spectrum.

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Late-onset epileptic spasms in a female patient with a CASK mutation.

Nakajiri T, Kobayashi K, Okamoto N, Oka M, Miya F, Kosaki K, Yoshinaga H

Brain & development （Brain and Development） 37 （ 9 ） 919 - 23 2015年10月

ISSN 0387-7604

We report a female patient with late-onset epileptic spasms (ESs) of a rare form, distinct from those seen in typical West syndrome, in association with a heterozygous frameshift CASK mutation (c.1896dupC (p.C633fs*2)). She has a phenotype of microcephaly with pontine and cerebellar hypoplasia (MICPCH), and has had intractable ESs in clusters since 3years 8months of age with multifocal, particularly bifrontal, epileptic discharges in electroencephalogram. The available literature on patients with both ESs and CASK mutations has been reviewed, revealing that four of the five female children, including the present girl, had late-onset ESs, in contrast to the four males, who tended toward early-onset ESs.

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A deletion mutation in myosin heavy chain 11 causing familial thoracic aortic dissection in two Japanese pedigrees.

Imai Y, Morita H, Takeda N, Miya F, Hyodo H, Fujita D, Tajima T, Tsunoda T, Nagai R, Kubo M, Komuro I

International journal of cardiology （International Journal of Cardiology） 195 290 - 2 2015年09月

ISSN 0167-5273

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Targeted next-generation sequencing in the diagnosis of neurodevelopmental disorders

Okamoto N., Miya F., Tsunoda T., Kato M., Saitoh S., Yamasaki M., Shimizu A., Torii C., Kanemura Y., Kosaki K.

Clinical Genetics （Clinical Genetics） 88 （ 3 ） 288 - 292 2015年09月

ISSN 00099163

We developed a next-generation sequencing (NGS) based mutation screening strategy for neurodevelopmental diseases. Using this system, we screened 284 genes in 40 patients. Several novel mutations were discovered. Patient 1 had a novel mutation in ACTB. Her dysmorphic feature was mild for Baraitser-Winter syndrome. Patient 2 had a truncating mutation of DYRK1A. She lacked microcephaly, which was previously assumed to be a constant feature of DYRK1A loss of function. Patient 3 had a novel mutation in GABRD gene. She showed Rett syndrome like features. Patient 4 was diagnosed with Noonan syndrome with PTPN11 mutation. He showed complete agenesis of corpus callosum. We have discussed these novel findings.

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Gene expression profiling of DBA/2J mice cochleae treated with l-methionine and valproic acid.

Miya F, Mutai H, Fujii M, Boroevich KA, Matsunaga T, Tsunoda T

Genomics data （Genomics Data） 5 323 - 5 2015年09月

ISSN 22135960

DBA/2J mice, which have homozygous mutations in Cdh23 and Fscn2, are characterized by early onset hearing loss at as early as three-weeks of age (Noben-Trauth et al., 2003 [1]) and are an animal model for progressive hearing loss research. Recently, it has been reported that epigenetic regulatory pathways likely play an important role in hearing loss (Provenzano and Domann, 2007 [2]; Mutai et al., 2009 [3]; Waldhaus et al., 2012 [4]). We previously reported that DBA/2J mice injected subcutaneously with a combination of epigenetic modifying reagents, l-methionine (MET) as methyl donor and valproic acid (VPA) as a pan-histone deacetylases (Hdac) inhibitor, showed a significant attenuation of progressive hearing loss by measuring their auditory brainstem response (ABR) thresholds (Mutai et al., 2015 [5]). Here we present genome wide expression profiling of the DBA/2J mice cochleae, with and without treatment of MET and VPA, to identify the genes involved in the reduction of progressive hearing loss. The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis.

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Primary microcephaly with anterior predominant pachygyria caused by novel compound heterozygous mutations in ASPM.

Nakamura K, Inui T, Miya F, Kanemura Y, Okamoto N, Saitoh S, Yamasaki M, Tsunoda T, Kosaki K, Tanaka S, Kato M

Pediatric neurology （Pediatric Neurology） 52 （ 5 ） e7 - 8 2015年05月

ISSN 0887-8994

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A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations.

