Faculty Profiles - OGI Tomoo

Loss of neuronal activity facilitates surface accumulation of p75NTR and cell death in avian cochlear nucleus Open Access

Ryosuke Sato, Ryota Adachi, Norihiko Yokoi, Keita Tsujimura, Ryo Egawa, Yuichiro Hara, Yuko Fukata, Masaki Fukata, Tomoo Ogi, Michihiko Sone, Hiroshi Kuba

Neuroscience Research Vol. 213 page： 23 - 34 2025.4

Novel FBN1 intron variant causes isolated ectopia lentis via in-frame exon skipping Open Access

Shimizu, N; Mashimo, Y; Yokouchi, H; Nishio, Y; Sawai, S; Ichikawa, T; Ogi, T; Baba, T; Onouchi, Y

JOURNAL OF HUMAN GENETICS Vol. 70 ( 4 ) page： 199 - 205 2025.4

Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Human Genetics

Mutations in fibrillin-1 (FBN1) cause various clinical conditions, such as Marfan syndrome (MFS). However, the genotype–phenotype relationships underlying MFS and other conditions relevant to FBN1 mutations have not been fully elucidated. We performed whole-exome sequencing on three participants, including an affected mother–daughter pair, in a three-generation Japanese family with isolated ectopia lentis (IEL). The sequencing identified a novel single-nucleotide variant (c.1327+3A>C) in intron 11 of FBN1 that was shared between the two patients. We confirmed the co-segregation of the variant with IEL in two additional affected relatives in the family. The Combined Annotation-Dependent Depletion score of the variant was 26.1, which was indicated by SpliceAI to influence splicing, with a score of 0.93. Reverse transcription-polymerase chain reaction (RT-PCR) of mRNAs isolated from peripheral blood mononuclear cells revealed aberrant bands in all four affected individuals. Subsequent sequencing revealed that these bands originated from FBN1 transcripts lacking exon 11. The causality of the variant in the skipping of exon 11, which results in an in-frame deletion of 60 amino acids corresponding to the “hinge” region of FBN1 protein, was confirmed in a minigene experiment. Interestingly, the same result was observed for a minigene for c.1327+1G>A, a variant previously identified in two unrelated EL families without MFS manifestations. These results suggest that the c.1327+3A>C mutation in FBN1 likely leads to IEL. The findings expand our knowledge of FBN1 and provide insights into FBN1-related diseases.

DOI： 10.1038/s10038-025-01318-0

Estimating the proportions of allele frequencies for SERPINA12 pathogenic variants in Japanese patients with Nagashima-type palmoplantar keratosis/keratoderma. International journal

Aoi Ebata, Takuya Takeichi, Kazuki Nishida, Basile Chretien, Akira Miyazaki, Takenori Yoshikawa, Yuika Suzuki, Kana Tanahashi, Ryo Fukaura, Mariko Seishima, Yasushi Suga, Yoshinao Muro, Yuka Nakazawa, Tomoo Ogi, Masashi Akiyama

The British journal of dermatology 2025.3

Whole-genome sequencing analysis of Japanese autism spectrum disorder trios Open Access

Furukawa, S; Kushima, I; Kato, H; Kimura, H; Nawa, Y; Aleksic, B; Banno, M; Yamamoto, M; Uematsu, M; Nagasaki, Y; Ogi, T; Ozaki, N; Ikeda, M

PSYCHIATRY AND CLINICAL NEUROSCIENCES Vol. 79 ( 3 ) page： 87 - 97 2025.3

Language：English Publishing type：Research paper (scientific journal) Publisher：Psychiatry and Clinical Neurosciences

Aim: Autism spectrum disorder (ASD) is a genetically and phenotypically heterogeneous neurodevelopmental disorder with a strong genetic basis. Conducting the first comprehensive whole-genome sequencing (WGS) analysis of Japanese ASD trios, this study aimed to elucidate the clinical significance of pathogenic variants and enhance the understanding of ASD pathogenesis. Methods: WGS was performed on 57 Japanese patients with ASD and their parents, investigating variants ranging from single-nucleotide variants to structural variants (SVs), short tandem repeats (STRs), mitochondrial variants, and polygenic risk score (PRS). Results: Potentially pathogenic variants that could explain observed phenotypes were identified in 18 patients (31.6%) overall and in 10 of 23 patients (43.5%) with comorbid intellectual developmental disorder (IDD). De novo variants in PTEN, CHD7, and HNRNPH2 were identified in patients referred for genetic counseling who exhibited previously reported phenotypes, including one patient with ASD who had profound IDD and macrocephaly with PTEN L320S. Analysis of the AlphaFold3 protein structure indicated potential inhibition of intramolecular interactions within PTEN. SV analysis identified deletions in ARHGAP11B and TMLHE. A pathogenic de novo mitochondrial variant was identified in a patient with ASD who had a history of encephalitis and cognitive decline. GO enrichment analysis of genes with nonsense variants and missense variants (Missense badness, PolyPhen-2, and Constraint >1) showed associations with regulation of growth and ATP-dependent chromatin remodeler activity. No reportable results were obtained in the analysis of STR and PRS. Conclusion: Characterizing the comprehensive genetic architecture and phenotypes of ASD is a fundamental step towards unraveling its complex biology.

DOI： 10.1111/pcn.13767

Pathophysiological significance of the p.E31G variant in RAC1 responsible for a neurodevelopmental disorder with microcephaly Reviewed

WHOLE GENOME SEQUENCING ANALYSIS OF JAPANESE ASD TRIOS: UNRAVELING PATHOGENIC VARIANTS Open Access

Furukawa, S; Kushima, I; Kimura, H; Kato, H; Nawa, Y; Aleksic, B; Ogi, T; Ozaki, N; Ikeda, M

INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY Vol. 28 page： i59 - i59 2025.2

Prenatal inflammation impairs early CD11c-positive microglia induction and delays myelination in neurodevelopmental disorders. International journal Open Access

Kazuya Fuma, Yukako Iitani, Kenji Imai, Takafumi Ushida, Sho Tano, Kosuke Yoshida, Akira Yokoi, Rika Miki, Hiroyuki Kidokoro, Yoshiaki Sato, Yuichiro Hara, Tomoo Ogi, Kohei Nomaki, Makoto Tsuda, Okiru Komine, Koji Yamanaka, Hiroaki Kajiyama, Tomomi Kotani

Communications biology Vol. 8 ( 1 ) page： 75 - 75 2025.1

Language：English Publishing type：Research paper (scientific journal)

Histological chorioamnionitis (HCA) is a form of maternal immune activation (MIA) linked to an increased risk of neurodevelopmental disorders in offspring. Our previous study identified neurodevelopmental impairments in an MIA mouse model mimicking HCA. Thus, this study investigated the role of CD11c+ microglia, key contributors to myelination through IGF-1 production, in this pathology. In the mouse model, the CD11c+ microglial population was significantly lower in the MIA group than in the control group on postnatal day 3 (PN3d). Furthermore, myelination-related protein levels significantly decreased in the MIA group at PN8d. In humans, preterm infants with HCA exhibited higher IL-6 and IL-17A cord-serum levels and lower IGF-1 levels than those without HCA, followed by a higher incidence of delayed myelination on magnetic resonance imaging at the term-equivalent age. In silico analysis revealed that the transient induction of CD11c+ microglia during early development occurred similarly in mice and humans. Notably, a lack of high CD11c+ microglial population has been observed in children with neurodevelopmental disorders. This study reports impaired induction of CD11c+ microglia during postnatal development in a mouse model of MIA associated with delayed myelination. Our findings may inform strategies for improving outcomes in infants with HCA.

DOI： 10.1038/s42003-025-07511-3

Nishikawa, M; Hayashi, S; Nakayama, A; Nishio, Y; Shiraki, A; Ito, H; Maruyama, K; Muramatsu, Y; Ogi, T; Mizuno, S; Nagata, K

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE Vol. 1871 ( 1 ) 2025.1

Language：English Publishing type：Research paper (scientific journal) Publisher：Biochimica et Biophysica Acta - Molecular Basis of Disease

RAC1 encodes a Rho family small GTPase that regulates actin cytoskeletal reorganization and intracellular signaling pathways. Pathogenic RAC1 variants lead to a neurodevelopmental disorder with diverse phenotypic manifestations, including abnormalities in brain size and facial dysmorphism. However, the underlying pathophysiological mechanisms have yet to be elucidated. Here, we present the case of a school-aged male who exhibited global developmental delay, intellectual disability, and acquired microcephaly. Through whole exome sequencing, we identified a novel de novo variant in RAC1, (NM_006908.5): c.92 A > G,p.(E31G). We then examined the pathophysiological significance of the p.E31G variant by focusing on brain development. Biochemical analyses revealed that the recombinant RAC1-E31G had no discernible impact on the intrinsic GDP/GTP exchange activity. However, it exhibited a slight inhibitory effect on GTP hydrolysis. Conversely, it demonstrated a typical response to both a guanine-nucleotide exchange factor and a GTPase-activating protein. In transient expression analyses using COS7 cells, RAC1-E31G exhibited minimal interaction with the downstream effector PAK1, even in its GTP-bound state. Additionally, overexpression of RAC1-E31G was observed to exert a weak inhibitory effect on the differentiation of primary cultured hippocampal neurons. Moreover, in vivo studies employing in utero electroporation revealed that acute expression of RAC1-E31G resulted in impairments in axonal elongation and dendritic arborization in the young adult stage. These findings suggest that the p.E31G variant functions as a dominant-negative version in the PAK1-mediated signaling pathway and is responsible for the clinical features observed in the patient under investigation, namely microcephaly and intellectual disability.

DOI： 10.1016/j.bbadis.2024.167520

Desulfovibrio falkowii sp. nov., Porphyromonas miyakawae sp. nov., Mediterraneibacter flintii sp. nov. and Owariibacterium komagatae gen. nov., sp. nov., isolated from human faeces. Open Access

Transcription‐coupled repair – mechanisms of action, regulation, and associated human disorders Open Access

Yuka Nakazawa, Yasuyoshi Oka, Tomoko Matsunaga, Tomoo Ogi

FEBS Letters Vol. 599 ( 2 ) page： 166 - 167 2025.1

Hamaguchi T, Ohara M, Hisatomi A, Sekiguchi K, Takeda JI, Ueyama J, Ito M, Nishiwaki H, Ogi T, Hirayama M, Ohkuma M, Sakamoto M, Ohno K

International journal of systematic and evolutionary microbiology Vol. 75 ( 1 ) 2025.1

Language：English Publishing type：Research paper (scientific journal) Publisher：International Journal of Systematic and Evolutionary Microbiology

Small, obligately anaerobic strains 13CB8CT, 13CB11CT, 13CB18CT and 13GAM1GT were isolated from a faecal sample in a patient with Parkinson’s disease with a history of duodenal resection. After conducting a comprehensive polyphasic taxonomic analysis including genomic analysis, we propose the establishment of one new genus and four new species. The novel bacteria are Desulfovibrio falkowii sp. nov. (type strain JCM 36128T = DSM 116810T), Porphyromonas miyakawae sp. nov. (type strain JCM 36129T = DSM 116947T), Mediterraneibacter flintii sp. nov. (type strain JCM 36130T = DSM 116866T) and Owariibacterium komaga-tae gen. nov. sp. nov. (type strain JCM 36131T = DSM 116982T), respectively.

DOI： 10.1099/ijsem.0.006636

Open Access

Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription, presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions Reviewed

Clinical and molecular overlap between nucleotide excision repair (NER) disorders and DYRK1A haploinsufficiency syndrome. Open Access

Le May N, Courraud J, Boujelbène I, Obringer C, Ogi T, Lehmann AR, Laffargue F, Lehalle D, Mizuno S, Mohammed S, Ormières C, Willems M, Laugel V, Calmels N

Frontiers in neuroscience Vol. 19 page： 1554093 2025

Neonatal myoclonus in Bryant-Li-Bhoj syndrome associated with a novel H3F3A variant Open Access

Hojo, M; Soma, N; Yamada, K; Kobayashi, Y; Miura, M; Fujii, H; Nyuzuki, H; Nishio, Y; Oso, T; Ogi, T; Ikeuchi, T; Tohyama, J

HUMAN GENOME VARIATION Vol. 11 ( 1 ) page： 45 2024.12

Language：English Publishing type：Research paper (scientific journal) Publisher：Human Genome Variation

Bryant-Li-Bhoj syndrome (BLBS; OMIM # 619720, 619721), caused by germline H3F3A and H3F3B variants encoding histone H3.3, is characterized by mild to severe developmental delay, intellectual disability, failure to thrive, muscle tone abnormalities, and dysmorphic facial features. Here, we present a Japanese patient with a novel heterozygous p.A48G variant in H3F3A, displaying previously unrecognized symptoms of neonatal myoclonus. This case helps broaden the phenotypic spectrum of BLBS.

DOI： 10.1038/s41439-024-00303-x

ALS-linked mutant TDP-43 in oligodendrocytes induces oligodendrocyte damage and exacerbates motor dysfunction in mice. International journal Open Access

Mai Horiuchi, Seiji Watanabe, Okiru Komine, Eiki Takahashi, Kumi Kaneko, Shigeyoshi Itohara, Mayuko Shimada, Tomoo Ogi, Koji Yamanaka

Acta neuropathologica communications Vol. 12 ( 1 ) page： 184 - 184 2024.11

Language：English Publishing type：Research paper (scientific journal)

Nuclear clearance and cytoplasmic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) are pathological hallmarks of amyotrophic lateral sclerosis (ALS) and its pathogenic mechanism is mediated by both loss-of-function and gain-of-toxicity of TDP-43. However, the role of TDP-43 gain-of-toxicity in oligodendrocytes remains unclear. To investigate the impact of excess TDP-43 on oligodendrocytes, we established transgenic mice overexpressing the ALS-linked mutant TDP-43M337V in oligodendrocytes through crossbreeding with Mbp-Cre mice. Two-step crossbreeding of floxed TDP-43M337V and Mbp-Cre mice resulted in the heterozygous low-level systemic expression of TDP-43M337V with (Cre-positive) or without (Cre-negative) oligodendrocyte-specific overexpression of TDP-43M337V. Although Cre-negative mice also exhibit subtle motor dysfunction, TDP-43M337V overexpression in oligodendrocytes aggravated clasping signs and gait disturbance accompanied by myelin pallor in the corpus callosum and white matter of the lumbar spinal cord in Cre-positive mice. RNA sequencing analysis of oligodendrocyte lineage cells isolated from whole brains of 12-month-old transgenic mice revealed downregulation of myelinating oligodendrocyte marker genes and cholesterol-related genes crucial for myelination, along with marked upregulation of apoptotic pathway genes. Immunofluorescence staining showed cleaved caspase 3-positive apoptotic oligodendrocytes surrounded by activated microglia and astrocytes in aged transgenic mice. Collectively, our findings demonstrate that an excess amount of ALS-linked mutant TDP-43 expression in oligodendrocytes exacerbates motor dysfunction in mice, likely through oligodendrocyte dysfunction and neuroinflammation. Therefore, targeting oligodendrocyte protection, particularly through ameliorating TDP-43 pathology, could represent a potential therapeutic approach for ALS.

DOI： 10.1186/s40478-024-01893-x

Yasuda T., Nakajima N., Ogi T., Yanaka T., Tanaka I., Gotoh T., Kagawa W., Sugasawa K., Tajima K.

PLoS ONE Vol. 19 ( 10 October ) 2024.10

Language：English Publishing type：Research paper (scientific journal) Publisher：PLoS ONE

Heavy water, containing the heavy hydrogen isotope, is toxic to cells, although the underlying mechanism remains incompletely understood. In addition, certain enzymatic proton transfer reactions exhibit kinetic isotope effects attributed to hydrogen isotopes and their temperature dependencies, indicative of quantum tunneling phenomena. However, the correlation between the biological effects of heavy water and the kinetic isotope effects mediated by hydrogen isotopes remains elusive. In this study, we elucidated the kinetic isotope effects arising from hydrogen isotopes of water and their temperature dependencies in vitro, focusing on deacetylation, DNA cleavage, and protein cleavage, which are crucial enzymatic reactions mediated by hydrolysis. Intriguingly, the intracellular isotope effects of heavy water, related to the in vitro kinetic isotope effects, significantly impeded multiple DNA double-strand break repair mechanisms crucial for cell survival. Additionally, heavy water exposure enhanced histone acetylation and associated transcriptional activation in cells, consistent with the in vitro kinetic isotope effects observed in histone deacetylation reactions. Moreover, as observed for the in vitro kinetic isotope effects, the cytotoxic effect on cell proliferation induced by heavy water exhibited temperature-dependency. These findings reveal the substantial impact of heavy water-induced isotope effects on cellular functions governed by hydrolytic enzymatic reactions, potentially mediated by quantum-level mechanisms underlying kinetic isotope effects.

