Publications by authors named "Richard J L F Lemmers"

52 Publications

Chromosome 10q-linked FSHD identifies as principal disease gene.

J Med Genet 2021 Jan 12. Epub 2021 Jan 12.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Background: Facioscapulohumeral dystrophy (FSHD) is an inherited muscular dystrophy clinically characterised by muscle weakness starting with the facial and upper extremity muscles. A disease model has been developed that postulates that failure in somatic repression of the transcription factor DUX4 embedded in the D4Z4 repeat on chromosome 4q causes FSHD. However, due to the position of the D4Z4 repeat close to the telomere and the complex genetic and epigenetic aetiology of FSHD, there is ongoing debate about the transcriptional deregulation of closely linked genes and their involvement in FSHD.

Method: Detailed genetic characterisation and gene expression analysis of patients with clinically confirmed FSHD and control individuals.

Results: Identification of two FSHD families in which the disease is caused by repeat contraction and expression from chromosome 10 due to a de novo D4Z4 repeat exchange between chromosomes 4 and 10. We show that the genetic lesion causal to FSHD in these families is physically separated from other candidate genes on chromosome 4. We demonstrate that muscle cell cultures from affected family members exhibit the characteristic molecular features of FSHD, including and DUX4 target gene expression, without showing evidence for transcriptional deregulation of other chromosome 4-specific candidate genes.

Conclusion: This study shows that in rare situations, FSHD can occur on chromosome 10 due to an interchromosomal rearrangement with the FSHD locus on chromosome 4q. These findings provide further evidence that derepression is the dominant disease pathway for FSHD. Hence, therapeutic strategies should focus on DUX4 as the primary target.
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http://dx.doi.org/10.1136/jmedgenet-2020-107041DOI Listing
January 2021

Homozygous nonsense variant in associated with facioscapulohumeral muscular dystrophy.

Neurology 2020 06 28;94(23):e2441-e2447. Epub 2020 May 28.

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.

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 gene in skeletal muscle. In this study, we tested the hypothesis whether , 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 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 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 and DUX4 target gene expression.

Conclusion: 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 expression in skeletal muscle.
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http://dx.doi.org/10.1212/WNL.0000000000009617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455367PMC
June 2020

Intronic variants in FSHD: testing the potential for CRISPR-Cas9 genome editing.

J Med Genet 2019 12 1;56(12):828-837. Epub 2019 Nov 1.

Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

Background: Facioscapulohumeral dystrophy (FSHD) is associated with partial chromatin relaxation of the retrogene containing D4Z4 macrosatellite repeats on chromosome 4, and transcriptional de-repression of in skeletal muscle. The common form of FSHD, FSHD1, is caused by a D4Z4 repeat array contraction. The less common form, FSHD2, is generally caused by heterozygous variants in .

Methods: We employed whole exome sequencing combined with Sanger sequencing to screen uncharacterised FSHD2 patients for extra-exonic mutations. We also used CRISPR-Cas9 genome editing to repair a pathogenic intronic variant from patient myoblasts.

Results: We identified intronic variants in two FSHD families. In the first family, an intronic variant resulted in partial intron retention and inclusion of the distal 14 nucleotides of intron 13 into the transcript. In the second family, a deep intronic variant in intron 34 resulted in exonisation of 53 nucleotides of intron 34. In both families, the aberrant transcripts are predicted to be non-functional. Deleting the pseudo-exon by CRISPR-Cas9 mediated genome editing in primary and immortalised myoblasts from the index case of the second family restored wild-type SMCHD1 expression to a level that resulted in efficient suppression of .

Conclusions: The estimated intronic mutation frequency of almost 2% in FSHD2, as exemplified by the two novel intronic variants identified here, emphasises the importance of screening for intronic variants in . Furthermore, the efficient suppression of after restoring SMCHD1 levels by genome editing of the mutant allele provides further guidance for therapeutic strategies.
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http://dx.doi.org/10.1136/jmedgenet-2019-106402DOI Listing
December 2019

Generation of genetically matched hiPSC lines from two mosaic facioscapulohumeral dystrophy type 1 patients.

Stem Cell Res 2019 10 28;40:101560. Epub 2019 Aug 28.

Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands. Electronic address:

Facioscapulohumeral dystrophy type 1 (FSHD1) is caused by contraction of the D4Z4 repeat array on chromosome 4q resulting in sporadic misexpression of the transcription factor DUX4 in skeletal muscle tissue. In ~4% of families, de novo D4Z4 contractions occur after fertilization resulting in somatic mosaicism with control and FSHD1 cell populations present within the same patient. Reprogramming of mosaic fibroblasts from two FSHD1 patients into human induced pluripotent stem cells (hiPSCs) generated genetically matched control and FSHD1 hiPSC lines. All hiPSC lines contained a normal karyotype, expressed pluripotency genes and differentiated into cells from the three germ layers.
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http://dx.doi.org/10.1016/j.scr.2019.101560DOI Listing
October 2019

SMCHD1 mutation spectrum for facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS) reveals disease-specific localisation of variants in the ATPase domain.