Miya F, Kato M, Shiohama T, Okamoto N, Saitoh S, Yamasaki M, Shigemizu D, Abe T, Morizono T, Boroevich KA, Kosaki K, Kanemura Y, Tsunoda T

Scientific reports （Scientific Reports） 5 9331 2015年03月

Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (∼97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis.

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A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.

Hirokawa M, Morita H, Tajima T, Takahashi A, Ashikawa K, Miya F, Shigemizu D, Ozaki K, Sakata Y, Nakatani D, Suna S, Imai Y, Tanaka T, Tsunoda T, Matsuda K, Kadowaki T, Nakamura Y, Nagai R, Komuro I, Kubo M

European journal of human genetics : EJHG （European Journal of Human Genetics） 23 （ 3 ） 374 - 80 2015年03月

ISSN 1018-4813

Despite considerable progress in preventive and therapeutic strategies, myocardial infarction (MI) is one of the leading causes of death throughout the world. A total of 55 susceptibility genes have been identified mostly in European genome-wide association studies (GWAS). Nevertheless, large-scale GWAS from other population could possibly find additional susceptibility loci. To identify as many MI susceptibility loci as possible, we performed a large-scale genomic analysis in Japanese population. To identify MI susceptibility loci in Japanese, we conducted a GWAS using 1666 cases and 3198 controls using the Illumina Human610-Quad BeadChip and HumanHap550v3 Genotyping BeadChip. We performed replication studies using a total of 11 412 cases and 28 397 controls in the Japanese population. Our study identified two novel susceptibility loci for MI: PLCL2 on chromosome 3p24.3 (rs4618210:A>G, P=2.60 × 10 -9, odds ratio (OR)=0.91) and AP3D1-DOT1L-SF3A2 on chromosome 19p13.3 (rs3803915:A>C, P=3.84 × 10 -9, OR=0.89). Besides, a total of 14 previously reported MI susceptibility loci were replicated in our study. In particular, we validated a strong association on chromosome 12q24 (rs3782886:A>G: P=1.14 × 10 -14, OR=1.46). Following pathway analysis using 265 genes related to MI or coronary artery disease, we found that these loci might be involved in the pathogenesis of MI via the promotion of atherosclerosis. In the present large-scale genomic analysis, we identified PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for MI in the Japanese population. Our findings will add novel findings for MI susceptibility loci.

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Sudden death in a case of megalencephaly capillary malformation associated with a de novo mutation in AKT3.

Harada A, Miya F, Utsunomiya H, Kato M, Yamanaka T, Tsunoda T, Kosaki K, Kanemura Y, Yamasaki M

Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery （Child's Nervous System） 31 （ 3 ） 465 - 71 2015年03月

ISSN 0256-7040

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Attenuation of progressive hearing loss in DBA/2J mice by reagents that affect epigenetic modifications is associated with up-regulation of the zinc importer Zip4.

Mutai H, Miya F, Fujii M, Tsunoda T, Matsunaga T

PloS one （PLoS ONE） 10 （ 4 ） e0124301 2015年

Various factors that are important for proper hearing have been identified, including serum levels of zinc. Here we investigated whether epigenetic regulatory pathways, which can be modified by environmental factors, could modulate hearing. RT-PCR detected expression of genes encoding DNA methyltransferase and histone deacetylase (Hdac) in the postnatal as well as adult mouse auditory epithelium. DBA/2J mice, which are a model for progressive hearing loss, were injected subcutaneously with one or a combination of the following reagents: 〈smallcaps〉L〈/smallcaps〉-methionine as a methyl donor, valproic acid as a pan-Hdac inhibitor, and folic acid and vitamin B12 as putative factors involved in age-related hearing loss. The mice were treated from ages 4 to 12 weeks (N ≥ 5), and auditory brainstem response (ABR) thresholds were measured at 8, 16, and 32 kHz. Treatment of the mice with a combination of 〈smallcaps〉L〈/smallcaps〉-methionine and valproic acid (M+V) significantly reduced the increase in the ABR threshold at 32 kHz. Treatment with any of these reagents individually produced no such effect. Microarray analyses detected 299 gene probes that were significantly up- or down-regulated in the cochleae of mice treated with M+V compared with the control vehicle-treated mice. Quantitative RT-PCR confirmed significant up-regulation of a zinc importer gene, Zip4, in the cochleae of mice treated with M+V. Immunohistochemistry demonstrated an intense Zip4 signal in cochlear tissues such as the lateral wall, organ of Corti, and spiral ganglion. Finally, mice treated with the Zip4 inducer (-)-epigallocatechin-3-O-gallate showed a significant reduction in the increase of the ABR threshold at 32 kHz and up-regulation of Zip4 expression in the cochlea. This study suggests that epigenetic regulatory pathways can modify auditory function and that zinc intake in the cochlea via Zip4 mediates maintenance of mammalian hearing.

