Article
Genetics & Heredity
Taku Miyagawa, Susumu Tanaka, Mihoko Shimada, Noriaki Sakai, Kotomi Tanida, Nozomu Kotorii, Tatayu Kotorii, Yu Ariyoshi, Yuji Hashizume, Kimihiro Ogi, Hiroshi Hiejima, Takashi Kanbayashi, Aya Imanishi, Azusa Ikegami, Yuichi Kamei, Akiko Hida, Yamato Wada, Masayuki Miyamoto, Masanori Takami, Hideaki Kondo, Yoshiyuki Tamura, Yukari Taniyama, Naoto Omata, Tomoyuki Mizuno, Shunpei Moriya, Hirokazu Furuya, Mitsuhiro Kato, Kayoko Kato, Jun Ishigooka, Kazuhito Tsuruta, Shigeru Chiba, Naoto Yamada, Masako Okawa, Koichi Hirata, Kenji Kuroda, Kazuhiko Kume, Naohisa Uchimura, Masaaki Kitada, Tohru Kodama, Yuichi Inoue, Seiji Nishino, Kazuo Mishima, Katsushi Tokunaga, Makoto Honda
Summary: Idiopathic hypersomnia is a rare sleep disorder characterized by excessive daytime sleepiness. A study in a Japanese population identified a rare variant associated with this disorder, which results in decreased signaling through orexin receptors, similar to narcolepsy type 1.
NPJ GENOMIC MEDICINE
(2022)
Article
Oncology
Marco Dicanio, Matteo Giaccherini, Alyssa Clay-Gilmour, Angelica Macauda, Juan Sainz, Mitchell J. Machiela, Malwina Rybicka-Ramos, Aaron D. Norman, Agata Tyczynska, Stephen J. Chanock, Torben Barington, Shaji K. Kumar, Parveen Bhatti, Wendy Cozen, Elizabeth E. Brown, Anna Suska, Eva K. Haastrup, Robert Z. Orlowski, Marek Dudzinski, Ramon Garcia-Sanz, Marcin Kruszewski, Joaquin Martinez-Lopez, Katia Beider, Elzbieta Iskierka-Jazdzewska, Matteo Pelosini, Sonja Berndt, Malgorzata Razny, Krzysztof Jamroziak, S. Vincent Rajkumar, Artur Jurczyszyn, Annette Juul Vangsted, Pilar Garrido Collado, Ulla Vogel, Jonathan N. Hofmann, Mario Petrini, Aleksandra Butrym, Susan L. Slager, Elad Ziv, Edyta Subocz, Graham G. Giles, Niels Frost Andersen, Grzegorz Mazur, Marzena Watek, Fabienne Lesueur, Michelle A. T. Hildebrandt, Daria Zawirska, Lene Hyldahl Ebbesen, Herlander Marques, Federica Gemignani, Charles Dumontet, Judit Varkonyi, Gabriele Buda, Arnon Nagler, Agnieszka Druzd-Sitek, Xifeng Wu, Katalin Kadar, Nicola J. Camp, Norbert Grzasko, Rosalie G. Waller, Celine Vachon, Federico Canzian, Daniele Campa
Summary: The aim of this study was to identify novel pleiotropic variants involved in multiple myeloma (MM) risk. Through analysis of 28,684 single nucleotide polymorphisms (SNPs), DNAJB4-rs34517439-A was found to be associated with an increased risk of developing MM.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Oncology
Kelsie Raspin, Liesel M. FitzGerald, James R. Marthick, Matt A. Field, Roslyn C. Malley, Annette Banks, Shaun Donovan, Russell J. Thomson, Georgea R. Foley, Janet L. Stanford, Joanne L. Dickinson
Summary: A rare variant (rs78589034) was identified as significantly associated with increased prostate cancer risk, potentially affecting EZH2 function in prostate tissue. This provides evidence for the variant as a potential therapeutic target.
INTERNATIONAL JOURNAL OF CANCER
(2021)
Article
Multidisciplinary Sciences
You Li, Zhiqiang Li, Ruiling Chen, Min Lian, Hanxiao Wang, Yiran Wei, Zhengrui You, Jun Zhang, Bo Li, Yikang Li, Bingyuan Huang, Yong Chen, Qiaoyan Liu, Zhuwan Lyu, Xueying Liang, Qi Miao, Xiao Xiao, Qixia Wang, Jingyuan Fang, YongYong Shi, Xiangdong Liu, Michael F. Seldin, M. Eric Gershwin, Ruqi Tang, Xiong Ma
Summary: Genome-wide association studies have identified a genetic locus, 19p13.3, associated with primary biliary cholangitis (PBC). Through functional annotations and experimental validations, the study suggests that a specific variant, rs2238574, may regulate the expression of ARID3A and affect the severity of PBC.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Taku Miyagawa, Mihoko Shimada, Yoshiko Honda, Tohru Kodama, Katsushi Tokunaga, Makoto Honda
Summary: Excessive daytime sleepiness is associated with genetic variants in OX2R, which can affect daytime sleepiness in the general population.