DOI： 10.1371/journal.pone.0309689

Treatment-resistant schizophrenia with 22q11.2 deletion and additional genetic defects Reviewed

Furukawa, S; Arafuka, S; Kato, H; Ogi, T; Ozaki, N; Ikeda, M; Kushima, I

NEUROPSYCHOPHARMACOLOGY REPORTS 2024.8

Language：English Publishing type：Research paper (scientific journal) Publisher：Neuropsychopharmacology Reports

We report a case of a 61-year-old female with 22q11.2 deletion syndrome (22q11.2DS) and a novel heterozygous nonsense variant in MAP1A, identified through whole-genome sequencing (WGS). The patient presented with intellectual developmental disorder, treatment-resistant schizophrenia (SCZ), and multiple congenital anomalies. Despite aggressive pharmacotherapy, she experienced persistent auditory hallucinations and negative symptoms. WGS revealed a 3 Mb deletion at 22q11.2 and a nonsense variant in MAP1A (c.4652T>G, p.Leu1551*). MAP1A, encoding microtubule-associated protein 1A, is crucial for axon and dendrite development and has been implicated in autism spectrum disorder and SCZ. The MAP1A variant may contribute to the severe psychiatric phenotype, as it is thought to influence synaptic plasticity, a process also affected by 22q11.2 deletion. This case highlights the importance of WGS in identifying additional pathogenic variants that may explain phenotypic variability in 22q11.2DS. Thus, WGS can lead to a better understanding of the genetic architecture of 22q11.2DS. However, further studies are needed to elucidate the role of secondary genetic contributors in the diverse clinical presentations of 22q11.2DS.

DOI： 10.1002/npr2.12477

The small CRL4CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics Reviewed

Localized epidermolysis bullosa simplex caused by a previously unreported substitution in the linker 12 domain of keratin 14. Reviewed International journal

Miyu Misaki, Takuya Takeichi, Michiya Omi, Yasutoshi Ito, Tomoo Ogi, Yoshinao Muro, Masashi Akiyama

The Journal of dermatology Vol. 51 ( 8 ) page： e264 - e265 2024.8

Schiffmacher, DAL; Lee, SH; Kliza, KW; Theil, AF; Akita, M; Helfricht, A; Bezstarosti, K; Gonzalo-Hansen, C; van Attikum, H; Verlaan-de Vries, M; Vertegaal, ACO; Hoeijmakers, JHJ; Marteijn, JA; Lans, H; Demmers, JAA; Vermeulen, M; Sixma, TK; Ogi, T; Vermeulen, W; Pines, A

NATURE COMMUNICATIONS Vol. 15 ( 1 ) 2024.7

Language：English Publishing type：Research paper (scientific journal) Publisher：Nature Communications

Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA polymerase II at DNA lesions, which triggers the assembly of the TC-NER-specific proteins CSA, CSB and UVSSA. CSA, a WD40-repeat containing protein, is the substrate receptor subunit of a cullin-RING ubiquitin ligase complex composed of DDB1, CUL4A/B and RBX1 (CRL4CSA). Although ubiquitination of several TC-NER proteins by CRL4CSA has been reported, it is still unknown how this complex is regulated. To unravel the dynamic molecular interactions and the regulation of this complex, we apply a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis shows that DDA1 is an integral component of the CRL4CSA complex. Functional analysis reveals that DDA1 coordinates ubiquitination dynamics during TC-NER and is required for efficient turnover and progression of this process.

DOI： 10.1038/s41467-024-50584-7

Dyssegmental dysplasia Rolland-Desbuquois type is caused by pathogenic variants in HSPG2 - a founder haplotype shared in five patients. Reviewed International journal

Paniz Farshadyeganeh, Takahiro Yamada, Hirofumi Ohashi, Gen Nishimura, Hiroki Fujita, Yuriko Oishi, Misa Nunode, Shuku Ishikawa, Jun Murotsuki, Yuri Yamashita, Shiro Ikegawa, Tomoo Ogi, Eri Arikawa-Hirasawa, Kinji Ohno

Journal of human genetics Vol. 69 ( 6 ) page： 235 - 244 2024.6

Language：English Publishing type：Research paper (scientific journal)

Dyssegmental dysplasia (DD) is a severe skeletal dysplasia comprised of two subtypes: lethal Silverman-Handmaker type (DDSH) and nonlethal Rolland-Desbuquois type (DDRD). DDSH is caused by biallelic pathogenic variants in HSPG2 encoding perlecan, whereas the genetic cause of DDRD remains undetermined. Schwartz-Jampel syndrome (SJS) is also caused by biallelic pathogenic variants in HSPG2 and is an allelic disorder of DDSH. In SJS and DDSH, 44 and 8 pathogenic variants have been reported in HSPG2, respectively. Here, we report that five patients with DDRD carried four pathogenic variants in HSPG2: c.9970 G > A (p.G3324R), c.559 C > T (p.R187X), c7006 + 1 G > A, and c.11562 + 2 T > G. Two patients were homozygous for p.G3324R, and three patients were heterozygous for p.G3324R. Haplotype analysis revealed a founder haplotype spanning 85,973 bp shared in the five patients. SJS, DDRD, and DDSH are allelic disorders with pathogenic variants in HSPG2.

DOI： 10.1038/s10038-024-01229-6

Two patients with Hailey-Hailey disease with novel pathogenic ATP2C1 variants suggesting possible genotype/phenotype correlations. Reviewed International journal

Michiya Omi, Takuya Takeichi, Yasutoshi Ito, Takenori Yoshikawa, Yuki Mizutani, Miki Nagai, Mariko Seishima, Tomoo Ogi, Yoshinao Muro, Masashi Akiyama

The Journal of dermatology Vol. 51 ( 6 ) page： e185 - e187 2024.6

Clearance of DNA damage-arrested RNAPII is selectively impaired in Cockayne syndrome cells Reviewed

Paula J. van der Meer, George Yakoub, Yuka Nakazawa, Tomoo Ogi, Martijn Luijsterburg

2024.5

Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair. Reviewed International journal

Yasuyoshi Oka, Yuka Nakazawa, Mayuko Shimada, Tomoo Ogi

Nature cell biology Vol. 26 ( 5 ) page： 784 - 796 2024.5

Language：English Publishing type：Research paper (scientific journal)

DNA-protein crosslinks (DPCs) induced by aldehydes interfere with replication and transcription. Hereditary deficiencies in DPC repair and aldehyde clearance processes cause progeria, including Ruijs-Aalfs syndrome (RJALS) and AMeD syndrome (AMeDS) in humans. Although the elimination of DPC during replication has been well established, how cells overcome DPC lesions in transcription remains elusive. Here we show that endogenous aldehyde-induced DPC roadblocks are efficiently resolved by transcription-coupled repair (TCR). We develop a high-throughput sequencing technique to measure the genome-wide distribution of DPCs (DPC-seq). Using proteomics and DPC-seq, we demonstrate that the conventional TCR complex as well as VCP/p97 and the proteasome are required for the removal of formaldehyde-induced DPCs. TFIIS-dependent cleavage of RNAPII transcripts protects against transcription obstacles. Finally, a mouse model lacking both aldehyde clearance and TCR confirms endogenous DPC accumulation in actively transcribed regions. Collectively, our data provide evidence that transcription-coupled DPC repair (TC-DPCR) as well as aldehyde clearance are crucial for protecting against metabolic genotoxin, thus explaining the molecular pathogenesis of AMeDS and other disorders associated with defects in TCR, such as Cockayne syndrome.

DOI： 10.1038/s41556-024-01401-2

TERT Promoter Mutations Increase Tumor Aggressiveness by Altering TERT mRNA Splicing in Papillary Thyroid Carcinoma Reviewed

Natal teeth, hypoplasia of the first toe, and growth retardation in a patient with severe epidermolysis bullosa simplex. Reviewed International journal

Maiko Shimomura-Ishihara, Takuya Takeichi, Tatsuhiro Noda, Haruka Koizumi, Teruyuki Mitsuma, Tomoo Ogi, Yoshinao Muro, Masashi Akiyama

The Journal of dermatology Vol. 51 ( 5 ) page： e175 - e177 2024.5

Sako, A; Matsuse, M; Saenko, V; Tanaka, A; Otsubo, R; Morita, M; Kuba, S; Nishihara, E; Suzuki, K; Ogi, T; Kawakami, A; Mitsutake, N

JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM Vol. 109 ( 10 ) page： e1827 - e1838 2024.4

Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Clinical Endocrinology and Metabolism

Context: Telomerase reverse transcriptase promoter (TERT-p) mutations, which upregulate TERT expression, are strongly associated with tumor aggressiveness and worse prognosis in papillary thyroid carcinomas (PTCs). TERT expression is also observed in a proportion of PTCs without TERT-p mutations, but such tumors show less aggressiveness and better prognosis than TERT-p mutation-positive tumors. Objective: TERT has multiple splicing variants whose relationships with the TERT-p status and clinicopathological characteristics remain poorly understood. We examined the relationship between the TERT-p mutational status, the TERT splicing pattern, and clinicopathological features. Methods: We investigated the expression of 2 major variants, α deletion (dA) and β deletion (dB), in a series of 207 PTCs operated on between November 2001 and March 2020 in Nagasaki University Hospital and Kuma Hospital. Results: The TERT-p mutations were found in 33 cases, and among 174 mutation-negative cases, 24 showed TERT expression. All cases were classified into 3 groups: the TERT-p mutation-negative/expression-negative group (mut-/exp-), the TERT-p mutation-negative/expression-positive group (mut-/exp+), and the TERT-p mutation-positive group (mut+/exp+). The +A+B/dB ratio in mut+/exp+ was significantly higher than that in mut-/exp+ PTCs. Analysis with clinicopathological data revealed that +A+B expression was associated with higher PTC aggressiveness, whereas dB expression counteracted this effect. Functional in vitro study demonstrated that dB strongly inhibited cell growth, migration, and clonogenicity, suggesting its tumor-suppressive role. Conclusion: These results provide evidence that the TERT-p mutations alter the expression of different TERT splice variants, which, in turn, associates with different tumor aggressiveness.

DOI： 10.1210/clinem/dgae220

MEFV variants are a predisposing factor for generalized pustular psoriasis Reviewed

Yoshikawa, T; Takeichi, T; Nishida, K; Kobayashi, Y; Sano, H; Shibata, A; Koizumi, H; Tsutsumi, R; Fukaura, R; Hayashi, M; Imanishi, A; Nakamura, K; Mikoshiba, Y; Ogawa, E; Sano, S; Kinoshita, M; Okamoto, T; Kageyama, R; Sano, Y; Kaneko, S; Aoi, J; Hara, T; Togawa, Y; Kishibe, M; Yoshida, Y; Yagi, H; Honda, T; Sugiura, K; Sano, S; Suzuki, T; Ogi, T; Muro, Y; Akiyama, M

JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY Vol. 90 ( 4 ) page： 852 - 854 2024.4

Updated mutational spectrum and genotype-phenotype correlations in ichthyosis patients with ABCA12 pathogenic variants. Reviewed International journal

Tatsuhiro Noda, Takuya Takeichi, Kana Tanahashi, Yasushi Ogawa, So Takeuchi, Takenori Yoshikawa, Erika Toriyama, Miwa Ashida, Sumihisa Imakado, Hitoshi Tsuchihashi, Takashi Okamoto, Yusuke Okuno, Tomoo Ogi, Kazumitsu Sugiura, Akiharu Kubo, Yoshinao Muro, Yasushi Suga, Akemi Ishida-Yamamoto, Masashi Akiyama

Experimental dermatology Vol. 33 ( 4 ) page： e15072 2024.4

Language：English Publishing type：Research paper (scientific journal)

Autosomal recessive congenital ichthyoses (ARCI) is a genetically heterogeneous condition that can be caused by pathogenic variants in at least 12 genes, including ABCA12. ARCI mainly consists of congenital ichthyosiform erythroderma (CIE), lamellar ichthyosis (LI) and harlequin ichthyosis (HI). The objective was to determine previously unreported pathogenic variants in ABCA12 and to update genotype-phenotype correlations for patients with pathogenic ABCA12 variants. Pathogenic variants in ABCA12 were detected using Sanger sequencing or a combination of Sanger sequencing and whole-exome sequencing. To verify the pathogenicity of a previously unreported large deletion and intron variant, cDNA analysis was performed using total RNA extracted from hair roots. Genetic analyses were performed on the patients with CIE, LI, HI and non-congenital ichthyosis with unusual phenotypes (NIUP), and 11 previously unreported ABCA12 variants were identified. Sequencing of cDNA confirmed the aberrant splicing of the variant ABCA12 in the patients with the previously unreported large deletion and intron variant. Our findings expand the phenotype spectrum of ichthyosis patients with ABCA12 pathogenic variants. The present missense variants in ABCA12 are considered to be heterogenous in pathogenicity, and they lead to varying disease severities in patients with ARCI and non-congenital ichthyosis with unusual phenotypes (NIUP).

DOI： 10.1111/exd.15072

Calcitriol ameliorates motor deficits and prolongs survival of Chrne-deficient mouse, a model for congenital myasthenic syndrome, by inducing Rspo2. Reviewed International journal

Bisei Ohkawara, Hiroyuki Tomita, Taro Inoue, Shaochuan Zhang, Shunsuke Kanbara, Hiroyuki Koshimizu, Yuki Miyasaka, Jun-Ichi Takeda, Hiroshi Nishiwaki, Hiroaki Nakashima, Mikako Ito, Akio Masuda, Naoki Ishiguro, Tomoo Ogi, Tamio Ohno, Shiro Imagama, Kinji Ohno

Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics Vol. 21 ( 2 ) page： e00318 2024.3

Language：English Publishing type：Research paper (scientific journal)

Signal transduction at the neuromuscular junction (NMJ) is compromised in a diverse array of diseases including congenital myasthenic syndromes (CMS). Germline mutations in CHRNE encoding the acetylcholine receptor (AChR) ε subunit are the most common cause of CMS. An active form of vitamin D, calcitriol, binds to vitamin D receptor (VDR) and regulates gene expressions. We found that calcitriol enhanced MuSK phosphorylation, AChR clustering, and myotube twitching in co-cultured C2C12 myotubes and NSC34 motor neurons. RNA-seq analysis of co-cultured cells showed that calcitriol increased the expressions of Rspo2, Rapsn, and Dusp6. ChIP-seq of VDR revealed that VDR binds to a region approximately 15 kbp upstream to Rspo2. Biallelic deletion of the VDR-binding site of Rspo2 by CRISPR/Cas9 in C2C12 myoblasts/myotubes nullified the calcitriol-mediated induction of Rspo2 expression and MuSK phosphorylation. We generated Chrne knockout (Chrne KO) mouse by CRISPR/Cas9. Intraperitoneal administration of calcitriol markedly increased the number of AChR clusters, as well as the area, the intensity, and the number of synaptophysin-positive synaptic vesicles, in Chrne KO mice. In addition, calcitriol ameliorated motor deficits and prolonged survival of Chrne KO mice. In the skeletal muscle, calcitriol increased the gene expressions of Rspo2, Rapsn, and Dusp6. We propose that calcitriol is a potential therapeutic agent for CMS and other diseases with defective neuromuscular signal transmission.

DOI： 10.1016/j.neurot.2024.e00318

Genetic background variation impacts microglial heterogeneity and disease progression in amyotrophic lateral sclerosis model mice. Reviewed International journal

Okiru Komine, Syuhei Ohnuma, Kunihiko Hinohara, Yuichiro Hara, Mayuko Shimada, Tomohiro Akashi, Seiji Watanabe, Akira Sobue, Noe Kawade, Tomoo Ogi, Koji Yamanaka

iScience Vol. 27 ( 2 ) page： 108872 - 108872 2024.2

Language：English Publishing type：Research paper (scientific journal)

Recent single-cell analyses have revealed the complexity of microglial heterogeneity in brain development, aging, and neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Disease-associated microglia (DAMs) have been identified in ALS mice model, but their role in ALS pathology remains unclear. The effect of genetic background variations on microglial heterogeneity and functions remains unknown. Herein, we established and analyzed two mice models of ALS with distinct genetic backgrounds of C57BL/6 and BALB/c. We observed that the change in genetic background from C57BL/6 to BALB/c affected microglial heterogeneity and ALS pathology and its progression, likely due to the defective induction of neurotrophic factor-secreting DAMs and impaired microglial survival. Single-cell analyses of ALS mice revealed new markers for each microglial subtype and a possible association between microglial heterogeneity and systemic immune environments. Thus, we highlighted the role of microglia in ALS pathology and importance of genetic background variations in modulating microglial functions.