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Truncating mutation in NFIA causes brain malformation and urinary tract defects.

Negishi Y, Miya F, Hattori A, Mizuno K, Hori I, Ando N, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S

Human genome variation 2 15007 2015年

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Exome Analyses of Long QT Syndrome Reveal Candidate Pathogenic Mutations in Calmodulin-Interacting Genes.

Shigemizu D, Aiba T, Nakagawa H, Ozaki K, Miya F, Satake W, Toda T, Miyamoto Y, Fujimoto A, Suzuki Y, Kubo M, Tsunoda T, Shimizu W, Tanaka T

PloS one （PLoS ONE） 10 （ 7 ） e0130329 2015年

Long QT syndrome (LQTS) is an arrhythmogenic disorder that can lead to sudden death. To date, mutations in 15 LQTS-susceptibility genes have been implicated. However, the genetic cause for approximately 20% of LQTS patients remains elusive. Here, we performed whole-exome sequencing analyses on 59 LQTS and 61 unaffected individuals in 35 families and 138 unrelated LQTS cases, after genetic screening of known LQTS genes. Our systematic analysis of familial cases and subsequent verification by Sanger sequencing identified 92 candidate mutations in 88 genes for 23 of the 35 families (65.7%): these included eleven de novo, five recessive (two homozygous and three compound heterozygous) and seventy-three dominant mutations. Although no novel commonly mutated gene was identified other than known LQTS genes, protein-protein interaction (PPI) network analyses revealed ten new pathogenic candidates that directly or indirectly interact with proteins encoded by known LQTS genes. Furthermore, candidate gene based association studies using an independent set of 138 unrelated LQTS cases and 587 controls identified an additional novel candidate. Together, mutations in these new candidates and known genes explained 37.1% of the LQTS families (13 in 35). Moreover, half of the newly identified candidates directly interact with calmodulin (5 in 11; comparison with all genes; p=0.042). Subsequent variant analysis in the independent set of 138 cases identified 16 variants in the 11 genes, of which 14 were in calmodulin-interacting genes (87.5%). These results suggest an important role of calmodulin and its interacting proteins in the pathogenesis of LQTS.

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KIF1A mutation in a patient with progressive neurodegeneration.

Okamoto N, Miya F, Tsunoda T, Yanagihara K, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K

Journal of human genetics （Journal of Human Genetics） 59 （ 11 ） 639 - 41 2014年11月

ISSN 1434-5161

Kinesins are a large superfamily of molecular motors. They move along microtubule filaments and are powered by the hydrolysis of ATP. This transport system is essential for neuronal function and survival. KIF1A belongs to the kinesin 3 family and involves in the anterograde transport of synaptic vesicle precursors along axons. Several studies confirmed that KIF1A mutations cause spastic paraplegia and sensory neuropathy in an autosomal-recessive fashion. A missense mutation in the KIF1A gene (p.Thr99Met) has been reported in a patient with intellectual disability (ID), axial hypotonia and peripheral spasticity. Mild atrophy of the cerebellar vermis was found on magnetic resonance imaging. The mutation was heterozygous and de novo. We identified the second patient with the p.T99M mutation in the KIF1A gene by whole-exome sequencing. He showed severe ID, spasticity, optic atrophy, neurogenic bladder, growth failure and progressive cerebellar atrophy. The p.T99M mutation may be a common recurrent mutation. We suppose that this specific mutation of KIF1A shows a novel neurodegenerative syndrome.

