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June 09, 2020; 94 (23) Article

Homozygous nonsense variant in LRIF1 associated with facioscapulohumeral muscular dystrophy

Kohei Hamanaka, Darina Šikrová, Satomi Mitsuhashi, Hiroki Masuda, Yukari Sekiguchi, Atsuhiko Sugiyama, Kazumoto Shibuya, Richard J.L.F. Lemmers, Remko Goossens, Megumu Ogawa, Koji Nagao, Chikashi Obuse, Satoru Noguchi, Yukiko K. Hayashi, Satoshi Kuwabara, Judit Balog, View ORCID ProfileIchizo Nishino, View ORCID ProfileSilvère M. van der Maarel
First published May 28, 2020, DOI: https://doi.org/10.1212/WNL.0000000000009617
Kohei Hamanaka
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Darina Šikrová
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Satomi Mitsuhashi
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Hiroki Masuda
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Yukari Sekiguchi
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Atsuhiko Sugiyama
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Kazumoto Shibuya
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Richard J.L.F. Lemmers
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Remko Goossens
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Megumu Ogawa
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Koji Nagao
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Chikashi Obuse
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Satoru Noguchi
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Yukiko K. Hayashi
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Satoshi Kuwabara
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Judit Balog
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Ichizo Nishino
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Silvère M. van der Maarel
From the Department of Neuromuscular Research (K.H., S.M., M.O., S.N., I.N.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neurology (K.H.), Graduate School of Medicine, Kyoto University, Japan; Department of Human Genetics (D.Š., R.J.L.F.L., R.G., J.B., S.M.M.), Leiden University Medical Center, the Netherlands; Department of Clinical Development (S.M., I.N.), Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo; Department of Neurology (H.M., Y.S., A.S., K.S., S.K.), Graduate School of Medicine, Chiba University; Department of Biological Sciences (K.N., C.O.), Graduate School of Science, Osaka University; and Department of Pathophysiology (Y.K.H.), Tokyo Medical University, Tokyo, Japan.
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Homozygous nonsense variant in LRIF1 associated with facioscapulohumeral muscular dystrophy
Kohei Hamanaka, Darina Šikrová, Satomi Mitsuhashi, Hiroki Masuda, Yukari Sekiguchi, Atsuhiko Sugiyama, Kazumoto Shibuya, Richard J.L.F. Lemmers, Remko Goossens, Megumu Ogawa, Koji Nagao, Chikashi Obuse, Satoru Noguchi, Yukiko K. Hayashi, Satoshi Kuwabara, Judit Balog, Ichizo Nishino, Silvère M. van der Maarel
Neurology Jun 2020, 94 (23) e2441-e2447; DOI: 10.1212/WNL.0000000000009617

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Abstract

Objective Facioscapulohumeral muscular dystrophy (FSHD) is a heterogenetic disorder predominantly characterized by progressive facial and scapular muscle weakness. Patients with FSHD either have a contraction of the D4Z4 repeat on chromosome 4q35 or mutations in D4Z4 chromatin modifiers SMCHD1 and DNMT3B, both causing D4Z4 chromatin relaxation and inappropriate expression of the D4Z4-encoded DUX4 gene in skeletal muscle. In this study, we tested the hypothesis whether LRIF1, a known SMCHD1 protein interactor, is a disease gene for idiopathic FSHD2.

Methods Clinical examination of a patient with idiopathic FSHD2 was combined with pathologic muscle biopsy examination and with genetic, epigenetic, and molecular studies.

Results A homozygous LRIF1 mutation was identified in a patient with a clinical phenotype consistent with FSHD. This mutation resulted in the absence of the long isoform of LRIF1 protein, D4Z4 chromatin relaxation, and DUX4 and DUX4 target gene expression in myonuclei, all molecular and epigenetic hallmarks of FSHD. In concordance, LRIF1 was shown to bind to the D4Z4 repeat, and knockdown of the LRIF1 long isoform in muscle cells results in DUX4 and DUX4 target gene expression.

Conclusion LRIF1 is a bona fide disease gene for FSHD2. This study further reinforces the unifying genetic mechanism, which postulates that FSHD is caused by D4Z4 chromatin relaxation, resulting in inappropriate DUX4 expression in skeletal muscle.

Glossary

FSHD=
facioscapulohumeral muscular dystrophy;
ChIP=
chromatin immunoprecipitation;
PAS=
polyadenylation sequence

Footnotes

  • Go to Neurology.org/N for full disclosures. Funding information and disclosures deemed relevant by the authors, if any, are provided at the end of the article.

  • ↵* These authors are shared first authors.

  • ↵# These authors are shared senior authors.

  • Editorial, page 1011

  • Received September 13, 2019.
  • Accepted in final form January 6, 2020.
  • © 2020 American Academy of Neurology
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