DOI： 10.1016/j.isci.2024.108872

Next-generation sequencing-based detection of Ureaplasma in the gastric fluid of neonates with respiratory distress and chorioamnionitis Reviewed

Okumura Toshihiko, Horiba Kazuhiro, Tetsuka Nobuyuki, Sato Yoshiaki, Sugiyama Yuichiro, Haruta Kazunori, Yamaguchi Makoto, Suzuki Takako, Torii Yuka, Kawada Jun-ichi, Ogi Tomoo, Hayakawa Masahiro, Ito Yoshinori

JOURNAL OF MATERNAL-FETAL & NEONATAL MEDICINE Vol. 36 ( 1 ) page： 2207113 2023.12

Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Maternal-Fetal and Neonatal Medicine

Background: Respiratory distress is common in neonates admitted to neonatal intensive care units. Additionally, infectious diseases such as intrauterine infections or vertical transmission are important underlying causes of respiratory failure. However, pathogens often cannot be identified in neonates, and there are many cases in which antibacterial drugs are empirically administered. Next-generation sequencing (NGS) is advantageous in that it can detect trace amounts of bacteria that cannot be detected by culturing or bacteria that are difficult to cultivate. However, there are few reports on the diagnosis of infectious diseases using NGS in the neonatal field, especially those targeting respiratory distress. Objective: The purpose of our study was to investigate the microorganisms associated with neonatal respiratory distress and to determine whether less invasive collection specimens such as plasma and gastric fluid are useful. Methods: Neonates were prospectively recruited between January and August 2020 from Nagoya University Hospital. The inclusion criteria were as follows: 1) admission to the neonatal intensive care unit; 2) respiratory distress presentation within 48 h of birth; and 3) suspected infection, collection of blood culture, and administration of antibiotics. Plasma samples and blood cultures were simultaneously collected. Gastric fluid samples were also collected if the patient was not started on enteral nutrition. Information on the patients and their mothers were collected from the medical records. DNA was extracted from 140 µL of plasma and gastric fluid samples. DNA sequencing libraries were prepared, and their quality was analyzed. DNA libraries were sequenced using high-throughput NGS. The NGS data of plasma and gastric fluid samples were analyzed using the metagenomic pipeline PATHDET, which calculated the number of reads assigned to microorganisms and their relative abundance. Putative pathogens were listed. Results: Overall, 30 plasma samples and 25 gastric fluid samples from 30 neonates were analyzed. Microorganism-derived reads of gastric fluid samples were significantly higher than those of plasma samples. Transient tachypnea of the newborn was the most common cause of respiratory distress with 13 cases (43%), followed by respiratory distress syndrome with 7 cases (23%). There were 8 cases (29%) of chorioamnionitis and 7 cases (25%) of funisitis pathologically diagnosed. All blood cultures were negative, and only two gastric fluid cultures were positive for group B Streptococcus (Patient 15) and Candida albicans (Patient 24). Putative pathogens that met the positive criteria for PATHET were detected in four gastric fluid samples, one of which was group B Streptococcus from Patient 15. In the gastric fluid sample of Patient 24, Candida albicans were detected by NGS but did not meet the positive criteria for PATHDET. Cluster analysis of the plasma samples divided them into two study groups, and the indicator genera of each cluster (Phormidium or Toxoplasma) are shown in Figure 1. Clinical findings did not show any significant differences between the two groups. Cluster analysis of the gastric fluid samples divided them into three study groups, and the indicator genera of each cluster (Ureaplasma, Nostoc, and Streptococcus) are shown in Figure 2. The incidence rate of chorioamnionitis was significantly higher in Ureaplasma group than in the other two groups. Conclusion: Gastric fluid may be useful for assessing neonatal patients with respiratory distress. To the best of our knowledge, this was the first study to reveal that the presence of Ureaplasma in the gastric fluid of neonates with respiratory distress was associated with chorioamnionitis. The early diagnosis of intra-amniotic infections using gastric fluid and its treatment may change the treatment strategy for neonatal respiratory distress. Screening for Ureaplasma in neonates with respiratory distress may reduce the need for empirical antibiotic administration. Further research is required to confirm these findings.

DOI： 10.1080/14767058.2023.2207113

Mitochondria-associated membrane collapse impairs TBK1-mediated proteostatic stress response in ALS. Reviewed International journal

Seiji Watanabe, Yuri Murata, Yasuyoshi Oka, Kotaro Oiwa, Mai Horiuchi, Yohei Iguchi, Okiru Komine, Akira Sobue, Masahisa Katsuno, Tomoo Ogi, Koji Yamanaka

Proceedings of the National Academy of Sciences of the United States of America Vol. 120 ( 47 ) page： e2315347120 2023.11

Language：English Publishing type：Research paper (scientific journal)

The organelle contact site of the endoplasmic reticulum and mitochondria, known as the mitochondria-associated membrane (MAM), is a multifunctional microdomain in cellular homeostasis. We previously reported that MAM disruption is a common pathological feature in amyotrophic lateral sclerosis (ALS); however, the precise role of MAM in ALS was uncovered. Here, we show that the MAM is essential for TANK-binding kinase 1 (TBK1) activation under proteostatic stress conditions. A MAM-specific E3 ubiquitin ligase, autocrine motility factor receptor, ubiquitinated nascent proteins to activate TBK1 at the MAM, which results in ribosomal protein degradation. MAM or TBK1 deficiency under proteostatic stress conditions resulted in increased cellular vulnerability in vitro and motor impairment in vivo. Thus, MAM disruption exacerbates proteostatic stress via TBK1 inactivation in ALS. Our study has revealed a proteostatic mechanism mediated by the MAM-TBK1 axis, highlighting the physiological importance of the organelle contact sites.

DOI： 10.1073/pnas.2315347120

Lysosomal cholesterol overload in macrophages promotes liver fibrosis in a mouse model of NASH. Reviewed International journal

Michiko Itoh, Atsushi Tamura, Sayaka Kanai, Miyako Tanaka, Yohei Kanamori, Ibuki Shirakawa, Ayaka Ito, Yasuyoshi Oka, Isao Hidaka, Taro Takami, Yasushi Honda, Mitsuyo Maeda, Yasuyuki Saito, Yoji Murata, Takashi Matozaki, Atsushi Nakajima, Yosky Kataoka, Tomoo Ogi, Yoshihiro Ogawa, Takayoshi Suganami

The Journal of experimental medicine Vol. 220 ( 11 ) 2023.11

Language：English Publishing type：Research paper (scientific journal)

Accumulation of lipotoxic lipids, such as free cholesterol, induces hepatocyte death and subsequent inflammation and fibrosis in the pathogenesis of nonalcoholic steatohepatitis (NASH). However, the underlying mechanisms remain unclear. We have previously reported that hepatocyte death locally induces phenotypic changes in the macrophages surrounding the corpse and remnant lipids, thereby promoting liver fibrosis in a murine model of NASH. Here, we demonstrated that lysosomal cholesterol overload triggers lysosomal dysfunction and profibrotic activation of macrophages during the development of NASH. β-cyclodextrin polyrotaxane (βCD-PRX), a unique supramolecule, is designed to elicit free cholesterol from lysosomes. Treatment with βCD-PRX ameliorated cholesterol accumulation and profibrotic activation of macrophages surrounding dead hepatocytes with cholesterol crystals, thereby suppressing liver fibrosis in a NASH model, without affecting the hepatic cholesterol levels. In vitro experiments revealed that cholesterol-induced lysosomal stress triggered profibrotic activation in macrophages predisposed to the steatotic microenvironment. This study provides evidence that dysregulated cholesterol metabolism in macrophages would be a novel mechanism of NASH.

DOI： 10.1084/jem.20220681

Extremely low-frequency electromagnetic field induces acetylation of heat shock proteins and enhances protein folding. Reviewed

Huang Z, Ito M, Zhang S, Toda T, Takeda JI, Ogi T, Ohno K

Ecotoxicology and environmental safety Vol. 264 page： 115482 2023.10

Language：English Publishing type：Research paper (scientific journal) Publisher：Ecotoxicology and Environmental Safety

The pervasive weak electromagnetic fields (EMF) inundate the industrialized society, but the biological effects of EMF as weak as 10 µT have been scarcely analyzed. Heat shock proteins (HSPs) are molecular chaperones that mediate a sequential stress response. HSP70 and HSP90 provide cells under undesirable situations with either assisting covalent folding of proteins or degrading improperly folded proteins in an ATP-dependent manner. Here we examined the effect of extremely low-frequency (ELF)-EMF on AML12 and HEK293 cells. Although the protein expression levels of HSP70 and HSP90 were reduced after an exposure to ELF-EMF for 3 h, acetylations of HSP70 and HSP90 were increased, which was followed by an enhanced binding affinities of HSP70 and HSP90 for HSP70/HSP90-organizing protein (HOP/STIP1). After 3 h exposure to ELF-EMF, the amount of mitochondria was reduced but the ATP level and the maximal mitochondrial oxygen consumption were increased, which was followed by the reduced protein aggregates and the increased cell viability. Thus, ELF-EMF exposure for 3 h activated acetylation of HSPs to enhance protein folding, which was returned to the basal level at 12 h. The proteostatic effects of ELF-EMF will be able to be applied to treat pathological states in humans.

DOI： 10.1016/j.ecoenv.2023.115482

Live cell transcription-coupled nucleotide excision repair dynamics revisited. Reviewed

Llerena Schiffmacher DA, Kliza KW, Theil AF, Kremers GJ, Demmers JAA, Ogi T, Vermeulen M, Vermeulen W, Pines A

DNA repair Vol. 130 page： 103566 2023.10

Language：English Publishing type：Research paper (scientific journal) Publisher：DNA Repair

Transcription–blocking lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which prevents DNA damage-induced cellular toxicity and maintains proper transcriptional processes. TC-NER is initiated by the stalling of RNA polymerase II (RNAPII), which triggers the assembly of TC-NER-specific proteins, namely CSB, CSA and UVSSA, which collectively control and drive TC-NER progression. Previous research has revealed molecular functions for these proteins, however, exact mechanisms governing the initiation and regulation of TC-NER, particularly at low UV doses have remained elusive, partly due to technical constraints. In this study, we employ knock-in cell lines designed to target the endogenous CSB gene locus with mClover, a GFP variant. Through live cell imaging, we uncover the intricate molecular dynamics of CSB in response to physiologically relevant UV doses. We showed that the DNA damage-induced association of CSB with chromatin is tightly regulated by the CSA-containing ubiquitin-ligase CRL complex (CRL4CSA). Combining the CSB-mClover knock-in cell line with SILAC-based GFP-mediated complex isolation and mass-spectrometry-based proteomics, revealed novel putative CSB interactors as well as discernible variations in complex composition during distinct stages of TC-NER progression. Our work not only provides molecular insight into TC-NER, but also illustrates the versatility of endogenously tagging fluorescent and affinity tags.

DOI： 10.1016/j.dnarep.2023.103566

Patients with keratinization disorders due to ABCA12 variants showing pityriasis rubra pilaris phenotypes. Reviewed

Takeichi T, Hamada T, Yamamoto M, Ito Y, Kawaguchi A, Kobashi H, Yoshikawa T, Koga H, Ishii N, Nakama T, Muro Y, Ogi T, Akiyama M

The Journal of dermatology 2023.9

Inducing multiple nicks promotes interhomolog homologous recombination to correct heterozygous mutations in somatic cells. Reviewed International journal

Akiko Tomita, Hiroyuki Sasanuma, Tomoo Owa, Yuka Nakazawa, Mayuko Shimada, Takahiro Fukuoka, Tomoo Ogi, Shinichiro Nakada

Nature communications Vol. 14 ( 1 ) page： 5607 - 5607 2023.9

Language：English Publishing type：Research paper (scientific journal)

CRISPR/Cas9-mediated gene editing has great potential utility for treating genetic diseases. However, its therapeutic applications are limited by unintended genomic alterations arising from DNA double-strand breaks and random integration of exogenous DNA. In this study, we propose NICER, a method for correcting heterozygous mutations that employs multiple nicks (MNs) induced by Cas9 nickase and a homologous chromosome as an endogenous repair template. Although a single nick near the mutation site rarely leads to successful gene correction, additional nicks on homologous chromosomes strongly enhance gene correction efficiency via interhomolog homologous recombination (IH-HR). This process partially depends on BRCA1 and BRCA2, suggesting the existence of several distinct pathways for MN-induced IH-HR. According to a genomic analysis, NICER rarely induces unintended genomic alterations. Furthermore, NICER restores the expression of disease-causing genes in cells derived from genetic diseases with compound heterozygous mutations. Overall, NICER provides a precise strategy for gene correction.

DOI： 10.1038/s41467-023-41048-5

Deep intronic founder mutations identified in the ERCC4/XPF gene are potential therapeutic targets for a high-frequency form of xeroderma pigmentosum. Reviewed International journal

Chikako Senju, Yuka Nakazawa, Taichi Oso, Mayuko Shimada, Kana Kato, Michiko Matsuse, Mariko Tsujimoto, Taro Masaki, Yasushi Miyazaki, Satoshi Fukushima, Satoshi Tateishi, Atsushi Utani, Hiroyuki Murota, Katsumi Tanaka, Norisato Mitsutake, Shinichi Moriwaki, Chikako Nishigori, Tomoo Ogi

Proceedings of the National Academy of Sciences of the United States of America Vol. 120 ( 27 ) page： e2217423120 2023.7

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal)

Xeroderma pigmentosum (XP) is a genodermatosis defined by cutaneous photosensitivity with an increased risk of skin tumors because of DNA repair deficiency. The worldwide prevalence of XP is ~1 to 4 in million, with higher incidence in some countries and regions including Japan (1 in 22,000) and North Africa due to founder mutations and a high degree of consanguinity. Among XP, the complementation group F (XP-F), is a rare form (1% of worldwide XP); however, this is underdiagnosed, because the ERCC4/XPF gene is essential for fetal development and most of previously reported ERCC4/XPF pathogenic variants are hypomorphs causing relatively mild phenotypes. From the largest Japanese XP cohort study, we report 17 XP-F cases bearing two pathogenic variants, both identified in deep intronic regions of the ERCC4/XPF gene. The first variant, located in intron 1, is a Japanese founder mutation, which additionally accounts for ~10% of the entire Japanese XP cases (MAF = 0.00196), causing an aberrant pre-mRNA splicing due to a miss-binding of U1snRNA. The second mutation located in intron eight induces an alternative polyadenylation. Both mutations cause a reduction of the ERCC4/XPF gene expression, resulting in XP clinical manifestations. Most cases developed early-onset skin cancers, indicating that these variants need critical attention. We further demonstrate that antisense oligonucleotides designed for the mutations can restore the XPF protein expression and DNA repair capacity in the patients' cells. Collectively, these pathogenic variants can be potential therapeutic targets for XP.

DOI： 10.1073/pnas.2217423120

Utility of nanopore sequencing for detecting pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure Reviewed

AP1B1の複合ヘテロ接合性変異によるMEDNIK-like syndrome

伊藤靖敏, 武市拓也, 竹内想, 室慶直, 秋山真志, 猪狩翔平, 森龍彦, 山本俊幸, 小野敦史, 陶山和秀, 細矢光亮, 荻朋男

角化症研究会記録集 Vol. 37 page： 22 - 25 2023.7

Yamaguchi Makoto, Horiba Kazuhiro, Haruta Kazunori, Takeuchi Suguru, Suzuki Takako, Torii Yuka, Kawabe Shinji, Wada Sho, Ikeyama Takanari, Ito Yoshinori, Ogi Tomoo, Kawada Jun-ichi

JOURNAL OF CLINICAL VIROLOGY PLUS Vol. 3 ( 2 ) 2023.6

Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Clinical Virology Plus

RNA viruses are the most frequent pathogens responsible for respiratory infections, particularly in pediatric patients. Next-generation sequencing, represented by Illumina sequencing, is one of the most comprehensive methods for identifying pathogens. Nanopore sequencing has been used to identify and analyze pathogens with a shorter sequencing time. In this study, we evaluated the utility of nanopore sequencing for the detection of RNA viruses in bronchoalveolar lavage fluid (BALF) of pediatric patients with respiratory failure. Using the seven BALF samples, we first compared the nanopore and Illumina sequencing results. The nanopore sequencing detected the same RNA viruses as the Illumina sequencing. Subsequently, BALF samples from 24 additional pediatric patients with respiratory failure were analyzed by nanopore sequencing, and RNA viral pathogens were detected in 10 out of 24 patients. Among these 10 patients, nanopore sequencing identified the same viral pathogens as detected by the PCR and viral antigen tests in five patients. Furthermore, additional RNA viral pathogens were detected by nanopore sequencing with high genome coverage in five patients that were not detected by PCR and viral antigen tests. In conclusion, nanopore sequencing could comprehensively detect RNA viral pathogens in BALF samples with equivalent sensitivity and genome coverage as Illumina sequencing. This rapid sequencing platform may be more beneficial for detecting RNA viruses in clinical settings.

DOI： 10.1016/j.jcvp.2023.100154

A case of Cockayne syndrome with unusually mild clinical manifestations Reviewed

Tsujimoto Mariko, Nakano Eiji, Nakazawa Yuka, Kanda Fumio, Ueda Takehiro, Ogi Tomoo, Nishigori Chikako

JOURNAL OF DERMATOLOGY Vol. 50 ( 4 ) page： 541 - 545 2023.4

Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Dermatology

We present a mild case of Cockayne syndrome that was referred to us with an extreme sunburn at the age of 3. In early teens, although her cutaneous symptoms alleviated without any medications, she developed tremor and dysarthria. Neurological examination and brain imaging suggested demyelination disorders. The patient's cells indicated a reduced recovery of RNA synthesis, which was partially restored by the introduction of CSB (Cockayne Syndrome B)-cDNA. In addition, her cells indicated a substantially reduced level of CSB protein. Despite the insidious progression of neurological symptoms, she gave birth to a child. Such mild cases of Cockayne syndrome may be misdiagnosed.