J Med Genet 2019 10 26;56(10):693-700. Epub 2019 Jun 26.

Human Genetics, Leids Universitair Medisch Centrum, Leiden, The Netherlands.

Background: Variants in the Structural Maintenance of Chromosomes flexible Hinge Domain-containing protein 1 () can cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) and the unrelated Bosma arhinia microphthalmia syndrome (BAMS). In FSHD2, pathogenic variants are found anywhere in SMCHD1 while in BAMS, pathogenic variants are restricted to the extended ATPase domain. Irrespective of the phenotypic outcome, both FSHD2-associated and BAMS-associated variants result in quantifiable local DNA hypomethylation. We compared FSHD2, BAMS and non-pathogenic variants to derive genotype-phenotype relationships.

Methods: Examination of variants and methylation of the SMCHD1-sensitive FSHD locus in 187 FSHD2 families, 41 patients with BAMS and in control individuals. Analysis of variants in a three-dimensional model of the ATPase domain of SMCHD1.

Results: methylation analysis is essential to establish pathogenicity of variants. Although the FSHD2 mutation spectrum includes all types of variants covering the entire locus, missense variants are significantly enriched in the extended ATPase domain. Identification of recurrent variants suggests disease-specific residues for FSHD2 and in BAMS, consistent with a largely disease-specific localisation of variants in SMCHD1.

Conclusions: The localisation of missense variants within the ATPase domain of SMCHD1 may contribute to the differences in phenotypic outcome.
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http://dx.doi.org/10.1136/jmedgenet-2019-106168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800092PMC
October 2019

FSHD1 and FSHD2 form a disease continuum.

Neurology 2019 05 12;92(19):e2273-e2285. Epub 2019 Apr 12.

From the Peripheral Nervous System (S.S., M.G., C.C., A.P.), Muscle & ALS Department, Pasteur 2 Hospital, Centre Hospitalier Universitaire de Nice, and Institute for Research on Cancer and Aging of Nice (S.S., C.B., N.L., P.N., G.C.), CNRS, INSERM, Université Côte d'Azur; Department of Genetics and Molecular Biology (A.B.-S., S.R., M.J.), Cochin Hospital, Paris, France; Department of Human Genetics (R.J.L.F.L., S.M.v.d.M.), Leiden University Medical Center, the Netherlands; Rare Neuromuscular Diseases Centre (C.C.), Department of Human Neuroscience, Sapienza University of Rome, Italy; Pathology Department (F.C.), CHRU of Caen, INSERM U1075, University of Caen, Normandy; Myology Institute (T.S., A.B., B.E.), Center of Research in Myology, APHP, Sorbonne Université, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Paris; Electromyography and Neuromuscular Department (C.V., F.B., P.P.), Neurologic Hospital, Lyon East Hospital Group, Lyon-Bron, France; Neuromuscular Center, Department of Neuroscience (M.C., E.P.), and Clinical Genetics Unit, Department of Women's and Children's Health (L.S.), University of Padova, Italy; Institut Imagine, Imagine Bioinfomatics Platform (M.B.), Paris Descartes University; Département de Neurologie (A.E.-L.), Hôpitaux Universitaires, Strasbourg; Nord/Est/Ile de France Neuromuscular Center (P.L.), Neurology Department, Raymond Poincaré Teaching Hospital, Garches; INSERM U1179 (P.L.), END-ICAP, Versailles Saint-Quentin-en-Yvelines University, Montigny-le-Bretonneux, France; and IRP Città della Speranza (L.S.), Padova, Italy.

Objective: To compare the clinical features of patients showing a classical phenotype of facioscapulohumeral muscular dystrophy (FSHD) with genetic and epigenetic characteristics of the FSHD1 and FSHD2 loci D4Z4 and .

Methods: This is a national multicenter cohort study. We measured motor strength, motor function, and disease severity by manual muscle testing sumscore, Brooke and Vignos scores, clinical severity score (CSS), and age-corrected CSS, respectively. We correlated these scores with genetic (D4Z4 repeat size and haplotype; variant status) and epigenetic (D4Z4 methylation) parameters.

Results: We included 103 patients: 54 men and 49 women. Among them, we identified 64 patients with FSHD1 and 20 patients with FSHD2. Seven patients had genetic and epigenetic characteristics of FSHD1 and FSHD2, all carrying repeats of 9-10 D4Z4 repeat units (RU) and a pathogenic variant. In the remaining patients, FSHD was genetically excluded or remained unconfirmed. All clinically affected mutation carriers had a D4Z4 repeat of 9-16 RU on a disease permissive 4qA haplotype. These patients are significantly more severely affected by all clinical scales when compared to patients with FSHD1 with upper-sized FSHD1 alleles (8-10 RU).