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Morphological and microarray analyses of human hepatocytes from xenogeneic host livers.

Tateno C, Miya F, Wake K, Kataoka M, Ishida Y, Yamasaki C, Yanagi A, Kakuni M, Wisse E, Verheyen F, Inoue K, Sato K, Kudo A, Arii S, Itamoto T, Asahara T, Tsunoda T, Yoshizato K

Laboratory investigation; a journal of technical methods and pathology （Laboratory Investigation） 93 （ 1 ） 54 - 71 2013年01月

ISSN 0023-6837

We previously produced mice with human hepatocyte (h-hep) chimeric livers by transplanting h-heps into albumin enhancer/promoter-driven urokinase-type plasminogen activator-transgenic severe combined immunodeficient (SCID) mice with liver disease. The chimeric livers were constructed with h-heps, mouse hepatocytes, and mouse hepatic sinusoidal cells (m-HSCs). Here, we investigated the morphological features of the chimeric livers and the h-hep gene expression profiles in the xenogeneic animal body. To do so, we performed immunohistochemistry, morphometric analyses, and electron microscopic observations on chimeric mouse livers, and used microarray analyses to compare gene expression patterns in hepatocytes derived from chimeric mouse hepatocytes (c-heps) and h-heps. Morphometric analysis revealed that the ratio of hepatocytes to m-HSCs in the chimeric mouse livers were twofold higher than those in the SCID mouse livers, corresponding to twin-cell plates in the chimeric mouse liver. The h-heps in the chimeric mouse did not show hypoxia even in the twin-cell plate structure, probably because of low oxygen consumption by the h-heps relative to the mouse hepatocytes (m-heps). Immunohistochemical and electron microscopic examinations revealed that the sinusoids in the chimeric mouse livers were normally constructed with h-heps and m-HSCs. However, a number of microvilli projected into the intercellular clefts on the lateral aspects of the hepatocytes, features typical of a growth phase. Microarray profiles indicated that ∼82% of 16 605 probes were within a twofold range difference between h-heps and c-heps. Cluster and principal component analyses showed that the gene expression patterns of c-heps were extremely similar to those of h-heps. In conclusion, the chimeric mouse livers were normally reconstructed with h-heps and m-HSCs, and expressed most human genes at levels similar to those in human livers, although the chimeric livers showed morphological characteristics typical of growth. © 2013 USCAP, Inc All rights reserved.

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Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators.

Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H

Nature genetics （Nature Genetics） 44 （ 7 ） 760 - 4 2012年05月

ISSN 1061-4036

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of 27 HCCs, 25 of which were associated with hepatitis B or C virus infections, including two sets of multicentric tumors. Although no common somatic mutations were identified in the multicentric tumor pairs, their whole-genome substitution patterns were similar, suggesting that these tumors developed from independent mutations, although their shared etiological backgrounds may have strongly influenced their somatic mutation patterns. Statistical and functional analyses yielded a list of recurrently mutated genes. Multiple chromatin regulators, including ARID1A, ARID1B, ARID2, MLL and MLL3, were mutated in ∼50% of the tumors. Hepatitis B virus genome integration in the TERT locus was frequently observed in a high clonal proportion. Our whole-genome sequencing analysis of HCCs identified the influence of etiological background on somatic mutation patterns and subsequent carcinogenesis, as well as recurrent mutations in chromatin regulators in HCCs. © 2012 Nature America, Inc. All rights reserved.

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Growth hormone-dependent pathogenesis of human hepatic steatosis in a novel mouse model bearing a human hepatocyte-repopulated liver.