DOI： 10.1111/1346-8138.16679

Two children with hypophosphatasia with a heterozygous c.1559delT variant in the ALPL gene, the most common variant in Japanese populations Reviewed

Kitoh Hiroshi, Izawa Masako, Kaneko Hiroshi, Kitamura Akiko, Matsuyama Saori, Kato Kohji, Ogi Tomoo

BONE REPORTS Vol. 17 page： 101626 2022.12

Language：English Publishing type：Research paper (scientific journal) Publisher：Bone Reports

Hypophosphatasia (HPP), a genetic disorder characterized by decreased tissue-nonspecific alkaline phosphatase (TNSALP) activity, is caused by loss-of-function mutations in the ALPL gene, which encodes TNSALP. The most frequent pathogenic variant in Japanese patients with HPP is a frameshift mutation in the ALPL gene, c.1559delT, and its carrier frequency is reported to be one in 480 in the Japanese population. We report the cases of two Japanese children with HPP who had a heterozygous c.1559delT variant in the ALPL gene. One case (involving a neonate) exhibited respiratory insufficiency associated with vitamin B6 dependent convulsions, significant defective mineralization similar to the severe form of HPP, and extremely low ALP activity. Enzyme replacement therapy (ERT) using asfotase alfa promptly improved her respiratory insufficiency, bone mineralization, and maintained her motor development during infancy. The second case involved a 10-year-old boy who demonstrated diffuse musculoskeletal pain and weakness that progressively disturbed mobility. Although he showed no bony lesions, the clinical symptoms and biochemical abnormalities were compatible with childhood HPP. ERT successfully relieved the severe generalized pain and significantly improved motor function.

DOI： 10.1016/j.bonr.2022.101626

A case of non-immune hydrops fetalis with maternal mirror syndrome diagnosed by trio-based exome sequencing: An autopsy case report and literature review

Tano Sho, Kotani Tomomi, Yoshihara Masato, Nakamura Noriyuki, Matsuo Seiko, Ushida Takafumi, Imai Kenji, Ito Miharu, Oka Yasuyoshi, Sato Emi, Hayashi Shin, Ogi Tomoo, Kajiyama Hiroaki

MOLECULAR GENETICS AND METABOLISM REPORTS Vol. 33 page： 100925 2022.12

Language：English Publishing type：Research paper (scientific journal) Publisher：Molecular Genetics and Metabolism Reports

Non-immune hydrops fetalis (NIHF) indicates the risk for stillbirth. Although the causes vary and most NIHFs have no identifiable cause, recent advances in exome sequencing have increased diagnostic rates. We report a case of NIHF that developed into a giant cystic hygroma complicated by maternal mirror syndrome. Trio-based exome sequencing showed a de novo heterozygous missense variant in the RIT1 (NM_006912: c.246 T > G [p.F82L]). The RIT1 variants are known causative variants of Noonan syndrome (NS; OMIM #163950). The location of the RIT1 variants in the previously reported NS cases with NIHF or/and maternal mirror syndrome was mainly in the switch II region, including the present case. While a further accumulation of cases is needed, exome sequencing, which can identify the variant type in detail, might help predict the phenotype and severity of NIHF.

DOI： 10.1016/j.ymgmr.2022.100925

Ceramide analysis in combination with genetic testing may provide a precise diagnosis for self-healing collodion babies. Reviewed International journal

Takuya Takeichi, Yusuke Ohno, Kana Tanahashi, Yasutoshi Ito, Ken Shiraishi, Ryo Utsunomiya, Satoshi Yoshida, Kenta Ikeda, Hayato Nomura, Shin Morizane, Koji Sayama, Tomoo Ogi, Yoshinao Muro, Akio Kihara, Masashi Akiyama

Journal of lipid research Vol. 63 ( 12 ) page： 100308 - 100308 2022.12

Language：English Publishing type：Research paper (scientific journal)

Self-healing collodion baby (SHCB), also called "self-improving collodion baby", is a rare mild variant of autosomal recessive congenital ichthyosis and is defined as a collodion baby who shows the nearly complete resolution of scaling within the first 3 months to 1 year of life. However, during the neonatal period, it is not easy to distinguish SHCB from other inflammatory forms of autosomal recessive congenital ichthyosis, such as congenital ichthyosiform erythroderma. Here, we report a case study of two Japanese SHCB patients with compound heterozygous mutations, c.235G>T (p.(Glu79*))/ c.1189C>T (p.(Arg397Cys)) and c.1295A>G (p.(Tyr432Cys))/ c.1138delG (p.(Asp380Thrfs*3)), in CYP4F22, which encodes cytochrome P450, family 4, subfamily F, polypeptide 22 (CYP4F22). Immunohistochemically, inflammation with the strong expression of IL-17C, IL-36γ, and TNF-α was seen in the skin at birth. CYP4F22 is an ultra-long-chain fatty acid (FA) ω-hydroxylase responsible for ω-O-acylceramide (acylceramide) production. Among the epidermal ceramides, acylceramide is a key lipid in maintaining the epidermal permeability barrier function. We found that the levels of ceramides with ω-hydroxy FAs including acylceramides and the levels of protein-bound ceramides were much lower in stratum corneum samples obtained by tape stripping from SHCB patients than in those from their unaffected parents and individuals without SHCB. Additionally, our cell-based enzyme assay revealed that two mutants, p.(Glu79*) and p.(Arg397Cys), had no enzyme activity. Our findings suggest that genetic testing coupled with non-invasive ceramide analyses using tape-stripped stratum corneum samples might be useful for the early and precise diagnosis of congenital ichthyoses, including SHCB.

DOI： 10.1016/j.jlr.2022.100308

経過観察中に水疱性類天疱瘡を発症した、MV遺伝子変異を有する高齢発症の汗孔角化症の2例

有沢友希, 武市拓也, 伊藤靖敏, 棚橋華奈, 室慶直, 荻朋男, 秋山真志

加齢皮膚医学セミナー Vol. 17 ( 2 ) page： 65 - 66 2022.12

Global landscape of replicative DNA polymerase usage in the human genome. International journal

Eri Koyanagi, Yoko Kakimoto, Tamiko Minamisawa, Fumiya Yoshifuji, Toyoaki Natsume, Atsushi Higashitani, Tomoo Ogi, Antony M Carr, Masato T Kanemaki, Yasukazu Daigaku

Nature communications Vol. 13 ( 1 ) page： 7221 - 7221 2022.11

Language：English Publishing type：Research paper (scientific journal)

The division of labour among DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequencing (Pu-seq) in HCT116 cells and mapped Polε and Polα usage genome wide. The polymerase usage profiles show Polε synthesises the leading strand and Polα contributes mainly to lagging strand synthesis. Combining the Polε and Polα profiles, we accurately predict the genome-wide pattern of fork directionality plus zones of replication initiation and termination. We confirm that transcriptional activity contributes to the pattern of initiation and termination and, by separately analysing the effect of transcription on co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands is compromised by transcription in both co-directional and convergent forks. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability. Together, our result demonstrated that Pu-seq in human cells provides a powerful and straightforward methodology to explore DNA polymerase usage and replication fork dynamics.

DOI： 10.1038/s41467-022-34929-8

Aicardi-Goutières syndrome with SAMHD1 deficiency can be diagnosed by unscheduled DNA synthesis test. International journal

Chikako Senju, Yuka Nakazawa, Mayuko Shimada, Dai Iwata, Michiko Matsuse, Katsumi Tanaka, Yasushi Miyazaki, Shinichi Moriwaki, Norisato Mitsutake, Tomoo Ogi

Frontiers in pediatrics Vol. 10 page： 1048002 - 1048002 2022.11

Language：English Publishing type：Research paper (scientific journal)

Aicardi-Goutières syndrome (AGS) is a rare genetic disorder characterised by progressive encephalopathy, involving microcephaly, intracranial calcification, and cerebrospinal fluid lymphocytosis with increased interferon-α concentrations. The clinical features of AGS overlap with fetal cerebral anomalies caused by congenital infections, such as TORCH (toxoplasmosis, other, rubella, cytomegalovirus, and herpes), or with those of other genetic disorders showing neonatal microcephaly, including Cockayne syndrome (CS) with transcription-coupled DNA repair deficiency, and Seckel syndrome (SS) showing aberrant cell-cycle checkpoint signaling. Therefore, a differential diagnosis to confirm the genetic cause or a proof of infection should be considered. In this report, we describe an individual who showed primordial dwarfism and encephalopathy, and whose initial diagnosis was CS. First, we conducted conventional DNA repair proficiency tests for the patient derived fibroblast cells. Transcription-coupled nucleotide excision repair (TC-NER) activity, which is mostly compromised in CS cases, was slightly reduced in the patient's cells. However, unscheduled DNA synthesis (UDS) was significantly diminished. These cellular traits were inconsistent with the diagnosis of CS. We further performed whole exome sequencing for the case and identified a compound heterozygous loss-of-function variants in the SAMHD1 gene, mutations in which are known to cause AGS. As SAMHD1 encodes deoxyribonucleoside triphosphate triphosphohydrolase, we reasoned that the deoxyribonucleoside triphosphate (dNTP) pool size in the patient's cells was elevated, and the labeling efficiency of UDS-test was hindered due to the reduced concentration of phosphorylated ethynyl deoxyuridine (EdU), a nucleoside analogue used for the assay. In conclusion, UDS assay may be a useful diagnostic tool to distinguish between AGS with SAMHD1 mutations and other related diseases.

DOI： 10.3389/fped.2022.1048002

Performance of Nanopore and Illumina Metagenomic Sequencing for Pathogen Detection and Transcriptome Analysis in Infantile Central Nervous System Infections

Horiba Kazuhiro, Torii Yuka, Aizawa Yuta, Yamaguchi Makoto, Haruta Kazunori, Okumura Toshihiko, Suzuki Takako, Kawano Yoshihiko, Kawada Jun-ichi, Hara Shinya, Saitoh Akihiko, Giske Christian G., Ogi Tomoo, Ito Yoshinori

OPEN FORUM INFECTIOUS DISEASES Vol. 9 ( 10 ) page： ofac504 2022.10

Language：English Publishing type：Research paper (scientific journal) Publisher：Open Forum Infectious Diseases

Background: Infantile central nervous system infections (CNSIs) can be life-threatening and cause severe sequelae. However, the causative microorganism remains unknown in >40% of patients with aseptic infections. This study aimed to analyze the metagenome for detection of pathogens and the transcriptome for host immune responses during infection in a single cerebrospinal fluid (CSF) sample using 2 different next-generation sequencing (NGS) platforms, Nanopore and Illumina. Methods: Twenty-eight CNSIs patients (<12 months) were enrolled, and 49 clinical samples (28 CSF and 21 blood) were collected. The DNA extracted from all 49 samples was sequenced using the Illumina sequencer for the detection of pathogens. Extracted RNA was obtained in sufficient quantities from 23 CSF samples and subjected to sequencing on both Nanopore and Illumina platforms. Human-derived reads subtracted during pathogen detection were used for host transcriptomic analysis from both Nanopore and Illumina sequencing. Results: RNA metagenomic sequencing using both sequencing platforms revealed putative viral pathogens in 10 cases. DNA sequencing using the Illumina sequencer detected 2 pathogens. The results of Nanopore and Illumina RNA sequencing were consistent; however, the mapping coverage and depth to the detected pathogen genome of Nanopore RNA sequencing were greater than those of Illumina. Host transcriptomic analysis of Nanopore sequencing revealed highly expressed genes related to the antiviral roles of innate immunity from pathogen-identified cases. Conclusions: The use of Nanopore RNA sequencing for metagenomic diagnostics of CSF samples should help to elucidate both pathogens and host immune responses of CNSI and could shed light on the pathogenesis of these infections.

DOI： 10.1093/ofid/ofac504

Metabolome and transcriptome analysis on muscle of sporadic inclusion body myositis

Murakami Ayuka, Noda Seiya, Kazuta Tomoyuki, Hirano Satoko, Kimura Seigo, Nakanishi Hirotaka, Matsuo Koji, Tsujikawa Koyo, Iida Madoka, Koike Haruki, Sakamoto Kazuma, Hara Yuichiro, Kuru Satoshi, Kadomatsu Kenji, Shimamura Teppei, Ogi Tomoo, Katsuno Masahisa

ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY Vol. 9 ( 10 ) page： 1602 - 1615 2022.10

Language：English Publishing type：Research paper (scientific journal) Publisher：Annals of Clinical and Translational Neurology

Objective: Sporadic inclusion body myositis (sIBM) is the most common acquired myopathy in patients older than 50 years of age. sIBM is hardly responds to any immunosuppressing theraphies, and its pathophysiology remains elusive. This study aims to explore pathogenic pathways underlying sIBM and identify novel therapeutic targets using metabolomic and transcriptomic analyses. Methods: In this retrospective observational study, we analyzed biopsied muscle samples from 14 sIBM patients and six non-diseased subjects to identify metabolic profiles. Frozen muscle samples were used to measure metabolites with cation and anion modes of capillary electrophoresis time of flight mass spectrometry. We validated the metabolic pathway altered in muscles of sIBM patients through RNA sequencing and histopathological studies. Results: A total of 198 metabolites were identified. Metabolomic and transcriptomic analyses identified specific metabolite changes in sIBM muscle samples. The pathways of histamine biosynthesis and certain glycosaminoglycan biosynthesis were upregulated in sIBM patients, whereas those of carnitine metabolism and creatine metabolism were downregulated. Histopathological examination showed infiltration of mast cells and deposition of chondroitin sulfate in skeletal muscle samples, supporting the results of metabolomic and transcriptomic analyses. Interpretation: We identified alterations of several metabolic pathways in muscle samples of sIBM patients. These results suggest that mast cells, chondroitin sulfate biosynthesis, carnitine, and creatine play roles in sIBM pathophysiology.

DOI： 10.1002/acn3.51657

Six years’ accomplishment of the Initiative on Rare and Undiagnosed Diseases: nationwide project in Japan to discover causes, mechanisms, and cures

Takahashi Y., Date H., Oi H., Adachi T., Imanishi N., Kimura E., Takizawa H., Kosugi S., Matsumoto N., Kosaki K., Matsubara Y., Ando Y., Anzai T., Ariga T., Fukushima Y., Furusawa Y., Ganaha A., Goto Y., Hata K., Honda M., Iijima K., Ikka T., Imoto I., Kaname T., Kobayashi M., Kojima S., Kurahashi H., Kure S., Kurosawa K., Maegaki Y., Makita Y., Morio T., Narita I., Nomura F., Ogata T., Ozono K., Oka A., Okamoto N., Saitoh S., Sakurai A., Takada F., Takahashi T., Tamaoka A., Umezawa A., Yachie A., Yoshiura K., Chinen Y., Eguchi M., Fujio K., Hosoda K., Ichikawa T., Kawarai T., Kosho T., Masuno M., Nakamura A., Nakane T., Ogi T., Okada S., Sakata Y., Seto T., Takahashi Y., Takano T., Ueda M., Yagasaki H., Yamamoto T., Watanabe A., Hotta Y., Kubo A., Maruyama H., Moriyama K., Nanba E., Sakai N., Sekijima Y., Shimosegawa T., Takeuchi T., Usami S., Yamamoto K., Mizusawa H.

Journal of Human Genetics Vol. 67 ( 9 ) page： 505 - 513 2022.9

Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Human Genetics

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

DOI： 10.1038/s10038-022-01025-0

A novel ZC4H2 variant in a female with severe respiratory complications

Wakabayashi Tomohiro, Mizukami Miyako, Terada Kojiro, Ishikawa Aki, Hinotsu Shiro, Kobayashi Masaki, Kato Koji, Ogi Tomoo, Tsugawa Takeshi, Sakurai Akihiro

BRAIN & DEVELOPMENT Vol. 44 ( 8 ) page： 571 - 577 2022.9

Language：English Publishing type：Research paper (scientific journal) Publisher：Brain and Development

Introduction: An X-linked ZC4H2 variant is associated with a variety of phenotypes that have abnormalities related to external malformation and neurodevelopment. There have been no reports on severe respiratory dysfunction resulting in surgical treatments not being possible due to the deformity resulting from in this disease. Here we report a female with arthrogryposis multiplex congenita with a severe respiratory complication. Case: A two-year-old girl had arthrogryposis multiplex congenita at delivery and subsequently had hypotonia and feeding difficulty. A novel ZC4H2 frameshift variant was identified by whole-exome sequencing in her genome. At eight months, she had recurrent aspiration pneumonia. A tracheostomy and gastrostomy were required; however, surgical intervention was not possible because of her short neck and complicated airway. Conclusion: We compared this case with previous reports. The truncation group had more described phenotypes than the non-truncation group. The patient had the most severe respiratory dysfunction in truncating variant.