JOURNAL OF HUMAN GENETICS
(2022)
Article
Immunology
Lener Santos da Silva, Jose do Espirito Santo Junior, Tirza Gabrielle Ramos de Mesquita, Veronica Alice Marinho Santos, Josue Lacerda de Souza, Felipe Jules de Araujo, Claudio Marcello da Silveira Junior, Cilana Chagas da Silva, Krys Layane Guimaraes Duarte Queiroz, Hector David Graterol Sequera, Marcus Vinitius de Farias Guerra, Mara Lucia Gomes de Souza, Rajendranath Ramasawmy
Summary: The study found an association between the IL-23R variant rs11805303 and the development of cutaneous leishmaniasis, indicating that the IL-17/IL-23 axis may play an important role in the pathogenesis of the disease.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biology
Yaqiong Jin, Jin Shi, Huanmin Wang, Jie Lu, Chenghao Chen, Yongbo Yu, Yaru Wang, Yeran Yang, Dong Ren, Qi Zeng, Xin Ni, Yongli Guo
Summary: The study found that the DDX1 gene polymorphism rs72780850 is associated with an increased risk of NB, especially in aggressive cases. This association may be due to the regulation of DDX1 gene expression affecting tumor risk. Additionally, the molecular mechanism of the rs72780850 polymorphism leading to increased NB risk may be related to the binding affinity of the MAX transcription factor.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Kugui Yoshida-Tanaka, Mihoko Shimada, Yoshiko Honda, Akihiro Fujimoto, Katsushi Tokunaga, Makoto Honda, Taku Miyagawa
Summary: This study found that HLA-DQB1 is associated with the pathogenesis of Narcolepsy type 1 (NT1) through DNA methylation and gene expression changes in CD4 (+) and CD8 (+) T cells.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, General & Internal
Lin-Lin Zhang, Xiao-Xiao Wu, Xu-Fan Wang, Dong-Sheng Di, Qian Huang, Rui-Shan Liu, Zong-Wen Shuai, Dong-Qing Ye, Rui-Xue Leng
Summary: The study investigated the association between SNPs in the miR-146a gene and susceptibility of RA, finding that the SNP rs2431697 in miR-146a gene is associated with RA risk. The effect size of this SNP was larger in Asian population compared to European population. Plasma TNF-alpha levels in healthy controls were inversely associated with the risk allele T of the SNP rs2431697.
ANNALS OF MEDICINE
(2021)
Article
Dentistry, Oral Surgery & Medicine
M. -J Li, P. Kumari, Y. -S Lin, M. -L Yao, B. -H Zhang, B. Yin, S. -J Duan, R. A. Cornell, M. L. Marazita, B. Shi, Z. - Jia
Summary: Targeted sequencing of 159 Han Chinese patients with NSCL/P identified an association between rs12403599 and all phenotypes of NSCL/P, specifically NSCLO and MCL. Further analysis revealed that the association between rs2235371 and NSCL/P was dependent on the presence of rs12403599. Functional assays demonstrated that rs12403599 was associated with increased promoter activity and expression of IRF6.
JOURNAL OF DENTAL RESEARCH
(2023)
Article
Medicine, Research & Experimental
Fabienne Gally, Sarah K. Sasse, Jonathan S. Kurche, Margaret A. Gruca, Jonathan H. Cardwell, Tsukasa Okamoto, Hong W. Chu, Xiaomeng Hou, Olivier B. Poirion, Justin Buchanan, Sebastian Preissl, Bing Ren, Sean P. Colgan, Robin D. Dowell, Ivana Yang, David A. Schwartz, Anthony N. Gerber
Summary: The G/T transversion rs35705950, located 3 kb upstream of the MUC5B start site, is identified as a key risk factor for idiopathic pulmonary fibrosis. Through analysis of accessible chromatin and nuclease sensitivity data, it is shown that this region affects the expression of MUC5B and is subject to epigenetic remodeling in IPF patients' lung tissue.