Conclusion: The overlap between FSHD1 and FSHD2 patients in the 9-10 D4Z4 RU range suggests that FSHD1 and FSHD2 form a disease continuum. The previously established repeat size threshold for FSHD1 (1-10 RU) and FSHD2 (11-20 RU) needs to be reconsidered.

Clinicaltrialsgov Identifier: NCT01970735.
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http://dx.doi.org/10.1212/WNL.0000000000007456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537132PMC
May 2019

Early onset as a marker for disease severity in facioscapulohumeral muscular dystrophy.

Neurology 2019 01 19;92(4):e378-e385. Epub 2018 Dec 19.

From the Department of Neurology (R.J.M.G., K.M., C.R.v.K., T.H.A.S., C.E.E., G.W.P., N.C.V., B.G.M.v.E.), Donders Center for Neuroscience, Radboud University Medical Center, Nijmegen; Department of Human Genetics (R.J.L.F.L., S.M.v.d.M.), Leiden University Medical Center, the Netherlands; and Department of Neurology (J.M.S.), Kansas University Medical Center, Kansas City.

Objective: To assess the relation between age at onset and disease severity in facioscapulohumeral muscular dystrophy (FSHD).

Methods: In this prospective cross-sectional study, we matched adult patients with FSHD with an early disease onset with 2 sex-matched FSHD control groups with a classic onset; the first group was age matched, and the second group was disease duration matched. Genetic characteristics, muscle performance, respiratory functioning, hearing loss, vision loss, epilepsy, educational level, and work status were compared with the 2 control groups.

Results: Twenty-eight patients with early-onset FSHD were age (n = 28) or duration (n = 27) matched with classic-onset patients. Patients with early-onset FSHD had more severe muscle weakness (mean FSHD clinical score 11 vs 5 in the age-matched and 9 in the duration-matched group, < 0.05) and a higher frequency of wheelchair dependency (57%, 0%, and 30%, respectively, < 0.05). In addition, systemic features were more frequent in early-onset FSHD, most important, hearing loss, decreased respiratory function and spinal deformities. There was no difference in work status. Genetically, the shortest D4Z4 repeat arrays (2-3 units) were found exclusively in the early-onset group, and the largest repeat arrays (8-9 units) were found only in the classic-onset groups. De novo mutations were more frequent in early-onset patients (46% vs 4%).

Conclusions: Patients with early-onset FSHD more often have severe muscle weakness and systemic features. The disease severity is greater than in patients with classic-onset FSHD who are matched for disease duration, suggesting that the progression is faster in early-onset patients.
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http://dx.doi.org/10.1212/WNL.0000000000006819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345117PMC
January 2019

Cis D4Z4 repeat duplications associated with facioscapulohumeral muscular dystrophy type 2.

Hum Mol Genet 2018 10;27(20):3488-3497

Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.

Facioscapulohumeral muscular dystrophy, known in genetic forms FSHD1 and FSHD2, is associated with D4Z4 repeat array chromatin relaxation and somatic derepression of DUX4 located in D4Z4. A complete copy of DUX4 is present on 4qA chromosomes, but not on the D4Z4-like repeats of chromosomes 4qB or 10. Normally, the D4Z4 repeat varies between 8 and 100 units, while in FSHD1 it is only 1-10 units. In the rare genetic form FSHD2, a combination of a 4qA allele with a D4Z4 repeat size of 8-20 units and heterozygous pathogenic variants in the chromatin modifier SMCHD1 causes DUX4 derepression and disease. In this study, we identified 11/79 (14%) FSHD2 patients with unusually large 4qA alleles of 21-70 D4Z4 units. By a combination of Southern blotting and molecular combing, we show that 8/11 (73%) of these unusually large 4qA alleles represent duplication alleles in which the long D4Z4 repeat arrays are followed by a small FSHD-sized D4Z4 repeat array duplication. We also show that these duplication alleles are associated with DUX4 expression. This duplication allele frequency is significantly higher than in controls (2.9%), FSHD1 patients (1.4%) and in FSHD2 patients with typical 4qA alleles of 8-20 D4Z4 units (1.5%). Segregation analysis shows that, similar to typical 8-20 units FSHD2 alleles, duplication alleles only cause FSHD in combination with a pathogenic variant in SMCHD1. We conclude that cis duplications of D4Z4 repeats explain DUX4 expression and disease presentation in FSHD2 families with unusual long D4Z4 repeats on 4qA chromosomes.
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http://dx.doi.org/10.1093/hmg/ddy236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168970PMC
October 2018

Phenotype-genotype relations in facioscapulohumeral muscular dystrophy type 1.

Clin Genet 2018 12 8;94(6):521-527. Epub 2018 Oct 8.

Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.