DOI： 10.1016/j.braindev.2022.04.009

Ceramide profiling of stratum corneum in Sjögren-Larsson syndrome. Reviewed International journal

Ayami Arai, Takuya Takeichi, Hiroyuki Wakamoto, Takayuki Sassa, Yasutoshi Ito, Yuya Murase, Tomoo Ogi, Masashi Akiyama, Akio Kihara

Journal of dermatological science Vol. 107 ( 3 ) page： 114 - 122 2022.9

Language：English Publishing type：Research paper (scientific journal)

BACKGROUND: Sjögren-Larsson syndrome (SLS) is a neurocutaneous disorder whose causative gene is the fatty aldehyde dehydrogenase ALDH3A2 and of which ichthyosis is the major skin symptom. The stratum corneum contains a variety of ceramides, among which ω-O-acylceramides (acylceramides) and protein-bound ceramides are essential for skin permeability barrier formation. OBJECTIVES: To determine the ceramide classes/species responsible for SLS pathogenesis and the enzymes that are impaired in SLS. METHODS: Genomic DNA was collected from peripheral blood samples from an SLS patient and her parents, and whole-genome sequencing and Sanger sequencing were performed. Lipids were extracted from stratum corneum samples from the SLS patient and healthy volunteers and subjected to ceramide profiling via liquid chromatography coupled with tandem mass spectrometry. RESULTS: A duplication (c.55_130dup) and a missense mutation (p.Lys447Glu) were found in the patient's ALDH3A2 gene. The patient had reduced levels of all acylceramide classes, with total acylceramide levels at 25 % of healthy controls. Reductions were also observed for several nonacylated ceramides: ceramides with phytosphingosine or 6-hydroxysphingosine in the long-chain base moiety were reduced to 24 % and 41 % of control levels, respectively, and ceramides with an α-hydroxy fatty acid as the fatty acid moiety were reduced to 29 %. The fatty acid moiety was shortened in many nonacylated ceramide classes. CONCLUSION: These results suggest that reduced acylceramide levels are a primary cause of the ichthyosis symptoms of SLS, but reductions in other ceramide classes may also be involved.

DOI： 10.1016/j.jdermsci.2022.08.003

Whole-exome analysis of 177 pediatric patients with undiagnosed diseases

Narita Kotaro, Muramatsu Hideki, Narumi Satoshi, Nakamura Yuji, Okuno Yusuke, Suzuki Kyogo, Hamada Motoharu, Yamaguchi Naoya, Suzuki Atsushi, Nishio Yosuke, Shiraki Anna, Yamamori Ayako, Tsumura Yusuke, Sawamura Fumi, Kawaguchi Masahiro, Wakamatsu Manabu, Kataoka Shinsuke, Kato Kohji, Asada Hideyuki, Kubota Tetsuo, Muramatsu Yukako, Kidokoro Hiroyuki, Natsume Jun, Mizuno Seiji, Nakata Tomohiko, Inagaki Hidehito, Ishihara Naoko, Yonekawa Takahiro, Okumura Akihisa, Ogi Tomoo, Kojima Seiji, Kaname Tadashi, Hasegawa Tomonobu, Saitoh Shinji, Takahashi Yoshiyuki

SCIENTIFIC REPORTS Vol. 12 ( 1 ) page： 14589 2022.8

Language：English Publishing type：Research paper (scientific journal) Publisher：Scientific Reports

Recently, whole-exome sequencing (WES) has been used for genetic diagnoses of patients who remain otherwise undiagnosed. WES was performed in 177 Japanese patients with undiagnosed conditions who were referred to the Tokai regional branch of the Initiative on Rare and Undiagnosed Diseases (IRUD) (TOKAI-IRUD). This study included only patients who had not previously received genome-wide testing. Review meetings with specialists in various medical fields were held to evaluate the genetic diagnosis in each case, which was based on the guidelines of the American College of Medical Genetics and Genomics. WES identified diagnostic single-nucleotide variants in 66 patients and copy number variants (CNVs) in 11 patients. Additionally, a patient was diagnosed with Angelman syndrome with a complex clinical phenotype upon detection of a paternally derived uniparental disomy (UPD) [upd(15)pat] wherein the patient carried a homozygous DUOX2 p.E520D variant in the UPD region. Functional analysis confirmed that this DUOX2 variant was a loss-of-function missense substitution and the primary cause of congenital hypothyroidism. A significantly higher proportion of genetic diagnoses was achieved compared to previous reports (44%, 78/177 vs. 24–35%, respectively), probably due to detailed discussions and the higher rate of CNV detection.

DOI： 10.1038/s41598-022-14161-6

Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes

Kimura Hiroki, Nakatochi Masahiro, Aleksic Branko, Guevara James, Toyama Miho, Hayashi Yu, Kato Hidekazu, Kushima Itaru, Morikawa Mako, Ishizuka Kanako, Okada Takashi, Tsurusaki Yoshinori, Fujita Atsushi, Miyake Noriko, Ogi Tomoo, Takata Atsushi, Matsumoto Naomichi, Buxbaum Joseph, Ozaki Norio, Sebat Jonathan

TRANSLATIONAL PSYCHIATRY Vol. 12 ( 1 ) page： 265 2022.7

Language：English Publishing type：Research paper (scientific journal) Publisher：Translational Psychiatry

Autism spectrum disorder (ASD) is a highly heritable, complex disorder in which rare variants contribute significantly to disease risk. Although many genes have been associated with ASD, there have been few genetic studies of ASD in the Japanese population. In whole exomes from a Japanese ASD sample of 309 cases and 299 controls, rare variants were associated with ASD within specific neurodevelopmental gene sets, including highly constrained genes, fragile X mental retardation protein target genes, and genes involved in synaptic function, with the strongest enrichment in trans-synaptic signaling (p = 4.4 × 10−4, Q-value = 0.06). In particular, we strengthen the evidence regarding the role of ABCA13, a synaptic function-related gene, in Japanese ASD. The overall results of this case-control exome study showed that rare variants related to synaptic function are associated with ASD susceptibility in the Japanese population.

DOI： 10.1038/s41398-022-02033-6

The iodide transporter Slc26a7 impacts thyroid function more strongly than Slc26a4 in mice

Yamaguchi Naoya, Suzuki Atsushi, Yoshida Aya, Tanaka Tatsushi, Aoyama Kohei, Oishi Hisashi, Hara Yuichiro, Ogi Tomoo, Amano Izuki, Kameo Satomi, Koibuchi Noriyuki, Shibata Yasuhiro, Ugawa Shinya, Mizuno Haruo, Saitoh Shinji

SCIENTIFIC REPORTS Vol. 12 ( 1 ) page： 11259 2022.7

Language：English Publishing type：Research paper (scientific journal) Publisher：Scientific Reports

SLC26A4 is a known iodide transporter, and is localized at the apical membrane of thyrocytes. Previously, we reported that SLC26A7 is also involved in iodide transport and that Slc26a7 is a novel causative gene for congenital hypothyroidism. However, its detailed role in vivo remains to be elucidated. We generated mice that were deficient in Slc26a7 and Slc26a4 to delineate differences and associations in their roles in iodide transport. Slc26a7−/− mice showed goitrous congenital hypothyroidism and mild growth failure on a normal diet. Slc26a7−/− mice with a low iodine environment showed marked growth failure. In contrast, Slc26a4−/− mice showed no growth failure and hypothyroidism in the same low iodine environment. Double-deficient mice showed more severe growth failure than Slc26a7−/− mice. RNA-seq analysis revealed that the number of differentially expressed genes (DEGs) in Slc26a7−/− mice was significantly higher than that in Slc26a4−/− mice. These indicate that SLC26A7 is more strongly involved in iodide transport and the maintenance of thyroid function than SLC26A4.

DOI： 10.1038/s41598-022-15151-4

Case of ichthyosis with confetti caused by KRT10 mutation, complicated with multiple malignant melanomas. International journal

Yasutoshi Ito, Takuya Takeichi, Koichi Nakagawa, Kana Tanahashi, Yoshinao Muro, Tomoo Ogi, Masashi Akiyama

The Journal of dermatology Vol. 49 ( 7 ) page： E228 - E229 2022.7

Deep Phenotyping of Superficial Epidermolytic Ichthyosis due to a Recurrent Mutation in KRT2. International journal

Yuika Suzuki, Takuya Takeichi, Kana Tanahashi, Yoshinao Muro, Yasushi Suga, Tomoo Ogi, Masashi Akiyama

International journal of molecular sciences Vol. 23 ( 14 ) 2022.7

Language：English Publishing type：Research paper (scientific journal)

Superficial epidermolytic ichthyosis (SEI) is an autosomal dominant inherited ichthyosis. SEI is caused by mutations in KRT2 and frequently shows erythroderma and widespread blistering at birth. We report the clinical manifestations of two patients from a Japanese family with SEI caused by a hotspot mutation, p.Glu487Lys, in KRT2. In addition, we summarize previous reports on SEI patients with the identical mutation. One of the two patients had disease onset at the age of 7 months. The other patient's age of onset is unknown, but it was in childhood. Neither of the two patients showed erythroderma. To perform deep phenotyping, we studied the age of onset and the frequency of erythroderma in 34 reported SEI cases with the p.Glu487Lys mutation, including the present cases. Among the cases with sufficient clinical information, 44.4% of the cases that were due to p.Glu487Lys in KRT2 occurred at birth. Erythroderma was observed in 11.1% of the cases with p.Glu487Lys in KRT2.

DOI： 10.3390/ijms23147791

Detection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study

Torii Yuka, Horiba Kazuhiro, Kawada Jun-ichi, Haruta Kazunori, Yamaguchi Makoto, Suzuki Takako, Uryu Hideko, Kashiwa Naoyuki, Goishi Keiji, Ogi Tomoo, Ito Yoshinori

BMC INFECTIOUS DISEASES Vol. 22 ( 1 ) page： 568 2022.6

Language：English Publishing type：Research paper (scientific journal) Publisher：BMC Infectious Diseases

Background: Congenital human cytomegalovirus (cCMV) infection can cause sensorineural hearing loss and neurodevelopmental disabilities in children. Ganciclovir and valganciclovir (GCV/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has been documented in some cases. Long-read sequencing can be used for the detection of drug resistance mutations. The objective of this study was to develop full-length analysis of UL97 and UL54, target genes with mutations that confer GCV/VGCV resistance using long-read sequencing, and investigate drug resistance mutation in patients with cCMV infection. Methods: Drug resistance mutation analysis was retrospectively performed in 11 patients with cCMV infection treated with GCV/VGCV. UL97 and UL54 genes were amplified using blood DNA. The amplicons were sequenced using a long-read sequencer and aligned with the reference gene. Single nucleotide variants were detected and replaced with the reference sequence. The replaced sequence was submitted to a mutation resistance analyzer, which is an open platform for drug resistance mutations. Results: Two drug resistance mutations (UL54 V823A and UL97 A594V) were found in one patient. Both mutations emerged after 6 months of therapy, where viral load increased. Mutation rates subsided after cessation of GCV/VGCV treatment. Conclusions: Antiviral drug resistance can emerge in patients with cCMV receiving long-term therapy. Full-length analysis of UL97 and UL54 via long-read sequencing enabled the rapid and comprehensive detection of drug resistance mutations.

DOI： 10.1186/s12879-022-07537-6

Expanding the phenotypic spectrum of ARCN1-related syndrome

Ritter Alyssa L., Gold Jessica, Hayashi Hiroshi, Ackermann Amanda M., Hanke Stephanie, Skraban Cara, Cuddapah Sanmati, Bhoj Elizabeth, Li Dong, Kuroda Yukiko, Wen Jessica, Takeda Ryojun, Bibb Audrey, El Chehadeh Salima, Piton Amelie, Ohl Jeanine, Kukolich Mary K., Nagasaki Keisuke, Kato Kohji, Ogi Tomoo, Bhatti Tricia, Russo Pierre, Krock Bryan, Murrell Jill R., Sullivan Jennifer A., Shashi Vandana, Stong Nicholas, Hakonarson Hakon, Sawano Kentaro, Torti Erin, Willaert Rebecca, Si Yue, Wilcox William Ross, Wirgenes Katrine Verena, Thomassen Kristian, Carlotti Katherine, Erwin Angelika, Lazier Joanna, Marquardt Thorsten, He Miao, Edmondson Andrew C., Izumi Kosuke

GENETICS IN MEDICINE Vol. 24 ( 6 ) page： 1227 - 1237 2022.6

Language：English Publishing type：Research paper (scientific journal) Publisher：Genetics in Medicine

Purpose: This study aimed to describe the phenotypic and molecular characteristics of ARCN1-related syndrome. Methods: Patients with ARCN1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. Results: In total, we identified 14 cases of ARCN1-related syndrome, (9 pediatrics, and 5 fetal cases from 3 families). The clinical features these newly identified cases were compared to 6 previously reported cases for a total of 20 cases. Intrauterine growth restriction, micrognathia, and short stature were present in all patients. Other common features included prematurity (11/15, 73.3%), developmental delay (10/14, 71.4%), genitourinary malformations in males (6/8, 75%), and microcephaly (12/15, 80%). Novel features of ARCN1-related syndrome included transient liver dysfunction and specific glycosylation abnormalities during illness, giant cell hepatitis, hepatoblastoma, cataracts, and lethal skeletal manifestations. Developmental delay was seen in 73% of patients, but only 3 patients had intellectual disability, which is less common than previously reported. Conclusion: ARCN1-related syndrome presents with a wide clinical spectrum ranging from a severe embryonic lethal syndrome to a mild syndrome with intrauterine growth restriction, micrognathia, and short stature without intellectual disability. Patients with ARCN1-related syndrome should be monitored for liver dysfunction during illness, cataracts, and hepatoblastoma. Additional research to further define the phenotypic spectrum and possible genotype–phenotype correlations are required.

DOI： 10.1016/j.gim.2022.02.005

Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome

経過観察中に水疱性類天疱瘡を発症した、MV遺伝子変異を有する高齢発症の汗孔角化症の2例

有沢友希, 武市拓也, 伊藤靖敏, 棚橋華奈, 室慶直, 荻朋男, 秋山真志

加齢皮膚医学セミナー Vol. 17 ( 1 ) page： 74 - 75 2022.6

経過観察中に水疱性類天疱瘡を発症した、MV遺伝子変異を有する高齢発症の汗孔角化症の2例

有沢友希, 武市拓也, 伊藤靖敏, 棚橋華奈, 室慶直, 荻朋男, 秋山真志

加齢皮膚医学セミナー Vol. 17 ( 1 ) page： 74 - 75 2022.6

Epithelioid cell granuloma formation in CARD14-associated papulosquamous eruptions. International journal

Takuya Takeichi, Kenta Ikeda, Yoshinao Muro, Tomoo Ogi, Shin Morizane, Masashi Akiyama

Journal of the European Academy of Dermatology and Venereology : JEADV Vol. 36 ( 5 ) page： E369 - E371 2022.5

Stephenson Sarah E. M., Costain Gregory, Blok Laura E. R., Silk Michael A., Nguyen Thanh Binh, Dong Xiaomin, Alhuzaimi Dana E., Dowling James J., Walker Susan, Amburgey Kimberly, Hayeems Robin Z., Rodan Lance H., Schwartz Marc A., Picker Jonathan, Lynch Sally A., Gupta Aditi, Rasmussen Kristen J., Schimmenti Lisa A., Klee Eric W., Niu Zhiyv, Agre Katherine E., Chilton Ilana, Chung Wendy K., Revah-Politi Anya, Au P. Y. Billie, Griffith Christopher, Racobaldo Melissa, Raas-Rothschild Annick, Ben Zeev Bruria, Barel Ortal, Moutton Sebastien, Morice-Picard Fanny, Carmignac Virginie, Cornaton Jenny, Marle Nathalie, Devinsky Orrin, Stimach Chandler, Wechsler Stephanie Burns, Hainline Bryan E., Sapp Katie, Willems Marjolaine, Bruel Angeline, Dias Kerith-Rae, Evans Carey-Anne, Roscioli Tony, Sachdev Rani, Temple Suzanna E. L., Zhu Ying, Baker Joshua J., Scheffer Ingrid E., Gardiner Fiona J., Schneider Amy L., Muir Alison M., Mefford Heather C., Crunk Amy, Heise Elizabeth M., Millan Francisca, Monaghan Kristin G., Person Richard, Rhodes Lindsay, Richards Sarah, Wentzensen Ingrid M., Cogne Benjamin, Isidor Bertrand, Nizon Mathilde, Vincent Marie, Besnard Thomas, Piton Amelie, Marcelis Carlo, Kato Kohji, Koyama Norihisa, Ogi Tomoo, Goh Elaine Suk-Ying, Richmond Christopher, Amor David J., Boyce Jessica O., Morgan Angela T., Hildebrand Michael S., Kaspi Antony, Bahlo Melanie, Fridriksdottir Run, Katrinardottir Hildigunnur, Sulem Patrick, Stefansson Kari, Bjornsson Hans Tomas, Mandelstam Simone, Morleo Manuela, Mariani Milena, Scala Marcello, Accogli Andrea, Torella Annalaura, Capra Valeria, Wallis Mathew, Jansen Sandra, Waisfisz Quinten, de Haan Hugoline, Sadedin Simon, Lim Sze Chern, White Susan M., Ascher David B., Schenck Annette, Lockhart Paul J., Christodoulou John, Tan Tiong Yang

AMERICAN JOURNAL OF HUMAN GENETICS Vol. 109 ( 4 ) page： 601 - 617 2022.4

Language：English Publishing type：Research paper (scientific journal) Publisher：American Journal of Human Genetics

Neurodevelopmental disorders are highly heterogenous conditions resulting from abnormalities of brain architecture and/or function. FBXW7 (F-box and WD-repeat-domain-containing 7), a recognized developmental regulator and tumor suppressor, has been shown to regulate cell-cycle progression and cell growth and survival by targeting substrates including CYCLIN E1/2 and NOTCH for degradation via the ubiquitin proteasome system. We used a genotype-first approach and global data-sharing platforms to identify 35 individuals harboring de novo and inherited FBXW7 germline monoallelic chromosomal deletions and nonsense, frameshift, splice-site, and missense variants associated with a neurodevelopmental syndrome. The FBXW7 neurodevelopmental syndrome is distinguished by global developmental delay, borderline to severe intellectual disability, hypotonia, and gastrointestinal issues. Brain imaging detailed variable underlying structural abnormalities affecting the cerebellum, corpus collosum, and white matter. A crystal-structure model of FBXW7 predicted that missense variants were clustered at the substrate-binding surface of the WD40 domain and that these might reduce FBXW7 substrate binding affinity. Expression of recombinant FBXW7 missense variants in cultured cells demonstrated impaired CYCLIN E1 and CYCLIN E2 turnover. Pan-neuronal knockdown of the Drosophila ortholog, archipelago, impaired learning and neuronal function. Collectively, the data presented herein provide compelling evidence of an F-Box protein-related, phenotypically variable neurodevelopmental disorder associated with monoallelic variants in FBXW7.

