ロングリードシーケンサーを用いた神経筋疾患の原因探索と病態解明

2022 Fiscal Year Annual Research Report

• Project/Area Number: 20K07907
• Research Institution: Yokohama City University
• Principal Investigator: 宮武 聡子 横浜市立大学, 附属病院, 准教授 (50637890)
• Project Period (FY): 2020-04-01 – 2023-03-31
• Keywords: ロングリードシーケンサー / 神経筋疾患 / 脊髄小脳変性症 / リピート伸長病 / CANVAS / RFC1 / ナノポアシーケンス / ターゲットロングリードシーケンス法

Outline of Annual Research Achievements

本研究は、ショートリード次世代シーケンサーの“次の世代”と位置付けられるロングリードシーケンサーを用いて、ショートリードシーケンサーの弱点を補完する全ゲノム解析系を構築し、全エクソーム解析で未解決の神経筋疾患症例の遺伝学的原因を同定することを目的とした。
研究全体の成果として、①脊髄小脳変性症の１つの病型である、小脳性運動失調、ニューロパチー、前庭機能障害を主徴とする小脳性運動失調・ニューロパチー・前庭反射消失症候群(Cerebellar ataxia, neuropathy, vestibular areflexia syndrome; CANVAS）の原因変異である、RFC1遺伝子のイントロン領域に存在する両アレル性リピート異常伸長の全配列(約2-8kb)を決定し、リピートユニットの組み合わせの多様性があることを発見、さらに配列パターンの組み合わせと臨床症状の関連について観察、報告したこと[Miyatake et al., Brain. Apr 29;145(3):1139-1150 (2022)]、②リピート伸長病の原因となる病的リピート伸長を、網羅的に一括スクリーニングできる迅速ロングリードシーケンス系を確立したこと[Miyatake et al., npj Genom. Med. 7, 62 (2022)]、が挙げられる。
前者は、長いリピート伸長の完全配列決定はこれまでほとんど行われてこなかったところ、ロングリードシーケンサーを用いて、リピート配列の全長を解読できたことが既存のゲノム手法の限界を打ち破る新たな知見であり、後者は、ナノポアシーケンサーのターゲットロングリードシーケンス法を利用したもので、従来のPCRを主体としたゲノム手法ではスクリーニングが困難であったリピート伸長病の簡便・迅速・正確な診断が可能となったことが有意義であった。