Article
Biochemistry & Molecular Biology
Bo Gong, Lulin Huang, Yongquan He, Wen Xie, Yi Yin, Yi Shi, Jialing Xiao, Ling Zhong, Yi Zhang, Zhilin Jiang, Fang Hao, Yu Zhou, Huan Li, Li Jiang, Xingxiang Yang, Xiangrong Song, Yan Kang, Lin Tuo, Yi Huang, Ping Shuai, Yuping Liu, Fang Zheng, Zhenglin Yang
Summary: A genetic variant in the IL-6 gene has been identified to protect against critical conditions with COVID-19 by decreasing IL-6 expression in the serum.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Siyuan Niu, Ke Shi, Xinying Yue, Miaoxin Pan, Lina Song, Linglong Gu, Yuqian Tan, Xiaoping Miao, Jianbo Tian, Jiang Chang
Summary: In this study, a two-stage case-control study and a series of biochemical experiments were conducted to explore the function of CYP26B1 and its common variants in the tumorigenesis of esophageal squamous cell carcinoma (ESCC). It was found that a common variant in CYP26B1 was significantly associated with ESCC risk and this variant affected the metabolism of retinoic acid in cells. Moreover, overexpression or knock-out of CYP26B1 affected cell proliferation rates both in vitro and in vivo, highlighting the role of CYP26B1 in ESCC risk.
MOLECULAR CARCINOGENESIS
(2023)
Article
Oncology
Matteo Giaccherini, Riccardo Farinella, Manuel Gentiluomo, Beatrice Mohelnikova-Duchonova, Emanuele Federico Kauffmann, Matteo Palmeri, Faik Uzunoglu, Pavel Soucek, Dalius Petrauskas, Giulia Martina Cavestro, Romanas Zykus, Silvia Carrara, Raffaele Pezzilli, Marta Puzzono, Andrea Szentesi, John Neoptolemos, Livia Archibugi, Orazio Palmieri, Anna Caterina Milanetto, Gabriele Capurso, Casper H. J. van Eijck, Hannah Stocker, Rita T. Lawlor, Pavel Vodicka, Martin Lovecek, Jakob R. Izbicki, Francesco Perri, Rita Kupcinskaite-Noreikiene, Mara Gotz, Juozas Kupcinskas, Tamas Hussein, Peter Hegyi, Olivier R. Busch, Thilo Hackert, Andrea Mambrini, Hermann Brenner, Maurizio Lucchesi, Daniela Basso, Francesca Tavano, Ben Schottker, Giuseppe Vanella, Stefania Bunduc, Agota Petranyi, Stefano Landi, Luca Morelli, Federico Canzian, Daniele Campa
Summary: This study analyzed the common genetic variability of PDAC familial genes and found that the CDKN2B-AS1/ANRIL gene located in the 9p21.3 region plays an important role in the development of PDAC. The results strongly support the association between genetic variability in the 9p21.3 region and PDAC pathogenesis.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Anna K. Miller, Gloria Tavera, Ricardo L. Dominguez, M. Constanza Camargo, Tim Waterboer, Keith T. Wilson, Scott M. Williams, Douglas R. Morgan
Summary: The primary cause of gastric cancer is chronic infection with Helicobacter pylori (H. pylori), particularly the high-risk genotype cagA, and risk modification by human genetic variants. Variants such as rs2302615 in ornithine decarboxylase (ODC1) are associated with gastric cancer risk.
Article
Biochemical Research Methods
Shinichi Morishita, Kazuki Ichikawa, Eugene W. Myers
Summary: This study presents an efficient algorithm that utilizes the characteristics of repetitive sequences to address the issue of high error rates in long-read sequencing technologies. The algorithm first estimates regions that may contain tandem repeats, and then assembles the k-mers of these regions into a consensus repeat unit by greedily traversing a de Bruijn graph. Experimental results demonstrate that the proposed algorithm outperforms the widely used Tandem Repeats Finder in terms of sensitivity.