To determine how much of the clinical variability in facioscapulohumeral muscular dystrophy type 1 (FSHD1) can be explained by the D4Z4 repeat array size, D4Z4 methylation and familial factors, we included 152 carriers of an FSHD1 allele (23 single cases, 129 familial cases from 37 families) and performed state-of-the-art genetic testing, extensive clinical evaluation and quantitative muscle MRI. Familial factors accounted for 50% of the variance in disease severity (FSHD clinical score). The explained variance by the D4Z4 repeat array size for disease severity was limited (approximately 10%), and varied per body region (facial muscles, upper and lower extremities approximately 30%, 15% and 3%, respectively). Unaffected gene carriers had longer repeat array sizes compared to symptomatic individuals (7.3 vs 6.0 units, P = 0.000) and slightly higher Delta1 methylation levels (D4Z4 methylation corrected for repeat size, 0.96 vs -2.46, P = 0.048). The D4Z4 repeat array size and D4Z4 methylation contribute to variability in disease severity and penetrance, but other disease modifying factors must be involved as well. The larger effect of the D4Z4 repeat array on facial muscle involvement suggests that these muscles are more sensitive to the influence of the FSHD1 locus itself, whereas leg muscle involvement seems highly dependent on modifying factors.
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http://dx.doi.org/10.1111/cge.13446DOI Listing
December 2018

Facioscapulohumeral Dystrophy in Childhood: A Nationwide Natural History Study.

Ann Neurol 2018 11 16;84(5):627-637. Epub 2018 Oct 16.

Department of Neurology, Donders Centre for Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands.

Objective: Facioscapulohumeral dystrophy (FSHD) is one of the most frequent heritable muscular dystrophies, with a large variety in age at onset and disease severity. The natural history and molecular characteristics of FSHD in childhood are incompletely understood. Our objective is to clinically and genetically characterize FSHD in childhood.

Methods: We performed a nationwide, single-investigator, natural history study on FSHD in childhood.

Results: Multiple-source recruitment resulted in 32 patients with FSHD (0-17 years), leading to an estimated prevalence of 1 in 100,000 children in The Netherlands. This series of 32 children with FSHD revealed a heterogeneous phenotype and genotype in childhood. The phenotypic hallmarks of FSHD in childhood are: facial weakness with normal or only mildly affected motor performance, decreased functional exercise capacity (6-minute walk test), lumbar hyperlordosis, and increased echo intensity on muscle ultrasonography. In addition, pain and fatigue were frequent and patients experienced a lower quality of life compared to healthy peers. In contrast to the literature on early-onset FSHD, systemic features such as hearing loss and retinal and cardiac abnormalities were infrequent and subclinical, and epilepsy and intellectual disability were absent. Genotypically, patients had a mean D4Z4 repeat array of 5 units (range, 2-9), and 14% of the mutations were de novo.

Interpretation: FSHD in childhood is more prevalent than previously known and the genotype resembles classic FSHD. Importantly, FSHD mainly affects functional exercise capacity and quality of life in children. As such, these results are paramount for counseling, clinical management, and stratification in clinical research. Ann Neurol 2018;84:635-645.
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http://dx.doi.org/10.1002/ana.25326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282793PMC
November 2018

FSHD type 2 and Bosma arhinia microphthalmia syndrome: Two faces of the same mutation.

Neurology 2018 08 6;91(6):e562-e570. Epub 2018 Jul 6.

From the Department of Neurology (K.M., N.C.V., B.G.M.v.E., C.G.C.H.), Radboud University Medical Center, Nijmegen; Departments of Human Genetics (R.J.L.F.L., P.J.v.d.V., M.L.v.d.B., S.M.v.d.M.), Clinical Genetics (M.K.), and Neurology (U.A.B.), Leiden University Medical Center, Leiden, the Netherlands; Department of Pediatrics (J.M.G.), Cedars Sinai Medical Center, Los Angeles, CA; Department of Medical Genetics (A.E.L.), MassGeneral Hospital for Children, Boston, MA; Center for Genomic Medicine and Department of Neurology (H.B.), Massachusetts General Hospital, Boston; Department of Pathology (S.A.M.), University of Iowa Hospitals and Clinics, Iowa City; The John Walton Muscular Dystrophy Research Centre (K.J., T.E., A.T., V.S.), Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK; Neuromuscular Consult Unit (S.K.G.), Bilbo-Basurtu Erakunde Sanitario Integratua, Organización Sanitaria Integrada Bilbao-Basurto, Spain; Centre de Référence des Maladies Neuromusculaires (S.S.), Nice, France; Department of Neurology (R.T.), University of Rochester Medical Center, NY; Division of Human Biology (S.J.T.), Fred Hutchinson Cancer Research Center, Seattle, WA; and National Institute of Environmental Health Sciences (N.D.S.), Research Triangle Park, NC.