Tateno C, Kataoka M, Utoh R, Tachibana A, Itamoto T, Asahara T, Miya F, Tsunoda T, Yoshizato K

Endocrinology （Endocrinology） 152 （ 4 ） 1479 - 91 2011年04月

ISSN 0013-7227

Clinical studies have shown a close association between nonalcoholic fatty liver disease and adult-onset GH deficiency, but the relevant molecular mechanisms are still unclear. No mouse model has been suitable to study the etiological relationship ofhumannonalcoholic fatty liver disease and human adult-onset GH deficiency under conditions similar to the human liver in vivo. We generated human (h-)hepatocyte chimeric mice with livers that were predominantly repopulated with h-hepatocytes in a h-GH-deficient state. The chimeric mouse liver was mostly repopulated with h-hepatocytes about 50 d after transplantation and spontaneously became fatty in the h-hepatocyte regions after about 70 d. Infusion of the chimeric mouse with h-GH drastically decreased steatosis, showing the direct cause ofh-GH deficiency in the generation of hepatic steatosis. Using microarray profiles aided by real-time quantitative RT-PCR, comparison between h-hepatocytes from h-GH-untreated and -treated mice identified 14 GH-up-regulated and four GH-down-regulated genes, including IGF-I, SOCS2, NNMT, IGFLS, P4AH1, SLC16A1, SRD5A1, FADS1, and AKR1B10, respectively. These GH-up- and -down-regulated genes were expressed in the chimeric mouse liver at lower and higher levels than in human livers, respectively. Treatment of the chimeric mice with h-GH ameliorated their altered expression. h-Hepatocytes were separated from chimeric mouse livers for testing in vitro effects of h-GH or h-IGF-I on gene expression, and results showed that GH directly regulated the expression of IGF-I, SOCS2, NNMT, IGFALS, P4AH1, FADS1, and AKR1B10. In conclusion, the chimeric mouse is a novel h-GH-deficient animal model for studying in vivo h-GH-dependent human liver dysfunctions. Copyright © 2011 by The Endocrine Society.

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Predicting response of bladder cancers to gemcitabine and carboplatin neoadjuvant chemotherapy through genome-wide gene expression profiling.

Kato Y, Zembutsu H, Takata R, Miya F, Tsunoda T, Obara W, Fujioka T, Nakamura Y

Experimental and therapeutic medicine （Experimental and Therapeutic Medicine） 2 （ 1 ） 47 - 56 2011年01月

ISSN 1792-0981

Neoadjuvant chemotherapy with gemcitabine and carboplatin (GC) for invasive bladder cancer increases the chance of a radical response for a subset of patients, while other patients suffer from severe adverse drug reactions without any benefit. To establish a method for predicting the response to chemotherapy with GC, the expression profiles of biopsy samples from 37 advanced bladder cancers were analyzed using a microarray consisting of 38,500 genes or ESTs. Upon analysis of 9 'responder' and 9 'non-responder' tumors, 12 'predictive' genes were found to be significantly differentially expressed between the 'responder' and 'non-responder' groups, and a numerical prediction scoring system that clearly separated the responder group from the non-responder group was established. This system accurately predicted the drug responses of 18 of 19 additional test cases that were reserved from the original 37 cases. Moreover, a quantitative PCR-based prediction system was developed that may be feasible for routine clinical use, and the sensitivity of invasive bladder cancer to neoadjuvant chemotherapy with GC was able to be predicted by the expression patterns in this set of genes. Nearly 50% of patients treated with GC or methotrexate, vinblastine, doxorubicin and cisplatin (M-VAC) therapy have been reported to achieve complete or partial response to either of these therapies. When we applied this prediction system as well as the system for M-VAC, we expected that approximately 80% of the patients would achieve significant tumor shrinking (>60%) by selection of either the GC or M-VAC regimens. Our results suggest that the two prediction scoring systems lead to achievement of 'personalized therapy' for the treatment of invasive bladder cancer and should improve the quality of life for patients with this disease.

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Hepatitis C virus infection suppresses the interferon response in the liver of the human hepatocyte chimeric mouse.