Article
Genetics & Heredity
Hiroya Naruse, Hiroyuki Ishiura, Jun Mitsui, Yuji Takahashi, Takashi Matsukawa, Jun Yoshimura, Koichiro Doi, Shinichi Morishita, Jun Goto, Tatsushi Toda, Shoji Tsuji
Summary: The study discovered that NEK1 LoF variants are associated with an increased risk of SALS in the Japanese population.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Genetics & Heredity
Yu Teranishi, Satoru Miyawaki, Hiroki Hongo, Shogo Dofuku, Atsushi Okano, Shunsaku Takayanagi, Takahiro Ota, Jun Yoshimura, Wei Qu, Jun Mitsui, Hirofumi Nakatomi, Shinichi Morishita, Shoji Tsuji, Nobuhito Saito
Summary: Improved diagnostic rate of mosaic NF2 was achieved by targeted deep sequencing of DNA from multiple tissues. Patients with mosaic NF2 showed significant differences in phenotype compared to those with NF2 germline variant, particularly in tumor growth rate and hearing outcome. Schwannoma behavior correlated with the extent of VAF in normal tissues carrying NF2 variant, unlike meningioma.
JOURNAL OF MEDICAL GENETICS
(2021)
Article
Genetics & Heredity
Hiroya Naruse, Hiroyuki Ishiura, Jun Mitsui, Yuji Takahashi, Takashi Matsukawa, Kaori Sakuishi, Kiyotaka Nakamagoe, Zenshi Miyake, Akira Tamaoka, Jun Goto, Jun Yoshimura, Koichiro Doi, Shinichi Morishita, Tatsushi Toda, Shoji Tsuji
Summary: The study revealed that LoF variants in the KIF5A gene accounted for 2.1% of all FALS families, while the frequency of missense variants in SALS patients and controls did not show a significant difference. FALS patients carrying pathogenic KIF5A variants exhibited ALS characterized by predominant involvement of upper motor neurons.
Article
Biochemical Research Methods
Bansho Masutani, Shin-ichi Arimura, Shinichi Morishita
Summary: Plant mitochondrial genomes exhibit large structural diversity, making it challenging to accurately assemble them using existing long-read sequencing technologies. This study introduces a novel method that leverages traditional sequence analysis models, hidden Markov model and partial order alignment, to identify strain-specific structures in plant mitochondrial genomes. Applying this method to PacBio Sequel data from Arabidopsis thaliana revealed putative but previously unknown structures, indicating the presence of recurrent and strain-specific structures in plant mitochondrial genomes.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Yuta Suzuki, Eugene W. Myers, Shinichi Morishita
Article
Biochemistry & Molecular Biology
Kyoko Ishino, Hidetoshi Hasuwa, Jun Yoshimura, Yuka W. Iwasaki, Hidenori Nishihara, Naomi M. Seki, Takamasa Hirano, Marie Tsuchiya, Hinako Ishizaki, Harumi Masuda, Tae Kuramoto, Kuniaki Saito, Yasubumi Sakakibara, Atsushi Toyoda, Takehiko Itoh, Mikiko C. Siomi, Shinichi Morishita, Haruhiko Siomi
Summary: In animal gonads, transposable elements are actively repressed through the PIWI-interacting RNA (piRNA) pathway to maintain genome integrity. Mice have abundant piRNA expression in male germ cells, while depletion of Piwi genes leads to male-specific sterility. Different from mice, most mammals have four PIWI genes, some of which are expressed in the ovary. PIWI complexes from golden hamster oocytes showed dynamic changes in the size and association of piRNAs during maturation, suggesting a complex and dynamic nature of piRNA biogenesis in hamster oocytes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Ryohei Nakamura, Yuichi Motai, Masahiko Kumagai, Candice L. Wike, Haruyo Nishiyama, Yoichiro Nakatani, Neva C. Durand, Kaori Kondo, Takashi Kondo, Tatsuya Tsukahara, Atsuko Shimada, Bradley R. Cairns, Erez Lieberman Aiden, Shinichi Morishita, Hiroyuki Takeda
Summary: Chromatin looping, an essential aspect of genome regulation, undergoes significant changes during early embryonic development, including the formation of loops and increased contact domain size during gastrulation. Loop formation occurs long after global transcriptional activation, suggesting they are not essential for zygotic transcription. The conservation of loop positions in synteny blocks between medaka and zebrafish indicates that 3D genome architecture has been preserved over 110-200 million years of evolution.
Review
Genetics & Heredity
Yuta Suzuki, Shinichi Morishita
Summary: The complete sequencing of human centromeres has long been difficult due to the presence of highly repetitive HOR units, which hamper sequence assembly. However, the recent availability of longer reads is expected to enable better observation of individual HOR occurrences.