Objective: To determine whether congenital arhinia/Bosma arhinia microphthalmia syndrome (BAMS) and facioscapulohumeral muscular dystrophy type 2 (FSHD2), 2 seemingly unrelated disorders both caused by heterozygous pathogenic missense variants in the gene, might represent different ends of a broad single phenotypic spectrum associated with SMCHD1 dysfunction.

Methods: We examined and/or interviewed 14 patients with FSHD2 and 4 unaffected family members with N-terminal pathogenic missense variants to identify BAMS subphenotypes.

Results: None of the patients with FSHD2 or family members demonstrated any congenital defects or dysmorphic features commonly found in patients with BAMS. One patient became anosmic after nasal surgery and one patient was hyposmic; one man was infertile (unknown cause) but reported normal pubertal development.

Conclusion: These data suggest that arhinia/BAMS and FSHD2 do not represent one phenotypic spectrum and that pathogenic variants by themselves are insufficient to cause either of the 2 disorders. More likely, both arhinia/BAMS and FSHD2 are caused by complex oligogenic or multifactorial mechanisms that only partially overlap at the level of
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http://dx.doi.org/10.1212/WNL.0000000000005958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105048PMC
August 2018

A 22-year follow-up reveals a variable disease severity in early-onset facioscapulohumeral dystrophy.

Eur J Paediatr Neurol 2018 Sep 3;22(5):782-785. Epub 2018 May 3.

Department of Neurology, Radboud University Medical Centre, Nijmegen, The Netherlands.

Aim: To assess the long-term natural course of early-onset facioscapulohumeral dystrophy (FSHD), which is important for patient management and trial-readiness, and is currently lacking.

Methods: We had the unique opportunity to evaluate 10 patients with early-onset FSHD after 22 years follow-up. Patients underwent a semi-structured interview, physical examination and additional genotyping.

Results: Nine initial study participants (median age 37 years) were included, one patient died shortly after first publication. At first examination, one patient was wheelchair dependent, one patient walked aided, and eight patients walked unaided. After 22 years, four patients were wheelchair dependent, three walked aided, and two walked unaided. Systemic features, including hearing loss (56%), intellectual disability (44%), and a decreased respiratory function (56%), were frequent. Patients participated socially and economically with most patients living in a regular house (n = 6) and/or having a paid job (n = 4).

Discussion: Patients with early-onset FSHD generally had a severe phenotype compared to classical onset FSHD. However, after 22 years of follow up they showed a wide variation in severity and, despite these physical limitations, participated socially and economically. These observations are important for patient management and should be taken into account in clinical trials.
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http://dx.doi.org/10.1016/j.ejpn.2018.04.013DOI Listing
September 2018

Monosomy 18p is a risk factor for facioscapulohumeral dystrophy.

J Med Genet 2018 07 21;55(7):469-478. Epub 2018 Mar 21.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Background: 18p deletion syndrome is a rare disorder caused by partial or full monosomy of the short arm of chromosome 18. Clinical symptoms caused by 18p hemizygosity include cognitive impairment, mild facial dysmorphism, strabismus and ptosis. Among other genes, structural maintenance of chromosomes flexible hinge domain containing 1 () is hemizygous in most patients with 18p deletions. Digenic inheritance of a mutation and a moderately sized D4Z4 repeat on a facioscapulohumeral muscular dystrophy (FSHD) permissive genetic background of chromosome 4 can cause FSHD type 2 (FSHD2).

Objectives: Since 12% of Caucasian individuals harbour moderately sized D4Z4 repeats on an FSHD permissive background, we tested if people with 18p deletions are at risk of developing FSHD.

Methods: To test our hypothesis we studied different cellular systems originating from individuals with 18p deletions not presenting FSHD2 phenotype for transcriptional and epigenetic characteristics of FSHD at D4Z4. Furthermore, individuals with an idiopathic muscle phenotype and an 18p deletion were subjected to neurological examination.

Results: Primary fibroblasts hemizygous for have a D4Z4 chromatin structure comparable with FSHD2 concomitant with DUX4 expression after transdifferentiation into myocytes. Neurological examination of 18p deletion individuals from two independent families with a moderately sized D4Z4 repeat identified muscle features compatible with FSHD.

Conclusions: 18p deletions leading to haploinsufficiency of , together with a moderately sized FSHD permissive D4Z4 allele, can associate with symptoms and molecular features of FSHD. We propose that patients with 18p deletion should be characterised for their D4Z4 repeat size and haplotype and monitored for clinical features of FSHD.
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http://dx.doi.org/10.1136/jmedgenet-2017-105153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019561PMC
July 2018

Adding quantitative muscle MRI to the FSHD clinical trial toolbox.

Neurology 2017 Nov 13;89(20):2057-2065. Epub 2017 Oct 13.

From the Department of Neurology (K.M., S.C.C.V., N.C.V., G.W.P., C.G.C.H., B.G.M.v.E.), Radboud University Medical Center, Nijmegen; and Department of Human Genetics (R.J.L.F.L., P.J.v.d.V., S.M.v.d.M.), Leiden University Medical Center, the Netherlands.