DOI： 10.1016/j.ajhg.2022.03.002

Mutations in SAM syndrome and palmoplantar keratoderma patients suggest genotype/phenotype correlations in DSG1 mutations

Takeuchi S., Takeichi T., Koike Y., Takama H., Tanahashi K., Okuno Y., Ishii N., Muro Y., Ogi T., Suga Y., Akiyama M.

JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY Vol. 36 ( 3 ) page： E215 - E218 2022.3

Clinical practice guidelines for pseudoxanthoma elasticum (2017): Clinical Practice Guidelines for Pseudoxanthoma Elasticum Drafting Committee: Clinical Practice Guidelines for Pseudoxanthoma Elasticum Drafting Committee. International journal

Akira Iwanaga, Atsushi Utani, Yuta Koike, Yumi Okubo, Yutaka Kuwatsuka, Yuichiro Endo, Hideaki Tanizaki, Mari Wataya-Kaneda, Atsushi Hatamochi, Kosuke Minaga, Tomoo Ogi, Yosuke Yamamoto, Satoshi Ikeda, Eiko Tsuiki, Hiroshi Tamura, Koji Maemura, Takashi Kitaoka, Hiroyuki Murota

The Journal of dermatology Vol. 49 ( 3 ) page： e91-e98 - e98 2022.1

Language：English Publishing type：Research paper (scientific journal)

Pseudoxanthoma elasticum (PXE) is a progressive hereditary disease that affects tissues such as the skin, retina, blood vessels, and gastrointestinal tracts. Therefore, comprehensive medical care across clinical departments specialized in specific organs is needed to provide the best clinical practices to PXE patients. The Japanese version of clinical guidelines developed by the Japanese Dermatological Association was published in 2017, and aimed to promote equal accessibility of PXE-related medical care. Here, the English version of Japanese guideline is reported, and is intended to be worldwide reference for medical care of PXE.

DOI： 10.1111/1346-8138.16301

Subtle infantile spasms presenting as hyperirritability in CK syndrome

Hagiwara Sho, Shiohama Tadashi, Ogi Tomoo, Ichikawa Tomohiko, Hamada Hiromichi

PEDIATRICS INTERNATIONAL Vol. 64 ( 1 ) page： e15335 2022.1

Exome sequencing of Japanese schizophrenia multiplex families supports the involvement of calcium ion channels

Toyama Miho, Takasaki Yuto, Branko Aleksic, Kimura Hiroki, Kato Hidekazu, Nawa Yoshihiro, Kushima Itaru, Ishizuka Kanako, Shimamura Teppei, Ogi Tomoo, Ozaki Norio

PLOS ONE Vol. 17 ( 5 ) page： e0268321 2022

Language：English Publishing type：Research paper (scientific journal) Publisher：PLoS ONE

Background Most sequencing studies of schizophrenia (SCZ) have focused on de novo genetic variants due to interpretability. However, investigating shared rare variants among patients in the same multiplex family is also important. Relatively large-scale analyses of SCZ multiplex families have been done in Caucasian populations, but whether detected variants are also pathogenic in the Japanese population is unclear because of ethnic differences in rare variants. Materials and methods We performed whole-exome sequencing (WES) of 14 Japanese SCZ multiplex families. After quality control and filtering, we identified rare variants shared among affected persons within the same family. A gene ontology (GO) analysis was performed to identify gene categories possibly affected by these candidate variants. Results We found 530 variants in 486 genes as potential candidate variants from the 14 SCZ multiplex families examined. The GO analysis demonstrated significant enrichment in calcium channel activity. Conclusion This study provides supporting evidence that calcium ion channel activity is involved in SCZ. WES of multiplex families is a potential means of identifying disease-associated rare variants for SCZ.

DOI： 10.1371/journal.pone.0268321

Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases

Kazuhiro Horiba, Yuka Torii, Toshihiko Okumura, Suguru Takeuchi, Takako Suzuki, Jun-ichi Kawada, Hideki Muramatsu, Yoshiyuki Takahashi, Tomoo Ogi, Yoshinori Ito

Open Forum Infectious Diseases Vol. 8 ( 11 ) page： ofab223 2021.11

Language：English Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP)

<title>Abstract</title>
<sec>
<title>Background</title>
Febrile neutropenia (FN) is a frequent complication in immunocompromised patients. However, causative microorganisms are detected in only 10% of patients. This study aimed to detect the microorganisms that cause FN using next-generation sequencing (NGS) to idenjpgy the genome derived from pathogenic microorganisms in the bloodstream. Here, we implemented a metagenomic approach to comprehensively analyze microorganisms present in clinical samples from patients with FN.

</sec>
<sec>
<title>Methods</title>
FN is defined as 1) a neutrophil count &lt; 500/µL, and 2) fever ≥ 37.5 °C. Plasma/serum samples of 112 pediatric patients with FN, 10 patients with neutropenia without fever (NE), were sequenced by NGS and analyzed by a metagenomic pipeline PATHDET.

</sec>
<sec>
<title>Results</title>
The putative pathogens were detected by NGS in 5 of 10 patients with FN with positive for blood culture results, 15 of 87 patients (17%) with negative for blood culture results, and 3 of 8 patients with NE. Several bacteria that were common in the oral, skin, and gut flora were commonly detected in blood samples, suggesting translocation of the human microbiota to the bloodstream in the setting of neutropenia. The cluster analysis of the microbiota in blood samples using NGS demonstrated that the representative bacteria of each cluster was mostly consistent with the pathogens in each patient.

</sec>
<sec>
<title>Conclusions</title>
NGS technique has a great potential for detecting causative pathogens in patients with FN. Cluster analysis, which extracts characteristic microorganisms from a complex microbial population, may be effective to detect pathogens in minute quantities of microbiota, such as those from the bloodstream.

</sec>

DOI： 10.1093/ofid/ofab223

Extensive multiple organ involvement in VEXAS syndrome

Noriyuki Takahashi, Takuya Takeichi, Tetsuya Nishida, Yasuhiro Takahashi, Juichi Sato, Masahiro Yamamura, Tomoo Ogi, Masashi Akiyama

Arthritis & Rheumatology Vol. 73 ( 10 ) page： 1896 - 1897 2021.10

Successful dupilumab treatment for ichthyotic and atopic features of Netherton syndrome

Murase C., Takeichi T., Taki T., Yoshikawa T., Suzuki A., Ogi T., Suga Y., Akiyama M.

JOURNAL OF INVESTIGATIVE DERMATOLOGY Vol. 141 ( 10 ) page： S177 - S177 2021.10

Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders

Jia Nan, Guo Chaowan, Nakazawa Yuka, Heuvel Diana van den, Luijsterburg Martijn S., Ogi Tomoo

DNA REPAIR Vol. 106 page： 103192 2021.10

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：DNA Repair

Transcription-blocking DNA lesions (TBLs) in genomic DNA are triggered by a wide variety of DNA-damaging agents. Such lesions cause stalling of elongating RNA polymerase II (RNA Pol II) enzymes and fully block transcription when unresolved. The toxic impact of DNA damage on transcription progression is commonly referred to as transcription stress. In response to RNA Pol II stalling, cells activate and employ transcription-coupled repair (TCR) machineries to repair cytotoxic TBLs and resume transcription. Increasing evidence indicates that the modification and processing of stalled RNA Pol II is an integral component of the cellular response to and the repair of TBLs. If TCR pathways fail, the prolonged stalling of RNA Pol II will impede global replication and transcription as well as block the access of other DNA repair pathways that may act upon the TBL. Consequently, such prolonged stalling will trigger profound genome instability and devastating clinical features. In this review, we will discuss the mechanisms by which various types of TBLs are repaired by distinct TCR pathways and how RNA Pol II processing is regulated during these processes. We will also discuss the clinical consequences of transcription stress and genotype-phenotype correlations of related TCR-deficiency disorders.

DOI： 10.1016/j.dnarep.2021.103192

Protein instability associated with AARS1 and MARS1 mutations causes trichothiodystrophy

Botta Elena, Theil Arjan F., Raams Anja, Caligiuri Giuseppina, Giachetti Sarah, Bione Silvia, Accadia Maria, Lombardi Anita, Smith Desiree E. C., Mendes Marisa I, Swagemakers Sigrid M. A., Van der Spek Peter J., Salomons Gajja S., Hoeijmakers Jan H. J., Yesodharan Dhanya, Nampoothiri Sheela, Ogi Tomoo, Lehmann Alan R., Orioli Donata, Vermeulen Wim

HUMAN MOLECULAR GENETICS Vol. 30 ( 18 ) page： 1711 - 1720 2021.9

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Human Molecular Genetics

Trichothiodystrophy (TTD) is a rare hereditary neurodevelopmental disorder defined by sulfur-deficient brittle hair and nails and scaly skin, but with otherwise remarkably variable clinical features. The photosensitive TTD (PS-TTD) forms exhibits in addition to progressive neuropathy and other features of segmental accelerated aging and is associated with impaired genome maintenance and transcription. New factors involved in various steps of gene expression have been identified for the different non-photosensitive forms of TTD (NPS-TTD), which do not appear to show features of premature aging. Here, we identify alanyl-tRNA synthetase 1 and methionyl-tRNA synthetase 1 variants as new gene defects that cause NPS-TTD. These variants result in the instability of the respective gene products alanyl- and methionyl-tRNA synthetase. These findings extend our previous observations that TTD mutations affect the stability of the corresponding proteins and emphasize this phenomenon as a common feature of TTD. Functional studies in skin fibroblasts from affected individuals demonstrate that these new variants also impact on the rate of tRNA charging, which is the first step in protein translation. The extension of reduced abundance of TTD factors to translation as well as transcription redefines TTD as a syndrome in which proteins involved in gene expression are unstable.

DOI： 10.1093/hmg/ddab123

The sodium-glucose cotransporter-2 inhibitor Tofogliflozin prevents the progression of nonalcoholic steatohepatitis-associated liver tumors in a novel murine model

Cutaneous malignant melanoma in an elderly patient with intermediate junctional epidermolysis bullosa. International journal

Yuta Yamashita, Tomoki Taki, Takuya Takeichi, Mao Okumura, Shoichiro Mori, Yasutoshi Ito, Tomoo Ogi, Motohito Yamada, Masashi Akiyama

The Journal of dermatology Vol. 48 ( 8 ) page： E384 - E385 2021.8

Yoshioka Naoki, Tanaka Miyako, Ochi Kozue, Watanabe Akiko, Ono Kenji, Sawada Makoto, Ogi Tomoo, Itoh Michiko, Ito Ayaka, Shiraki Yukihiro, Enomoto Atsushi, Ishigami Masatoshi, Fujishiro Mitsuhiro, Ogawa Yoshihiro, Suganami Takayoshi

BIOMEDICINE & PHARMACOTHERAPY Vol. 140 page： 111738 2021.8

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Biomedicine and Pharmacotherapy

Background: Diabetes and obesity contribute to the pathogenesis of nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). However, how diabetes and obesity accelerate liver tumorigenesis remains to be fully understood. Moreover, to verify the therapeutic potential of anti-diabetic drugs, there exists a strong need for appropriate animal models that recapitulate human pathophysiology of NASH and HCC. Methods: We established a novel murine model of NASH-associated liver tumors using genetically obese melanocortin 4 receptor-deficient mice fed on Western diet in combination with a chemical procarcinogen, and verified the validity of our model in evaluating drug efficacy. Findings: Our model developed multiple liver tumors together with obesity, diabetes, and NASH within a relatively short period (approximately 3 months). In this model, sodium glucose cotransporter 2 inhibitor Tofogliflozin prevented the development of NASH-like liver phenotypes and the progression of liver tumors. Tofogliflozin attenuated p21 expression of hepatocytes in non-tumorous lesions in the liver. Interpretation: Tofogliflozin treatment attenuates cellular senescence of hepatocytes under obese and diabetic conditions. This study provides a unique animal model of NASH-associated liver tumors, which is applicable for assessing drug efficacy to prevent or treat NASH-associated HCC.

DOI： 10.1016/j.biopha.2021.111738

Updated allele frequencies of SERPINB7 founder mutations in Asian patients with Nagashima-type palmoplantar keratosis/keratoderma

Yasutoshi Ito, Takuya Takeichi, Kenta Ikeda, Kana Tanahashi, Takenori Yoshikawa, Yuya Murase, Yoshinao Muro, Yoshio Kawakami, Yasuo Nakamura, Kanako Matsuyama, Jun Muto, Naoki Oiso, Shin Morizane, Kazumitsu Sugiura, Yasushi Suga, Mariko Seishima, Akira Kawada, Tomoo Ogi, Masashi Akiyama

Journal of Dermatological Science Vol. 103 ( 2 ) page： 116 - 119 2021.8

Paradoxical Reaction in a Patient with Hidradenitis Suppurativa Undergoing Adalimumab Treatment. International journal

Soichiro Ikeya, Takuya Takeichi, Tomoki Taki, Yoshinao Muro, Tomoo Ogi, Masashi Akiyama

Acta dermato-venereologica Vol. 101 ( 6 ) page： adv00484 2021.6

Pediatric sepsis cases diagnosed with group B streptococcal meningitis using next-generation sequencing: a report of two cases

Horiba Kazuhiro, Suzuki Michio, Tetsuka Nobuyuki, Kawano Yoshihiko, Yamaguchi Makoto, Okumura Toshihiko, Suzuki Takako, Torii Yuka, Kawada Jun-ichi, Morita Makoto, Hara Shinya, Ogi Tomoo, Ito Yoshinori

BMC INFECTIOUS DISEASES Vol. 21 ( 1 ) page： 531 2021.6

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：BMC Infectious Diseases

Background: Group B Streptococcus (GBS) is an important cause of invasive infection in neonates and infants. Cerebrospinal fluid (CSF) findings and culture may not show evidence of infection early in GBS meningitis. Next-generation sequencing (NGS) has the potential to detect microbial genetic material in patients with infectious diseases. We report two cases of infantile sepsis of GBS meningitis with negative results for CSF culture tests, but positive results for NGS analysis. Case presentation: Patient 1 was a 22-day-old male infant diagnosed with sepsis and meningitis. His CSF findings showed pleocytosis, decreased glucose, and increased protein levels. However, CSF and blood culture results at admission were negative. He received a total of 3 weeks of treatment with ampicillin and cefotaxime, and showed clinical improvement. GBS was detected through NGS analysis of CSF collected at admission. Patient 2 was a 51-day-old male infant with sepsis. CSF findings on admission were normal, and blood and CSF cultures were also negative. Intravenous ampicillin and cefotaxime treatment were initiated. Treatment was de-escalated to ampicillin alone because Enterococcus faecalis was cultured from urine. He was discharged after a total of 1 week of antibiotic treatment. Six days after discharge, he was re-hospitalized for sepsis. Blood and CSF cultures were negative, and E. faecalis was again cultured from urine. He received a total of 3 weeks of ampicillin treatment for enterococcal-induced nephritis and did not relapse thereafter. NGS pathogen searches were retrospectively performed on both blood and CSF collected at the first and second admission. GBS was detected in the CSF collected at the first admission, but no significant pathogen was detected in the other samples. Inadequate treatment for GBS meningitis at the first admission may have caused the recurrence of the disease. Conclusion: Infantile sepsis may present bacterial meningitis that is not diagnosed by either culture testing or CSF findings. NGS analysis for CSF may be useful for confirming the diagnosis of bacterial meningitis.