Tsuge M, Fujimoto Y, Hiraga N, Zhang Y, Ohnishi M, Kohno T, Abe H, Miki D, Imamura M, Takahashi S, Ochi H, Hayes CN, Miya F, Tsunoda T, Chayama K

PloS one （PLoS ONE） 6 （ 8 ） e23856 2011年

Background and Aims: Recent studies indicate that hepatitis C virus (HCV) can modulate the expression of various genes including those involved in interferon signaling, and up-regulation of interferon-stimulated genes by HCV was reported to be strongly associated with treatment outcome. To expand our understanding of the molecular mechanism underlying treatment resistance, we analyzed the direct effects of interferon and/or HCV infection under immunodeficient conditions using cDNA microarray analysis of human hepatocyte chimeric mice. Methods: Human serum containing HCV genotype 1b was injected into human hepatocyte chimeric mice. IFN-α was administered 8 weeks after inoculation, and 6 hours later human hepatocytes in the mouse livers were collected for microarray analysis. Results: HCV infection induced a more than 3-fold change in the expression of 181 genes, especially genes related to Organismal Injury and Abnormalities, such as fibrosis or injury of the liver (P = 5.90E-16 ~ 3.66E-03). IFN administration induced more than 3-fold up-regulation in the expression of 152 genes. Marked induction was observed in the anti-fibrotic chemokines such as CXCL9, suggesting that IFN treatment might lead not only to HCV eradication but also prevention and repair of liver fibrosis. HCV infection appeared to suppress interferon signaling via significant reduction in interferon-induced gene expression in several genes of the IFN signaling pathway, including Mx1, STAT1, and several members of the CXCL and IFI families (P = 6.0E-12). Genes associated with Antimicrobial Response and Inflammatory Response were also significantly repressed (P = 5.22×10 -10 ~ 1.95×10 -2). Conclusions: These results provide molecular insights into possible mechanisms used by HCV to evade innate immune responses, as well as novel therapeutic targets and a potential new indication for interferon therapy. © 2011 Tsuge et al.

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Identification of a set of genes associated with response to interleukin-2 and interferon-α combination therapy for renal cell carcinoma through genome-wide gene expression profiling.

Mizumori O, Zembutsu H, Kato Y, Tsunoda T, Miya F, Morizono T, Tsukamoto T, Fujioka T, Tomita Y, Kitamura T, Ozono S, Miki T, Naito S, Akaza H, Nakamura Y

Experimental and therapeutic medicine （Experimental and Therapeutic Medicine） 1 （ 6 ） 955 - 961 2010年11月

ISSN 1792-0981

Interleukin (IL)-2 and interferon (IFN)-α combination therapy for metastatic renal cell carcinoma (RCC) improves the prognosis for a subset of patients, while some patients suffer from severe adverse drug reactions with little benefit. To establish a method to predict responses to this combination therapy (approximately 30% response rate), the gene expression profiles of primary RCCs were analyzed using an oligo DNA microarray consisting of 38,500 genes or ESTs, after enrichment of the cancer cell population by laser microbeam microdissection. The analysis of 10 responders and 18 non-responders identified 24 genes that exhibited significant differential expression between the two groups. In addition, the patients whose tumors did not express HLA-DQA1 or HLA-DQB1 molecules demonstrated poor clinical response. Exclusion of patients with tumors lacking either of these two genes is likely to improve the response rate to IL-2 and IFN-α combination therapy from 30 to 67%, indicating that a simple pretreatment test provides useful information with which to subselect patients with renal cancer in order to improve the efficacy of this treatment and reduce unnecessary medical costs.

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C-MYC overexpression with loss of Ink4a/Arf transforms bone marrow stromal cells into osteosarcoma accompanied by loss of adipogenesis

Shimizu T., Ishikawa T., Sugihara E., Kuninaka S., Miyamoto T., Mabuchi Y., Matsuzaki Y., Tsunoda T., Miya F., Morioka H., Nakayama R., Kobayashi E., Toyama Y., Kawai A., Ichikawa H., Hasegawa T., Okada S., Ito T., Ikeda Y., Suda T., Saya H.