Objective: To add quantitative muscle MRI to the clinical trial toolbox for facioscapulohumeral muscular dystrophy (FSHD) by correlating it to clinical outcome measures in a large cohort of genetically and clinically well-characterized patients with FSHD comprising the entire clinical spectrum.

Methods: Quantitative MRI scans of leg muscles of 140 patients with FSHD1 and FSHD2 were assessed for fatty infiltration and TIRM hyperintensities and were correlated to multiple clinical outcome measures.

Results: The mean fat fraction of the total leg musculature correlated highly with the motor function measure, FSHD clinical score, Ricci score, and 6-minute walking test (correlation coefficients -0.845, 0.835, 0.791, -0.701, respectively). Fat fraction per muscle group correlated well with corresponding muscle strength (correlation coefficients up to -0.82). The hamstring muscles, adductor muscles, rectus femoris, and gastrocnemius medialis were affected most frequently, also in early stage disease and in patients without leg muscle weakness. Muscle involvement was asymmetric in 20% of all muscle pairs and fatty infiltration within muscles showed a decrease from distal to proximal of 3.9%. TIRM hyperintense areas, suggesting inflammation, were found in 3.5% of all muscles, with and without fatty infiltration.

Conclusions: We show a strong correlation between quantitative muscle MRI and clinical outcome measures. Muscle MRI is able to detect muscle pathology before clinical involvement of the leg muscles. This indicates that quantitative leg muscle MRI is a promising biomarker that captures disease severity and motor functioning and can thus be included in the FSHD trial toolbox.
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http://dx.doi.org/10.1212/WNL.0000000000004647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711504PMC
November 2017

SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes.

Skelet Muscle 2017 06 6;7(1):12. Epub 2017 Jun 6.

Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance.

Methods: To investigate the global effects of harboring heterozygous SMCHD1 mutations on DNA methylation in humans, we combined 450k methylation analysis on mononuclear monocytes from female heterozygous SMCHD1 mutation carriers and unaffected controls with reduced representation bisulfite sequencing (RRBS) on FSHD2 and control myoblast cell lines. Candidate loci were then evaluated for SMCHD1 binding using ChIP-qPCR and expression was evaluated using RT-qPCR.

Results: We identified a limited number of clustered autosomal loci with CpG hypomethylation in SMCHD1 mutation carriers: the protocadherin (PCDH) cluster on chromosome 5, the transfer RNA (tRNA) and 5S rRNA clusters on chromosome 1, the HOXB and HOXD clusters on chromosomes 17 and 2, respectively, and the D4Z4 repeats on chromosomes 4 and 10. Furthermore, minor increases in RNA expression were seen in FSHD2 myoblasts for some of the PCDHβ cluster isoforms, tRNA isoforms, and a HOXB isoform in comparison to controls, in addition to the previously reported effects on DUX4 expression. SMCHD1 was bound at DNAseI hypersensitivity sites known to regulate the PCDHβ cluster and at the chromosome 1 tRNA cluster, with decreased binding in SMCHD1 mutation carriers at the PCDHβ cluster sites.

Conclusions: Our study is the first to investigate the global methylation effects in humans resulting from heterozygous mutations in SMCHD1. Our results suggest that SMCHD1 acts as a repressor on a limited set of autosomal gene clusters, as an observed reduction in methylation associates with a loss of SMCHD1 binding and increased expression for some of the loci.
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http://dx.doi.org/10.1186/s13395-017-0129-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461771PMC
June 2017

whole-genome assembly of a wild type yeast isolate using nanopore sequencing.

F1000Res 2017;6:618. Epub 2017 May 3.

Institute of Biology, Leiden University, Leiden, 2300 RA, Netherlands.

The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for assembly of complex genomes without using other technologies. Furthermore, Nanopore data combined with other sequencing technologies is highly useful for accurate annotation of all genes in the genome. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. We compared various technical and software developments for the nanopore sequencing protocol, showing that the R9 chemistry is, as predicted, higher in quality than R7.3 chemistry. The R9 chemistry is an essential improvement for assembly of the extremely AT-rich mitochondrial genome. We double corrected assemblies from four different assemblers with PILON and assessed sequence correctness before and after PILON correction with a set of 290 Fungi genes using BUSCO. In this study, we used this new technology to sequence and assemble the genome of a recently isolated ethanologenic yeast strain, and compared the results with those obtained by classical Illumina short read sequencing. This strain was originally named ( ) based on ribosomal RNA sequencing. We show that the assembly using nanopore data is much more contiguous than the assembly using short read data. We also compared various technical and software developments for the nanopore sequencing protocol, showing that nanopore-derived assemblies provide the highest contiguity. The mitochondrial and chromosomal genome sequences showed that our strain is clearly distinct from other yeast taxons and most closely related to published species. In conclusion, MinION-mediated long read sequencing can be used for high quality assembly of new eukaryotic microbial genomes.
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http://dx.doi.org/10.12688/f1000research.11146.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081980PMC
May 2017

Analyzing Copy Number Variation Using Pulsed-Field Gel Electrophoresis: Providing a Genetic Diagnosis for FSHD1.