DOI： 10.1186/s12879-021-06231-3

Predominant cellular mitochondrial dysfunction in the TOP3A gene-caused Bloom syndrome-like disorder

Jiang Wenjun, Jia Nan, Guo Chaowan, Wen Juan, Wu Lingqian, Ogi Tomoo, Zhang Huiwen

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE Vol. 1867 ( 6 ) page： 166106 2021.6

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Biochimica et Biophysica Acta - Molecular Basis of Disease

TOP3A promotes processing of double Holliday junction dissolution and also plays an important role in decatenation and segregation of human mtDNA. Recently, TOP3A mutations have been reported to cause Bloom syndrome-like disorder. However, whether the two function play equal roles in the disease pathogenesis is unclear. We retrospectively studied the disease progression of two siblings with Bloom-like syndrome caused by two novel mutations of TOP3A, p.Q788* and p.D479G. Beside the common clinical manifestations, our patients exhibited liver lipid storage with hepatomegaly. In cellular and molecular biological studies, TOP3A deficiency moderately increased sister chromatid exchanges and decreased cell proliferation compared with BLM or RMI2 deficiency. These changes were rescued by ectopic expression of either of the wildtype TOP3A or TOP3A-D479G. In contrast, reduced mitochondrial ATP generation and oxygen consumption rates observed in TOP3A defective cells were rescued by over-expression of the wildtype TOP3A, but not TOP3A-D479G. Considering the different impact of the TOP3A-D479G mutation on the genome stability and mitochondrial metabolism, we propose that the impaired mitochondrial metabolism plays an important role in the pathogenesis of TOP3A-deficient Bloom-like disease.

DOI： 10.1016/j.bbadis.2021.166106

Hereditary Mucoepithelial Dysplasia and Autosomal-Dominant IFAP Syndrome Is a Clinical Spectrum Due to SREBF1 Variants. International journal

Chiaki Murase, Takuya Takeichi, Toshifumi Nomura, Tomoo Ogi, Masashi Akiyama

The Journal of investigative dermatology Vol. 141 ( 6 ) page： 1596 - 1598 2021.6

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. International journal

Yana van der Weegen, Klaas de Lint, Diana van den Heuvel, Yuka Nakazawa, Tycho E T Mevissen, Janne J M van Schie, Marta San Martin Alonso, Daphne E C Boer, Román González-Prieto, Ishwarya V Narayanan, Noud H M Klaassen, Annelotte P Wondergem, Khashayar Roohollahi, Josephine C Dorsman, Yuichiro Hara, Alfred C O Vertegaal, Job de Lange, Johannes C Walter, Sylvie M Noordermeer, Mats Ljungman, Tomoo Ogi, Rob M F Wolthuis, Martijn S Luijsterburg

Nature cell biology Vol. 23 ( 6 ) page： 595 - 607 2021.6

Language：English Publishing type：Research paper (scientific journal)

Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.

DOI： 10.1038/s41556-021-00688-9

Transcription-Coupled DNA Repair: From Mechanism to Human Disorder

van den Heuvel Diana, van der Weegen Yana, Boer Daphne E. C., Ogi Tomoo, Luijsterburg Martijn S.

TRENDS IN CELL BIOLOGY Vol. 31 ( 5 ) page： 359 - 371 2021.5

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Trends in Cell Biology

DNA lesions pose a major obstacle during gene transcription by RNA polymerase II (RNAPII) enzymes. The transcription-coupled DNA repair (TCR) pathway eliminates such DNA lesions. Inherited defects in TCR cause severe clinical syndromes, including Cockayne syndrome (CS). The molecular mechanism of TCR and the molecular origin of CS have long remained enigmatic. Here we explore new advances in our understanding of how TCR complexes assemble through cooperative interactions between repair factors stimulated by RNAPII ubiquitylation. Mounting evidence suggests that RNAPII ubiquitylation activates TCR complex assembly during repair and, in parallel, promotes processing and degradation of RNAPII to prevent prolonged stalling. The fate of stalled RNAPII is therefore emerging as a crucial link between TCR and associated human diseases.

DOI： 10.1016/j.tcb.2021.02.007

MEDNIK-like syndrome due to compound heterozygous mutations in AP1B1

Successful dupilumab treatment for ichthyotic and atopic features of Netherton syndrome. International journal

Chiaki Murase, Takuya Takeichi, Tomoki Taki, Takenori Yoshikawa, Akiko Suzuki, Tomoo Ogi, Yasushi Suga, Masashi Akiyama

Journal of dermatological science Vol. 102 ( 2 ) page： 126 - 129 2021.5

Ito Y., Takeichi T., Igari S., Mori T., Ono A., Suyama K., Takeuchi S., Muro Y., Ogi T., Hosoya M., Yamamoto T., Akiyama M.

JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY Vol. 35 ( 5 ) page： E345 - E347 2021.5

Odontogenic keratocysts are an important clue for diagnosing basal cell nevus syndrome.

Kaori Kaibuchi-Ando, Takuya Takeichi, Yasutoshi Ito, So Takeuchi, Yuta Yamashita, Motohito Yamada, Yoshinao Muro, Tomoo Ogi, Masashi Akiyama

Nagoya journal of medical science Vol. 83 ( 2 ) page： 393 - 396 2021.5

Language：Japanese Publishing type：Research paper (scientific journal)

Basal cell nevus syndrome (BCNS) is an autosomal dominant skin disorder characterized by multiple basal cell nevi. Patients with BCNS tend to develop basal cell carcinoma (BCC) and frequently show skeletal abnormalities. Most cases of BCNS are caused by mutations in patched 1 (PTCH1). PTCH1 encodes a transmembrane receptor protein for the secreted molecule sonic hedgehog, which plays a key role in the development of animals ranging from insects to mammals. We analyzed two Japanese BCNS patients from two independent families. Both of our patients had multiple jaw keratocysts. In one patient, these were the key to noticing his BCNS, as he had no skin tumors. The early detection of PTCH1 mutations would enable BCNS patients to be carefully followed up for the occurrence of BCC. The diagnosis of BCC at the early stage leads to prompt surgical treatments, resulting in a good prognosis. The present cases suggest that keratocysts of the jaw might be an important clue for diagnosing BCNS.

DOI： 10.18999/nagjms.83.2.393

[A case of Charcot-Marie-Tooth disease type 2Z caused by MORC2 S87L mutation mimicking spinal muscular atrophy].

Yamamoto D, Oda R, Hisahara S, Ishikawa A, Ogi T, Shimohama S

Rinsho shinkeigaku = Clinical neurology Vol. 61 ( 4 ) page： 262 - 264 2021.4

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Clinical Neurology

A 33-year-old man with an unremarkable family history has had limb muscle weakness, joint contracture and skeleton deformation from early childhood. He was diagnosed with spinal muscular atrophy (SMA) by a pediatrician. He needed assistance and used orthoses in his daily life. There was no subjective sensory disturbance. However, physical examination showed slight sensory impairment, and nerve conduction study indicated sensory motor axonal neuropathy. This finding suggested Charcot-Marie-Tooth disease (CMT). Gene analysis detected MORC2 S87L mutation, leading to a diagnosis of CMT type 2Z. Patients with MORC2 S87L mutation are known to exhibit a severe phenotype, and may mimic SMA. It is important to demonstrate subclinical sensory neuropathy in patients with MORC2 S87L mutation mimicking SMA.

DOI： 10.5692/clinicalneurol.cn-001542

Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study

Okumura Toshihiko, Horiba Kazuhiro, Kamei Hideya, Takeuchi Suguru, Suzuki Takako, Torii Yuka, Kawada Jun-ichi, Takahashi Yoshiyuki, Ogura Yasuhiro, Ogi Tomoo, Ito Yoshinori

BMC MICROBIOLOGY Vol. 21 ( 1 ) page： 104 2021.4

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：BMC Microbiology

Background: Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection but poses a risk for severe infectious diseases. Immune modulation and antimicrobials affect the plasma microbiome. Thus, determining the impact of immunosuppression on the microbiome may be important to understand immunocompetence, elucidate the source of infection, and predict the risk of infection in LT recipients. We characterized the plasma microbiome of LT recipients at early post-LT and assessed the association between the microbiome and clinical events. Results: In this study, 51 patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected at the following time points: 1) within a week after LT; 2) 4 ± 1 weeks after LT; 3) 8 ± 1 weeks after LT; and 4) within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS) with the PATHDET pipeline. Relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period. Microbiome diversity was higher within a week after LT than that at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly increased and the plasma microbiome diversity was significantly lower in patients with acute cellular rejection (ACR) than non-ACR patients. Sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples, and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe clinical condition. Conclusions: The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients.

DOI： 10.1186/s12866-021-02154-w

The wide-ranging clinical and genetic features in Japanese families with valosin-containing protein proteinopathy. International journal

Takashi Ando, Ryoichi Nakamura, Satoshi Kuru, Daichi Yokoi, Naoki Atsuta, Haruki Koike, Masashi Suzuki, Kazuhiro Hara, Yohei Iguchi, Yumiko Harada, Yusuke Yoshida, Makoto Hattori, Ayuka Murakami, Seiya Noda, Seigo Kimura, Jun Sone, Tomohiko Nakamura, Yoji Goto, Kazuo Mano, Hisashi Okada, Satoshi Okuda, Ichizo Nishino, Tomoo Ogi, Gen Sobue, Masahisa Katsuno

Neurobiology of aging Vol. 100 page： 120.e1 - 120.e6 2021.4

Language：Japanese Publishing type：Research paper (scientific journal)

Mutations in the valosin-containing protein (VCP) gene are known to cause various neurodegenerative disorders. Here, we report 8 Japanese patients [6 men, 2 women; median age at onset: 49.5 (range, 35-58) years] from 5 unrelated families with VCP missense mutations. Although 7 of 8 patients were diagnosed with either inclusion body myopathy or amyotrophic lateral sclerosis, 1 patient showed demyelinating polyneuropathy, which was confirmed by longitudinal nerve conduction studies. Sural nerve biopsy of the patient revealed intranuclear ubiquitin staining in Schwann cells. Three known pathogenic VCP mutations (p.Arg191Gln, p.Arg155Cys, and p.Ile126Phe) were detected. A novel mutation, c.293 A>T (p.Asp98Val), was also identified in a patient with amyotrophic lateral sclerosis and frontotemporal dementia. This mutation was predicted to be "deleterious" or "disease causing" using in silico mutation analyses. In conclusion, demyelinating polyneuropathy may be a novel phenotype caused by VCP mutations. The p.Asp98Val mutation was found to be a novel pathogenic mutation of VCP proteinopathy. We believe our cases represent a wide clinical spectrum of VCP mutations.

DOI： 10.1016/j.neurobiolaging.2020.10.028

Two Cases of Porokeratosis with MVD Mutations, in Association with Bullous Pemphigoid. International journal

Yuki Arisawa, Yasutoshi Ito, Kana Tanahashi, Yoshinao Muro, Tomoo Ogi, Takuya Takeichi, Masashi Akiyama

Acta dermato-venereologica Vol. 101 ( 3 ) page： adv00423 2021.3

Identification of a novel causative mutation in KRT1 in diffuse palmoplantar keratoderma, facilitated by whole-exome sequencing. International journal

So Takeuchi, Takuya Takeichi, Yasutoshi Ito, Kana Tanahashi, Yoshinao Muro, Tomoo Ogi, Masashi Akiyama

European journal of dermatology : EJD Vol. 31 ( 2 ) page： 264 - 265 2021.3

Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer's disease. International journal

Akira Sobue, Okiru Komine, Yuichiro Hara, Fumito Endo, Hiroyuki Mizoguchi, Seiji Watanabe, Shigeo Murayama, Takashi Saito, Takaomi C Saido, Naruhiko Sahara, Makoto Higuchi, Tomoo Ogi, Koji Yamanaka

Acta neuropathologica communications Vol. 9 ( 1 ) page： 1 - 1 2021.1

Language：Japanese Publishing type：Research paper (scientific journal)

Microglia-mediated neuroinflammation has been implicated in the pathogenesis of Alzheimer's disease (AD). Although microglia in aging and neurodegenerative disease model mice show a loss of homeostatic phenotype and activation of disease-associated microglia (DAM), a correlation between those phenotypes and the degree of neuronal cell loss has not been clarified. In this study, we performed RNA sequencing of microglia isolated from three representative neurodegenerative mouse models, AppNL-G-F/NL-G-F with amyloid pathology, rTg4510 with tauopathy, and SOD1G93A with motor neuron disease by magnetic activated cell sorting. In parallel, gene expression patterns of the human precuneus with early Alzheimer's change (n = 11) and control brain (n = 14) were also analyzed by RNA sequencing. We found that a substantial reduction of homeostatic microglial genes in rTg4510 and SOD1G93A microglia, whereas DAM genes were uniformly upregulated in all mouse models. The reduction of homeostatic microglial genes was correlated with the degree of neuronal cell loss. In human precuneus with early AD pathology, reduced expression of genes related to microglia- and oligodendrocyte-specific markers was observed, although the expression of DAM genes was not upregulated. Our results implicate a loss of homeostatic microglial function in the progression of AD and other neurodegenerative diseases. Moreover, analyses of human precuneus also suggest loss of microglia and oligodendrocyte functions induced by early amyloid pathology in human.

DOI： 10.1186/s40478-020-01099-x

Expanding the phenotype of biallelic loss-of-function variants in the NSUN2 gene: Description of four individuals with juvenile cataract, chronic nephritis, or brain anomaly as novel complications. International journal

Kohji Kato, Seiji Mizuno, Jenny Morton, Miho Toyama, Yuichiro Hara, Evangeline Wasmer, Alan Lehmann, Tomoo Ogi

American journal of medical genetics. Part A Vol. 185 ( 1 ) page： 282 - 285 2021.1

Language：English Publishing type：Research paper (scientific journal)

The NSUN2 gene encodes a tRNA cytosine methyltransferase that functions in the maturation of leucyl tRNA (Leu) (CAA) precursors, which is crucial for the anticodon-codon pairing and correct translation of mRNA. Biallelic loss of function variants in NSUN2 are known to cause moderate to severe intellectual disability. Microcephaly, postnatal growth retardation, and dysmorphic facial features are common complications in this genetic disorder, and delayed puberty is occasionally observed. Here, we report four individuals, two sets of siblings, with biallelic loss-of-function variants in the NSUN2 gene. The first set of siblings have compound heterozygous frameshift variants: c.546_547insCT, p.Met183Leufs*13; c.1583del, p.Pro528Hisfs*19, and the other siblings carry a homozygous frameshift variant: c.1269dup, p.Val424Cysfs*14. In addition to previously reported clinical features, the first set of siblings showed novel complications of juvenile cataract and chronic nephritis. The other siblings showed hypomyelination and simplified gyral pattern in neuroimaging. NSUN2-related intellectual disability is a very rare condition, and less than 20 cases have been reported previously. Juvenile cataract, chronic nephritis, and brain anomaly shown in the present patients have not been previously described. Our report suggests clinical diversity of NSUN2-related intellectual disability.

DOI： 10.1002/ajmg.a.61927

Digenic mutations in ALDH2 and ADH5 impair formaldehyde clearance and cause a multisystem disorder, AMeD syndrome

Yasuyoshi Oka, Motoharu Hamada, Yuka Nakazawa, Hideki Muramatsu, Yusuke Okuno, Koichiro Higasa, Mayuko Shimada, Honoka Takeshima, Katsuhiro Hanada, Taichi Hirano, Toshiro Kawakita, Hirotoshi Sakaguchi, Takuya Ichimura, Shuichi Ozono, Kotaro Yuge, Yoriko Watanabe, Yuko Kotani, Mutsumi Yamane, Yumiko Kasugai, Miyako Tanaka, Takayoshi Suganami, Shinichiro Nakada, Norisato Mitsutake, Yuichiro Hara, Kohji Kato, Seiji Mizuno, Noriko Miyake, Yosuke Kawai, Katsushi Tokunaga, Masao Nagasaki, Seiji Kito, Keiichi Isoyama, Masafumi Onodera, Hideo Kaneko, Naomichi Matsumoto, Fumihiko Matsuda, Keitaro Matsuo, Yoshiyuki Takahashi, Tomoji Mashimo, Seiji Kojima, Tomoo Ogi

Science Advances Vol. 6 ( 51 ) page： eabd7197 - eabd7197 2020.12

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：American Association for the Advancement of Science (AAAS)

Rs671 in the aldehyde dehydrogenase 2 gene (<italic>ALDH2</italic>) is the cause of Asian alcohol flushing response after drinking. ALDH2 detoxifies endogenous aldehydes, which are the major source of DNA damage repaired by the Fanconi anemia pathway. Here, we show that the rs671 defective allele in combination with mutations in the alcohol dehydrogenase 5 gene, which encodes formaldehyde dehydrogenase (<italic>ADH5FDH</italic>), causes a previously unidentified disorder, AMeD (aplastic anemia, mental retardation, and dwarfism) syndrome. Cellular studies revealed that a decrease in the formaldehyde tolerance underlies a loss of differentiation and proliferation capacity of hematopoietic stem cells. Moreover, <italic>Adh5−/−Aldh2</italic>E506K/E506K double-deficient mice recapitulated key clinical features of AMeDS, showing short life span, dwarfism, and hematopoietic failure. Collectively, our results suggest that the combined deficiency of formaldehyde clearance mechanisms leads to the complex clinical features due to overload of formaldehyde-induced DNA damage, thereby saturation of DNA repair processes.