Research Products

• [Journal Article] Molecular diagnosis of 405 individuals with autism spectrum disorder (2023)
  • Author(s): Miyake N, Tsurusaki Y, Fukai R, Kushima I, Okamoto N, Ohashi K, Nakamura K, Miyatake S, Matsumoto N.
  • Journal Title: Eur J Hum Genet Volume: 27-Mar Pages: -
  • DOI: 10.1038/s41431-023-01335-7
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Publisher Correction: A novel NONO variant that causes developmental delay and cardiac phenotypes (2023)
  • Author(s): Itai T, Sugie A, Nitta Y, Maki R, Suzuki T, Shinkai Y, Watanabe Y, Nakano Y, Ichikawa K, Okamoto N, Utsuno Y, Koshimizu E, Fujita A, Hamanaka K, Uchiyama Y, Tsuchida N, Miyake N, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N.
  • Journal Title: Sci Rep Volume: Mar 9;13(1) Pages: 3954
  • DOI: 10.1038/s41598-023-30968-3
  • Peer Reviewed / Open Access
• [Journal Article] An integrated genetic analysis of epileptogenic brain malformed lesions (2023)
  • Author(s): Fujita A, Kato M, Sugano H, Iimura Y, Suzuki H, Tohyama J, Fukuda M, Miyatake S, Mizuguchi T, Nakashima M, Saitsu H, Miyake N, Kakita A, Matsumoto N.
  • Journal Title: Acta Neuropathol Commun Volume: Mar 2;11(1) Pages: 33
  • DOI: 10.1186/s40478-023-01532-x
  • Peer Reviewed / Open Access
• [Journal Article] A case of early-infantile onset, rapidly progressive leukoencephalopathy with calcifications and cysts caused by biallelic SNORD118 variants (2023)
  • Author(s): Kodama K, Aoyama H, Murakami Y, Takanashi JI, Koshimizu E, Miyatake S, Iwama K, Mizuguchi T, Matsumoto N, Omata T.
  • Journal Title: Radiol Case Rep Volume: Jan 12;18(3) Pages: 1217-1220
  • DOI: 10.1016/j.radcr.2022.11.033
  • Peer Reviewed / Open Access
• [Journal Article] A novel NONO variant that causes developmental delay and cardiac phenotypes (2023)
  • Author(s): Itai T, Sugie A, Nitta Y, Maki R, Suzuki T, Shinkai Y, Watanabe Y, Nakano Y, Ichikawa K, Okamoto N, Utsuno Y, Koshimizu E, Fujita A, Hamanaka K, Uchiyama Y, Tsuchida N, Miyake N, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N.
  • Journal Title: Sci Rep Volume: Jan 18;13(1) Pages: 975
  • DOI: 10.1038/s41598-023-27770-6
  • Peer Reviewed / Open Access
• [Journal Article] Brain monoamine vesicular transport disease caused by homozygous SLC18A2 variants: A study in 42 affected individuals (2023)
  • Author(s): Saida K, Maroofian R, Sengoku T, Mitani T, Pagnamenta AT, Marafi D, Miyatake S, Lupski JR, Houlden H, Matsumoto N.
  • Journal Title: Genet Med Volume: Jan;25(1) Pages: 90-102
  • DOI: 10.1016/j.gim.2022.09.010
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genetic and clinical landscape of childhood cerebellar hypoplasia and atrophy (2022)
  • Author(s): Sakamoto M, Iwama K, Sasaki M, Ishiyama A, Komaki H, Saito T, Miyatake S, Mizuguchi T, Miyake N, Matsumoto N.
  • Journal Title: Genet Med Volume: Dec;24(12) Pages: 2453-2463
  • DOI: 10.1016/j.gim.2022.08.007
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A case of generalized dystonia DYT28 with a novel de novo mutation in the KMT2B gene (2022)
  • Author(s): Hara K, Ouchi H, Hamanaka K, Miyatake S, Matsumoto N.
  • Journal Title: Rinsho Shinkeigaku Volume: Nov 26;62(11) Pages: 856-859
  • DOI: 10.5692/clinicalneurol.cn-001773
  • Peer Reviewed
• [Journal Article] Distal 2q duplication in a patient with intellectual disability (2022)
  • Author(s): Suzuki T, Osaka H, Miyake N, Fujita A, Uchiyama Y, Seyama R, Koshimizu E, Miyatake S, Mizuguchi T, Takeda S, Matsumoto N.
  • Journal Title: Hum Genome Var Volume: Nov 10;9(1) Pages: 39
  • DOI: 10.1038/s41439-022-00215-8
  • Peer Reviewed / Open Access
• [Journal Article] A case of ALG11-congenital disorders of glycosylation diagnosed by post-mortem whole exome sequencing (2022)
  • Author(s): Arai Y, Okanishi T, Kanai S, Okazaki T, Koshimizu E, Miyatake S, Maeoka Y, Fujimoto A, Matsumoto N, Maegaki Y.
  • Journal Title: Brain Dev Volume: Nov;44(10) Pages: 732-736
  • DOI: 10.1016/j.braindev.2022.07.005
  • Peer Reviewed
• [Journal Article] Monogenic causes of pigmentary mosaicism (2022)
  • Author(s): Saida K, Chong PF, Yamaguchi A, Saito N, Ikehara H, Koshimizu E, Miyata R, Ishiko A, Nakamura K, Ohnishi H, Fujioka K, Sakakibara T, Asada H, Ogawa K, Kudo K, Ohashi E, Kawai M, Abe Y, Tsuchida N, Uchiyama Y, Hamanaka K, Fujita A, Mizuguchi T, Miyatake S, Miyake N, Kato M, Kira R, Matsumoto N.
  • Journal Title: Hum Genet Volume: Nov;141(11) Pages: 1771-1784
  • DOI: 10.1007/s00439-022-02437-w
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing (2022)