Methods Mol Biol 2017 ;1492:107-125

Department of Human Genetics, Leiden University Medical Center, 2333, ZA, Leiden, The Netherlands.

The myopathy facioscapulohumeral muscular dystrophy type 1 (FSHD1) is caused by copy number variation of the D4Z4 macrosatellite repeat on chromosome 4. In unaffected individuals the number of 3.3 kb D4Z4 units varies between 8 and 100, whereas 1-10 units are seen in FSHD1 cases. A homologous and heterogenous D4Z4 array can be found on chromosome 10q, but contractions of this array are typically not associated with FSHD. Discriminating between the chromosome 4 and chromosome 10 D4Z4 arrays, as well as determining the array size, requires the use of pulsed-field gel electrophoresis, Southern blotting, and the isolation of high-quality DNA.
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http://dx.doi.org/10.1007/978-1-4939-6442-0_7DOI Listing
January 2018

Mutations in DNMT3B Modify Epigenetic Repression of the D4Z4 Repeat and the Penetrance of Facioscapulohumeral Dystrophy.

Am J Hum Genet 2016 05;98(5):1020-1029

Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands. Electronic address:

Facioscapulohumeral dystrophy (FSHD) is associated with somatic chromatin relaxation of the D4Z4 repeat array and derepression of the D4Z4-encoded DUX4 retrogene coding for a germline transcription factor. Somatic DUX4 derepression is caused either by a 1-10 unit repeat-array contraction (FSHD1) or by mutations in SMCHD1, which encodes a chromatin repressor that binds to D4Z4 (FSHD2). Here, we show that heterozygous mutations in DNA methyltransferase 3B (DNMT3B) are a likely cause of D4Z4 derepression associated with low levels of DUX4 expression from the D4Z4 repeat and increased penetrance of FSHD. Recessive mutations in DNMT3B were previously shown to cause immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome. This study suggests that transcription of DUX4 in somatic cells is modified by variations in its epigenetic state and provides a basis for understanding the reduced penetrance of FSHD within families.
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http://dx.doi.org/10.1016/j.ajhg.2016.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863565PMC
May 2016

Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2.

J Med Genet 2016 05 1;53(5):348-55. Epub 2016 Feb 1.

Institute of Cell Biology and Neurobiology, National Research Council of Italy, Monterotondo (Rome), Italy.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is associated with an epigenetic defect on 4qter. Two clinically indistinguishable forms of FSHD are known, FSHD1 and FSHD2. FSHD1 is caused by contraction of the highly polymorphic D4Z4 macrosatellite repeat array on chromosome 4q35. FSHD2 is caused by pathogenic mutations of the SMCHD1 gene.Both genetic defects lead to D4Z4 DNA hypomethylation. In the presence of a polymorphic polyadenylation signal (PAS), DNA hypomethylation leads to inappropriate expression of the D4Z4-encoded DUX4 transcription factor in skeletal muscle. Currently, hypomethylation is not diagnostic per se because of the interference of non-pathogenic arrays and the lack of information about the presence of DUX4-PAS.

Methods: We investigated, by bisulfite sequencing, the DNA methylation levels of the region distal to the D4Z4 array selectively in PAS-positive alleles.

Results: Comparison of FSHD1, FSHD2 and Control subjects showed a highly significant difference of methylation levels in all CpGs tested. Importantly, using a cohort of 112 samples, one of these CpGs (CpG6) is able to discriminate the affected individuals with a sensitivity of 0.95 supporting this assay potential for FSHD diagnosis. Moreover, our study showed a relationship between PAS-specific methylation and severity of the disease.

Conclusions: These data point to the CpGs distal to the D4Z4 array as a critical region reflecting multiple factors affecting the epigenetics of FSHD. Additionally, methylation analysis of this region allows the establishment of a rapid and sensitive tool for FSHD diagnosis.
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http://dx.doi.org/10.1136/jmedgenet-2015-103436DOI Listing
May 2016

Increased DUX4 expression during muscle differentiation correlates with decreased SMCHD1 protein levels at D4Z4.

Epigenetics 2015 ;10(12):1133-42

a Department of Human Genetics; Leiden University Medical Center; 2333ZA Leiden , The Netherlands.