DOI： 10.1126/sciadv.abd7197

Astrocytic phagocytosis is a compensatory mechanism for microglial dysfunction. International journal

Hiroyuki Konishi, Takayuki Okamoto, Yuichiro Hara, Okiru Komine, Hiromi Tamada, Mitsuyo Maeda, Fumika Osako, Masaaki Kobayashi, Akira Nishiyama, Yosky Kataoka, Toshiyuki Takai, Nobuyuki Udagawa, Steffen Jung, Keiko Ozato, Tomohiko Tamura, Makoto Tsuda, Koji Yamanaka, Tomoo Ogi, Katsuaki Sato, Hiroshi Kiyama

The EMBO journal Vol. 39 ( 22 ) page： e104464 2020.11

Language：Japanese Publishing type：Research paper (scientific journal)

Microglia are the principal phagocytes that clear cell debris in the central nervous system (CNS). This raises the question, which cells remove cell debris when microglial phagocytic activity is impaired. We addressed this question using Siglechdtr mice, which enable highly specific ablation of microglia. Non-microglial mononuclear phagocytes, such as CNS-associated macrophages and circulating inflammatory monocytes, did not clear microglial debris. Instead, astrocytes were activated, exhibited a pro-inflammatory gene expression profile, and extended their processes to engulf microglial debris. This astrocytic phagocytosis was also observed in Irf8-deficient mice, in which microglia were present but dysfunctional. RNA-seq demonstrated that even in a healthy CNS, astrocytes express TAM phagocytic receptors, which were the main astrocytic phagocytic receptors for cell debris in the above experiments, indicating that astrocytes stand by in case of microglial impairment. This compensatory mechanism may be important for the maintenance or prolongation of a healthy CNS.

DOI： 10.15252/embj.2020104464

Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study

A heterozygous SERPINB7 mutation is a possible modifying factor for epidermolytic palmoplantar keratoderma. International journal

Takenori Yoshikawa, Takuya Takeichi, Tomoo Ogi, Yasushi Suga, Yoshinao Muro, Masashi Akiyama

Journal of dermatological science Vol. 100 ( 2 ) page： 148 - 151 2020.11

Torii Yuka, Horiba Kazuhiro, Hayano Satoshi, Kato Taichi, Suzuki Takako, Kawada Jun-ichi, Takahashi Yoshiyuki, Kojima Seiji, Okuno Yusuke, Ogi Tomoo, Ito Yoshinori

BMC PEDIATRICS Vol. 20 ( 1 ) page： 482 2020.10

Gene Expression Profile at the Motor Endplate of the Neuromuscular Junction of Fast-Twitch Muscle. International journal

Kun Huang, Jin Li, Mikako Ito, Jun-Ichi Takeda, Bisei Ohkawara, Tomoo Ogi, Akio Masuda, Kinji Ohno

Frontiers in molecular neuroscience Vol. 13 page： 154 - 154 2020.9

Language：Japanese Publishing type：Research paper (scientific journal)

The neuromuscular junction (NMJ) is a prototypic chemical synapse between the spinal motor neuron and the motor endplate. Gene expression profiles of the motor endplate are not fully elucidated. Collagen Q (ColQ) is a collagenic tail subunit of asymmetric forms of acetylcholinesterase and is driven by two distinct promoters. pColQ1 is active throughout the slow-twitch muscle, whereas pColQ1a is active at the motor endplate of fast-twitch muscle. We made a transgenic mouse line that expresses nuclear localization signal (NLS)-attached Cre recombinase under the control of pColQ1a (pColQ1a-Cre mouse). RiboTag mouse expresses an HA-tagged ribosomal subunit, RPL22, in cells expressing Cre recombinase. We generated pColQ1a-Cre:RiboTag mouse, and confirmed that HA-tagged RPL22 was enriched at the NMJ of tibialis anterior (TA) muscle. Next, we confirmed that Chrne and Musk that are specifically expressed at the NMJ were indeed enriched in HA-immunoprecipitated (IP) RNA, whereas Sox10 and S100b, markers for Schwann cells, and Icam1, a marker for vascular endothelial cells, and Pax3, a marker for muscle satellite cells, were scarcely detected. Gene set enrichment analysis (GSEA) of RNA-seq data showed that "phosphatidylinositol signaling system" and "extracellular matrix receptor interaction" were enriched at the motor endplate. Subsequent analysis revealed that genes encoding diacylglycerol kinases, phosphatidylinositol kinases, phospholipases, integrins, and laminins were enriched at the motor endplate. We first characterized the gene expression profile under translation at the motor endplate of TA muscle using the RiboTag technique. We expect that our gene expression profiling will help elucidate molecular mechanisms of the development, maintenance, and pathology of the NMJ.

DOI： 10.3389/fnmol.2020.00154

NUS1 mutation in a family with epilepsy, cerebellar ataxia, and tremor. Reviewed International journal

Kunihiko Araki, Ryoichi Nakamura, Daisuke Ito, Kohji Kato, Yohei Iguchi, Kentaro Sahashi, Miho Toyama, Kensuke Hamada, Nobuhiko Okamoto, Yoshinao Wada, Tomohiko Nakamura, Tomoo Ogi, Masahisa Katsuno

Epilepsy research Vol. 164 page： 106371 - 106371 2020.8

Language：Japanese Publishing type：Research paper (scientific journal)

We report on familial 5 epilepsy patients with autosomal dominant inheritance of a novel heterozygous NUS1 frameshift mutation. All patients had cerebellar ataxia and tremor. Three patients were diagnosed with childhood absence epilepsy, 1 patient with generalized epilepsy, and 1 patient with parkinsonism without epilepsy. Our cases and previously reported cases with deletions of chromosome 6q22 that include NUS1 share these common symptoms. In a cellular experiment, NUS1 mutation led to a substantial reduction of the protein level of NUS1. NUS1 mutation could contribute to epilepsy pathogenesis and also constitute a distinct syndromic entity with cerebellar ataxia and tremor.

DOI： 10.1016/j.eplepsyres.2020.106371

Topoisomerase I-driven repair of UV-induced damage in NER-deficient cells. Reviewed International journal

Liton Kumar Saha, Mitsuo Wakasugi, Salma Akter, Rajendra Prasad, Samuel H Wilson, Naoto Shimizu, Hiroyuki Sasanuma, Shar-Yin Naomi Huang, Keli Agama, Yves Pommier, Tsukasa Matsunaga, Kouji Hirota, Shigenori Iwai, Yuka Nakazawa, Tomoo Ogi, Shunichi Takeda

Proceedings of the National Academy of Sciences of the United States of America Vol. 117 ( 25 ) page： 14412 - 14420 2020.6

Language：Japanese Publishing type：Research paper (scientific journal)

Nucleotide excision repair (NER) removes helix-destabilizing adducts including ultraviolet (UV) lesions, cyclobutane pyrimidine dimers (CPDs), and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). In comparison with CPDs, 6-4PPs have greater cytotoxicity and more strongly destabilizing properties of the DNA helix. It is generally believed that NER is the only DNA repair pathway that removes the UV lesions as evidenced by the previous data since no repair of UV lesions was detected in NER-deficient skin fibroblasts. Topoisomerase I (TOP1) constantly creates transient single-strand breaks (SSBs) releasing the torsional stress in genomic duplex DNA. Stalled TOP1-SSB complexes can form near DNA lesions including abasic sites and ribonucleotides embedded in chromosomal DNA. Here we show that base excision repair (BER) increases cellular tolerance to UV independently of NER in cancer cells. UV lesions irreversibly trap stable TOP1-SSB complexes near the UV damage in NER-deficient cells, and the resulting SSBs activate BER. Biochemical experiments show that 6-4PPs efficiently induce stable TOP1-SSB complexes, and the long-patch repair synthesis of BER removes 6-4PPs downstream of the SSB. Furthermore, NER-deficient cancer cell lines remove 6-4PPs within 24 h, but not CPDs, and the removal correlates with TOP1 expression. NER-deficient skin fibroblasts weakly express TOP1 and show no detectable repair of 6-4PPs. Remarkably, the ectopic expression of TOP1 in these fibroblasts led them to completely repair 6-4PPs within 24 h. In conclusion, we reveal a DNA repair pathway initiated by TOP1, which significantly contributes to cellular tolerance to UV-induced lesions particularly in malignant cancer cells overexpressing TOP1.

DOI： 10.1073/pnas.1920165117

InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution

Jun-ichi Takeda, Kentaro Nanatsue, Ryosuke Yamagishi, Mikako Ito, Nobuhiko Haga, Hiromi Hirata, Tomoo Ogi, Kinji Ohno

NAR Genomics and Bioinformatics Vol. 2 ( 2 ) page： lqaa038 2020.6

Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Oxford University Press (OUP)

<title>Abstract</title>
In predicting the pathogenicity of a nonsynonymous single-nucleotide variant (nsSNV), a radical change in amino acid properties is prone to be classified as being pathogenic. However, not all such nsSNVs are associated with human diseases. We generated random forest (RF) models individually for each amino acid substitution to differentiate pathogenic nsSNVs in the Human Gene Mutation Database and common nsSNVs in dbSNP. We named a set of our models ‘Individual Meta RF’ (InMeRF). Ten-fold cross-validation of InMeRF showed that the areas under the curves (AUCs) of receiver operating characteristic (ROC) and precision–recall curves were on average 0.941 and 0.957, respectively. To compare InMeRF with seven other tools, the eight tools were generated using the same training dataset, and were compared using the same three testing datasets. ROC-AUCs of InMeRF were ranked first in the eight tools. We applied InMeRF to 155 pathogenic and 125 common nsSNVs in seven major genes causing congenital myasthenic syndromes, as well as in VANGL1 causing spina bifida, and found that the sensitivity and specificity of InMeRF were 0.942 and 0.848, respectively. We made the InMeRF web service, and also made genome-wide InMeRF scores available online (https://www.med.nagoya-u.ac.jp/neurogenetics/InMeRF/).

DOI： 10.1093/nargab/lqaa038

Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair. Reviewed International journal

Yuka Nakazawa, Yuichiro Hara, Yasuyoshi Oka, Okiru Komine, Diana van den Heuvel, Chaowan Guo, Yasukazu Daigaku, Mayu Isono, Yuxi He, Mayuko Shimada, Kana Kato, Nan Jia, Satoru Hashimoto, Yuko Kotani, Yuka Miyoshi, Miyako Tanaka, Akira Sobue, Norisato Mitsutake, Takayoshi Suganami, Akio Masuda, Kinji Ohno, Shinichiro Nakada, Tomoji Mashimo, Koji Yamanaka, Martijn S Luijsterburg, Tomoo Ogi

Cell Vol. 180 ( 6 ) page： 1228 - + 2020.3

Authorship：Corresponding author Language：Japanese Publishing type：Research paper (scientific journal)

Transcription-coupled nucleotide excision repair (TC-NER) is initiated by the stalling of elongating RNA polymerase II (RNAPIIo) at DNA lesions. The ubiquitination of RNAPIIo in response to DNA damage is an evolutionarily conserved event, but its function in mammals is unknown. Here, we identified a single DNA damage-induced ubiquitination site in RNAPII at RPB1-K1268, which regulates transcription recovery and DNA damage resistance. Mechanistically, RPB1-K1268 ubiquitination stimulates the association of the core-TFIIH complex with stalled RNAPIIo through a transfer mechanism that also involves UVSSA-K414 ubiquitination. We developed a strand-specific ChIP-seq method, which revealed RPB1-K1268 ubiquitination is important for repair and the resolution of transcriptional bottlenecks at DNA lesions. Finally, RPB1-K1268R knockin mice displayed a short life-span, premature aging, and neurodegeneration. Our results reveal RNAPII ubiquitination provides a two-tier protection mechanism by activating TC-NER and, in parallel, the processing of DNA damage-stalled RNAPIIo, which together prevent prolonged transcription arrest and protect against neurodegeneration.

DOI： 10.1016/j.cell.2020.02.010

Severe achondroplasia due to two de novo variants in the transmembrane domain of FGFR3 on the same allele: A case report. Reviewed International journal

Tadashi Nagata, Masaki Matsushita, Kenichi Mishima, Yasunari Kamiya, Kohji Kato, Miho Toyama, Tomoo Ogi, Naoki Ishiguro, Hiroshi Kitoh

Molecular genetics & genomic medicine Vol. 8 ( 3 ) page： e1148 2020.3

Language：Japanese Publishing type：Research paper (scientific journal)

BACKGROUND: Achondroplasia (ACH), the most common form of short-limbed skeletal dysplasia, is caused by gain-of-function mutations in the fibroblast growth factor receptor 3 (FGFR3) gene. More than 97% of patients result from a heterozygous p.G380R mutation in the FGFR3 gene. We present here a child who had two de novo variants in the FGFR3 on the same allele, a common p.G380R mutation and a novel p.S378N variant. METHODS: A 3-year-old Japanese girl born from non-consanguineous healthy parents showed more severe clinical and radiological phenotypes than classic ACH, including severe short-limbed short stature with marked ossification defects in the metaphysis and epiphysis, hydrocephalus and cervicomedullary compression due to foramen magnum stenosis, prolonged pulmonary hypoplasia, and significant delay in the gross motor development. Genomic DNA was extracted from the proband and whole-exome sequencing was performed. The variants were subsequently confirmed by Sanger sequencing. RESULTS: Mutation analysis demonstrated that the proband had p.S378N (c.1133G>A) and p.G380R (c.1138G>A) variants in the FGFR3 gene. Both variants were not detected in her parents and therefore considered de novo. An allele-specific PCR was developed in order to determine whether these mutations were on the same allele (cis) or on different alleles (trans). The c.1138G>A mutation was found in the PCR product generated with the primer for the mutant 1133A, but it was not detected in the product with the wild-type 1133G, confirming that p.S378N and p.G380R variants were located on the same allele (cis). CONCLUSION: This is the second case who had two FGFR3 variants in the transmembrane domain on the same allele. The p.S378N variant may provide an additive effect on the activating receptor with the p.G380R mutation and alter the protein function, which could be responsible for the severe phenotype of the present case.

DOI： 10.1002/mgg3.1148

Reduced stratum corneum acylceramides in autosomal recessive congenital ichthyosis with a NIPAL4 mutation. Reviewed International journal

Yuya Murase, Takuya Takeichi, Akane Kawamoto, Kana Tanahashi, Yusuke Okuno, Hiroyuki Takama, Eri Shimizu, Junko Ishikawa, Tomoo Ogi, Masashi Akiyama

Journal of dermatological science Vol. 97 ( 1 ) page： 50 - 56 2020.1

Language：Japanese Publishing type：Research paper (scientific journal)

BACKGROUND: NIPAL4, encoding the NIPA-like domain containing 4 protein (NIPAL4), is one of the causative genes of autosomal recessive congenital ichthyosis (ARCI). The physiological role of NIPAL4 and the pathogenetic mechanisms of ARCI caused by NIPAL4 mutations remain unclear. OBJECTIVE: To clarify the changes of ceramide components in the lesional stratum corneum (SC) and the gene expression profile in the lesional skin of an ARCI patient with a novel frameshift mutation in NIPAL4. METHODS: We performed ultrastructural and immunohistochemical analyses of the skin. We used RNA sequencing to determine the mRNA expression in the skin of the patient and healthy individuals. We investigated ceramide components using tape stripped SC samples from the patient. RESULTS: mRNA expression profiling in the patient's skin showed significant upregulation of IL-17/TNFα-related genes (IL17C, IL36A, IL36G, S100A7A, S100A9) and psoriasis hallmark genes (VNN3, LCE3D, PLA2G4D), and significant downregulation of lipid-associated genes (GAL, HAO2, FABP7). Ceramide analysis in the patient's SC revealed amounts of CER[NS] with carbon chain-length (C) 32-52 were increased, while amounts of most acylceramide with C66:2 - C72:2 were reduced relatively to those in healthy individuals. After the retinoid treatment, CER[NS] with carbon chains C46-54, CER[EOH] and CER[EOP] increased. CONCLUSION: IL-17C and IL-36 family cytokines might be involved in the pathogenetic process of ARCI with NIPAL4 mutations. Reduced amounts of the acylceramides in the SC are associated with the skin phenotype due to NIPAL4 mutations. Efficacy of the oral retinoid treatment might be due to restored amounts of CER[EOH] and CER[EOP] in the SC.

DOI： 10.1016/j.jdermsci.2019.12.001