  • Author(s): Miyatake S, Koshimizu E, Fujita A, Doi H, Okubo M, Wada T, Hamanaka K, Ueda N, Kishida H, Minase G, Matsuno A, Kodaira M, Ogata K, Kato R, Sugiyama A, Sasaki A, Miyama T, Satoh M, Uchiyama Y, Tsuchida N, Hamanoue H, Misawa K, Hayasaka K, Sekijima Y, Adachi H, Yoshida K, Tanaka F, Mizuguchi T, Matsumoto N.
  • Journal Title: NPJ Genom Med Volume: Oct 26;7(1) Pages: 62
  • DOI: 10.1038/s41525-022-00331-y
  • Peer Reviewed / Open Access
• [Journal Article] Pathogenic variants detected by RNA sequencing in Cornelia de Lange syndrome (2022)
  • Author(s): Seyama R, Uchiyama Y, Ceroni JRM, Kim VEH, Furquim I, Honjo RS, Castro MAA, Pires LVL, Aoi H, Iwama K, Hamanaka K, Fujita A, Tsuchida N, Koshimizu E, Misawa K, Miyatake S, Mizuguchi T, Makino S, Itakura A, Bertola DR, Kim CA, Matsumoto N.
  • Journal Title: Genomics Volume: Sep;114(5) Pages: 110468
  • DOI: 10.1016/j.ygeno.2022.110468
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Patients with biallelic GGC repeat expansions in NOTCH2NLC exhibiting a typical neuronal intranuclear inclusion disease phenotype (2022)
  • Author(s): Kameyama S, Mizuguchi T, Doi H, Koyano S, Okubo M, Tada M, Shimizu H, Fukuda H, Tsuchida N, Uchiyama Y, Koshimizu E, Hamanaka K, Fujita A, Misawa K, Miyatake S, Kanai K, Tanaka F, Matsumoto N.
  • Journal Title: Genomics Volume: Sep;114(5) Pages: 110469
  • DOI: 10.1016/j.ygeno.2022.110469
  • Peer Reviewed / Open Access
• [Journal Article] A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode (2022)
  • Author(s): Marafi D, Kozar N, Duan R, Bradley S, Yokochi K, Kato M, Arai H, Miyatake S, Matsumoto N, Wagner M.
  • Journal Title: Am J Hum Genet Volume: Sep 1;109(9) Pages: 1713-1723
  • DOI: 10.1016/j.ajhg.2022.07.006
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] De novo heterozygous variants in KIF5B cause kyphomelic dysplasia (2022)
  • Author(s): Itai T, Wang Z, Nishimura G, Ohashi H, Guo L, Wakano Y, Sugiura T, Hayakawa H, Okada M, Saisu T, Kitta A, Doi H, Kurosawa K, Hotta Y, Hosono K, Sato M, Shimizu K, Takikawa K, Watanabe S, Ikeda N, Suzuki M, Fujita A, Uchiyama Y, Tsuchida N, Miyatake S, Miyake N, Matsumoto N, Ikegawa S.
  • Journal Title: Clin Genet Volume: Jul;102(1) Pages: 3-11
  • DOI: 10.1111/cge.14133
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Actin-binding protein filamin-A drives tau aggregation and contributes to progressive supranuclear palsy pathology (2022)
  • Author(s): Tsujikawa K, Hamanaka K, Riku Y, Miyatake S, Japanese Longitudinal Biomarker Study in PSP and CBD (JALPAC) Consortium; Sobue G, Matsumoto N, Sahashi K, Katsuno M.
  • Journal Title: Sci Adv Volume: May 27;8(21) Pages: eabm5029
  • DOI: 10.1126/sciadv.abm5029
  • Peer Reviewed / Open Access
• [Journal Article] Repeat conformation heterogeneity in cerebellar ataxia, neuropathy, vestibular areflexia syndrome (2022)
  • Author(s): Miyatake S, Yoshida K, Koshimizu E, Doi H, Tanaka F, Mizuguchi T, Matsumoto N.
  • Journal Title: Brain Volume: Apr 29;145(3) Pages: 1139-1150
  • DOI: 10.1093/brain/awab363
  • Peer Reviewed
• [Journal Article] Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants (2022)
  • Author(s): Hamanaka K, Miyake N, Mizuguchi T, Miyatake S, Uchiyama Y, Tsuchida N, Sekiguchi F, Mitsuhashi S, Tsurusaki Y, Nakashima M, Saitsu H, Yamada K, Sakamoto M, Fukuda H, Ohori S, Saida K, Itai T, Azuma Y, Koshimizu E, Fujita A, Erturk B, Hiraki Y, Ch'ng GS, Kato M, Okamoto N, Takata A, Matsumoto N.
  • Journal Title: Genome Med Volume: Apr 26;14(1) Pages: 40
  • DOI: 10.1186/s13073-022-01042-w
  • Peer Reviewed / Open Access
• [Journal Article] Long-term course of early onset developmental and epileptic encephalopathy associated with 2q24.3 microduplication (2022)
  • Author(s): Masuda T, Osaka H, Tsuchida N, Miyatake S, Nishimura K, Takenouchi T, Takahashi T, Matsumoto N, Yamagata T.
  • Journal Title: Epilepsy Behav Rep Volume: Apr 25;19 Pages: 100547
  • DOI: 10.1016/j.ebr.2022.100547
  • Peer Reviewed / Open Access
• [Presentation] CANVASはrepeat conformation heterogeneityを有する (2022)
  • Author(s): 宮武聡子
  • Organizer: 日本人類遺伝学会第67回大会
• [Presentation] ホットトピックス06: 小児神経疾患の分子機構最前線～成人との懸け橋 (2022)
  • Author(s): 宮武聡子
  • Organizer: 第63回日本神経学会学術大会
  • Invited
• [Presentation] 教育コース08: 神経内科医が知っておきたい小児神経 (2022)
  • Author(s): 宮武聡子
  • Organizer: 第63回日本神経学会学術大会
  • Invited
• [Presentation] Cerebellar ataxia, neuropathy, vestibular areflexia syndrome has repeat conformation heterogeneity (2022)
  • Author(s): 宮武聡子
  • Organizer: 第63回日本神経学会学術大会