Oncogene （Oncogene） 29 （ 42 ） 5687 - 5699 2010年10月

ISSN 09509232

The development of cancer is due to the growth and proliferation of transformed normal cells. Recent evidence suggests that the nature of oncogenic stress and the state of the cell of origin critically affect both tumorigenic activity and tumor histological type. However, this mechanistic relationship in mesenchymal tumors is currently largely unexplored. To clarify these issues, we established a mouse osteosarcoma (OS) model through overexpression of c-MYC in bone marrow stromal cells (BMSCs) derived from Ink4a/Arf (/) mice. Single-cell cloning revealed that c-MYC-expressing BMSCs are composed of two distinctly different clones: highly tumorigenic cells, similar to bipotent-committed osteochondral progenitor cells, and low-tumorigenic tripotent cells, similar to mesenchymal stem cells (MSCs). It is noteworthy that both bipotent and tripotent cells were capable of generating histologically similar, lethal OS, suggesting that both committed progenitor cells and MSCs can become OS cells of origin. Shifting mesenchymal differentiation by depleting PPARγ in tripotent MSC-like cells and overexpressing PPARγ in bipotent cells affected cell proliferation and tumorigenic activity. Our findings indicate that differentiation potential has a key role in OS tumorigenic activity, and that the suppression of adipogenic ability is a critical factor for the development of OS. © 2010 Macmillan Publishers Limited All rights reserved.

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Recombination rates of genes expressed in human tissues.

Kato M, Miya F, Kanemura Y, Tanaka T, Nakamura Y, Tsunoda T

Human molecular genetics （Human Molecular Genetics） 17 （ 4 ） 577 - 86 2008年02月

ISSN 0964-6906

High-resolution recombination rates have recently been revealed in the human genome, and considerable variation in patterns of recombination rates has been found along the chromosomes. Although the associations between this variation and genomic sequence features, such as genic regions, provide information on haplotype diversity and natural selection in these regions, the associations are not well understood. Here, we performed microarray experiments to identify genes specifically expressed in human tissues and investigated tendencies of recombination rates within tissue-specific genes. We found that some types of tissue-specific genes (in the frontal lobe, fetal brain, testis, thymus and thyroid) tended to have extremely low recombination rates, whereas other types (in the brain cerebellum, brain whole, stomach, lung and bone marrow) tended to have relatively high recombination rates. Surprisingly, genes specifically expressed in the frontal lobe, which is a brain region involved in human cognitive abilities, had low recombination rates, whereas genes specifically expressed in the cerebellum, which is a brain region with primitive functions shared by all vertebrate species, had high rates. These findings suggest that natural selection forms the recombination rate tendencies according to the physiological functions exerted in the tissues. For example, the low recombination rates in frontal lobe-specific genes may indicate that a few haplotypes have been rapidly widespread across the population because higher cognitive abilities are advantageous. Frontal lobe-specific genes with extremely low recombination rates may be candidates for genes related to cognitive abilities that human species have recently obtained. © 2007 The Author(s).

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Pravastatin at 10 mg/day does not decrease plasma levels of either amyloid-beta (Abeta) 40 or Abeta 42 in humans.

Ishii K, Tokuda T, Matsushima T, Miya F, Shoji S, Ikeda S, Tamaoka A

Neuroscience letters （Neuroscience Letters） 350 （ 3 ） 161 - 4 2003年10月

ISSN 0304-3940

It has been assumed that statins work as a preventative drug for Alzheimer's disease (AD). Although some epidemiological observations raise doubts to the effectiveness of statins for AD, many in vitro and clinical studies insist on the effectiveness of statins decreasing amyloid-β (Aβ) levels in medium or blood. To explore the effect of pravastatin on Aβ production, we followed the longitudinal plasma levels of both Aβ 40 and Aβ 42 during the allocation of pravastatin in 46 patients with hyperlipidemia. We found no correlation between plasma cholesterol levels or the decreasing values of total cholesterol and those of Aβ 40 or Aβ 42. Patients having Apolipoprotein E4 (ApoE4) had higher low-density lipoprotein levels and lower Aβ 40 levels in plasma, suggesting ApoE4 seems to influence plasma Aβ levels via cholesterol metabolism. © 2003 Elsevier Ireland Ltd. All rights reserved.

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Molecular cloning of ubiquitin-activating enzyme (E1) from Xenopus laevis

Miya F., Tokumoto M., Nagahama Y., Okida N., Ishikawa K., Tokumoto T.

Mitochondrial DNA （Mitochondrial DNA） 11 （ 3-4 ） 349 - 352 2000年12月

ISSN 19401736

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