Article
Biotechnology & Applied Microbiology
Yusuke Takahashi, Massa Shoura, Andrew Fire, Shinichi Morishita
Summary: The paper presents an analysis of high IPD loci in two genomes, E. coli and C. elegans. By comparing native genomic DNA with whole-genome amplified material, the study distinguishes the effects of DNA modification on DNA polymerization speed. Adenine modification sites in E. coli showed expected IPD shifts, while C. elegans did not exhibit such differences, suggesting DNA modification may not be the main driver for high IPD segments in this organism.
Article
Peripheral Vascular Disease
Hiroki Hongo, Satoru Miyawaki, Yu Teranishi, Jun Mitsui, Hiroto Katoh, Daisuke Komura, Kinya Tsubota, Takashi Matsukawa, Masakatsu Watanabe, Masakazu Kurita, Jun Yoshimura, Shogo Dofuku, Kenta Ohara, Daiichiro Ishigami, Atsushi Okano, Motoi Kato, Fumihiko Hakuno, Ayaka Takahashi, Akiko Kunita, Hiroyuki Ishiura, Masahiro Shin, Hirofumi Nakatomi, Toshitaka Nagao, Hiroshi Goto, Shin-Ichiro Takahashi, Tetsuo Ushiku, Shumpei Ishikawa, Mutsumi Okazaki, Shinichi Morishita, Shoji Tsuji, Nobuhito Saito
Summary: Our study identified a somatic missense mutation in GJA4 gene that may be a driver mutation for OCVM. Our findings suggested that hyperactive hemichannel plays a role in the development of this vascular phenotype.
Article
Medicine, General & Internal
Naoki Takegami, Akihiko Mitsutake, Tatsuo Mano, Yukako Shintani-Domoto, Atsushi Unuma, Nanaka Yamaguchi-Takegami, Hiroyuki Ishiura, Kaori Sakuishi, Masahiko Ando, Haruo Yamauchi, Minoru Ono, Shinichi Morishita, Jun Mitsui, Jun Shimizu, Shoji Tsuji, Tatsushi Toda
Summary: Desminopathy is a cardiac and skeletal myopathy caused by disease-causing variants in the DES gene. In this report, we describe a 28-year-old Japanese patient who was initially diagnosed with sporadic hypertrophic cardiomyopathy with atrioventricular block and developed weakness in the soft palate and extremities. Genetic testing confirmed a de novo mutation of the DES gene. The challenging molecular diagnosis of desminopathy makes the pathological findings of endomyocardial proteinase K-resistant desmin aggregates helpful in clinical practice.
Article
Multidisciplinary Sciences
Kazuki Ichikawa, Riki Kawahara, Takeshi Asano, Shinichi Morishita
Summary: This study uses a high-precision algorithm to determine complex TR structures from long accurate sequences, revealing the abundance and diversity of TRs. It finds that complex TRs are more common than single-unit TRs, and that they tend to consist of <10-bp units. Several known disease-associated TRs are found in loci with extended TRs, making them potential candidates for disease association.
NATURE COMMUNICATIONS
(2023)
Article
Neurosciences
Yu Teranishi, Satoru Miyawaki, Masahiro Nakatochi, Atsushi Okano, Kenta Ohara, Hiroki Hongo, Daiichiro Ishigami, Yu Sakai, Daisuke Shimada, Shunsaku Takayanagi, Masako Ikemura, Daisuke Komura, Hiroto Katoh, Jun Mitsui, Shinichi Morishita, Tetsuo Ushiku, Shumpei Ishikawa, Hirofumi Nakatomi, Nobuhito Saito
Summary: This study investigated the characteristics of meningiomas in NF2 patients and found that these tumors showed less aggressive behavior but had a marked immune response compared to sporadic NF2-altered meningiomas, with a higher immune cell infiltration, particularly of macrophages.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2023)
Article
Endocrinology & Metabolism
Jun Hosoe, Fuyuki Miya, Hiroko Kadowaki, Toyofumi Fujiwara, Ken Suzuki, Takashi Kato, Hironori Waki, Takayoshi Sasako, Katsuya Aizu, Natsumi Yamamura, Fusako Sasaki, Makoto Kurano, Kazuo Hara, Masaki Tanaka, Hiroyuki Ishiura, Shoji Tsuji, Kenjiro Honda, Jun Yoshimura, Shinichi Morishita, Fumiko Matsuzawa, Sei-Ichi Aikawa, Keith A. Boroevich, Masaomi Nangaku, Yukinori Okada, Tatsuhiko Tsunoda, Nobuhiro Shojima, Toshimasa Yamauchi, Takashi Kadowaki
DIABETES RESEARCH AND CLINICAL PRACTICE
(2020)