Facioscapulohumeral muscular dystrophy is caused by incomplete epigenetic repression of the transcription factor DUX4 in skeletal muscle. A copy of DUX4 is located within each unit of the D4Z4 macrosatellite repeat array and its derepression in somatic cells is caused by either repeat array contraction (FSHD1) or by mutations in the chromatin repressor SMCHD1 (FSHD2). While DUX4 expression has thus far only been detected in FSHD muscle and muscle cell cultures, and increases with in vitro myogenic differentiation, the D4Z4 chromatin structure has only been studied in proliferating myoblasts or non-myogenic cells. We here show that SMCHD1 protein levels at D4Z4 decline during muscle cell differentiation and correlate with DUX4 derepression. In FSHD2, but not FSHD1, the loss of SMCHD1 repressor activity is partially compensated by increased Polycomb Repressive Complex 2 (PRC2)-mediated H3K27 trimethylation at D4Z4, a situation that can be mimicked by SMCHD1 knockdown in control myotubes. In contrast, moderate overexpression of SMCHD1 results in DUX4 silencing in FSHD1 and FSHD2 myotubes demonstrating that DUX4 derepression in FSHD is reversible. Together, we show that in FSHD1 and FSHD2 the decline in SMCHD1 protein levels during muscle cell differentiation renders skeletal muscle sensitive to DUX4.
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http://dx.doi.org/10.1080/15592294.2015.1113798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844215PMC
November 2016

Milder phenotype in facioscapulohumeral dystrophy with 7-10 residual D4Z4 repeats.

Neurology 2015 Dec 11;85(24):2147-50. Epub 2015 Nov 11.

From the Department of Neurology (J.M.S.), University of Kansas Medical Center, Kansas City; the Department of Neurology (C.M.D., R.T.), University of Rochester Medical Center, NY; the Division of Human Biology (S.J.T.), Fred Hutchinson Cancer Research Center, Seattle, WA; and the Department of Human Genetics (R.J.L.F.L., S.M.v.d.M.), Leiden University Medical Center, the Netherlands.

Objective: To examine the relationship of clinical and genetic features of patients with facioscapulohumeral muscular dystrophy (FSHD) with 7-10 residual D4Z4 repeats in a large genetically defined FSHD1 cohort.

Methods: We performed a prospective cross-sectional observational study of 74 clinically affected patients with FSHD1. Measures of clinical severity were compared between patients with 1-6 D4Z4 repeats and 7-10 repeats, and included D4Z4 CpG methylation, age at diagnosis, age-adjusted clinical severity score, a muscle pathology grade of quadriceps biopsies (0 = normal, 12 = severe dystrophic changes), quantitative myometry of biopsied muscles, global manual muscle testing scores, and frequency of wheelchair use.

Results: Twenty-eight (37.8%) participants had 7-10 D4Z4 repeats, and compared to participants with 1-6 repeats, were diagnosed 6.6 years older (p = 0.17); had lower CpG methylation than would be predicted by D4Z4 repeat size (p = 0.04); had age-adjusted clinical severity 39.8 points lower (p = 0.004); had muscle pathology grades that were 2.4 points less severe (p < 0.0001); had quantitative myometry 28.3% predicted of normal higher (p = 0.002); had global manual muscle testing scores 0.6 higher (p = 0.005); and did not require wheelchairs.

Conclusion: Patients with FSHD with 7-10 D4Z4 repeats have milder disease than other genetically defined patients with FSHD1. The lower than predicted methylation in the 7-10 residual repeat group may suggest that additional epigenetic factors play a role in the severity of disease expression.
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http://dx.doi.org/10.1212/WNL.0000000000002217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691686PMC
December 2015

Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome.

Nat Commun 2015 Jul 28;6:7870. Epub 2015 Jul 28.

Division of Epigenomics and Development, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.

The life-threatening Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome is a genetically heterogeneous autosomal recessive disorder. Twenty percent of patients cannot be explained by mutations in the known ICF genes DNA methyltransferase 3B or zinc-finger and BTB domain containing 24. Here we report mutations in the cell division cycle associated 7 and the helicase, lymphoid-specific genes in 10 unexplained ICF cases. Our data highlight the genetic heterogeneity of ICF syndrome; however, they provide evidence that all genes act in common or converging pathways leading to the ICF phenotype.
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http://dx.doi.org/10.1038/ncomms8870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519989PMC
July 2015

Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation.

Proc Natl Acad Sci U S A 2015 Jul 19;112(27):E3535-44. Epub 2015 Jun 19.

The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia;

Structural maintenance of chromosomes flexible hinge domain containing 1 (Smchd1) is an epigenetic repressor with described roles in X inactivation and genomic imprinting, but Smchd1 is also critically involved in the pathogenesis of facioscapulohumeral dystrophy. The underlying molecular mechanism by which Smchd1 functions in these instances remains unknown. Our genome-wide transcriptional and epigenetic analyses show that Smchd1 binds cis-regulatory elements, many of which coincide with CCCTC-binding factor (Ctcf) binding sites, for example, the clustered protocadherin (Pcdh) genes, where we show Smchd1 and Ctcf act in opposing ways. We provide biochemical and biophysical evidence that Smchd1-chromatin interactions are established through the homodimeric hinge domain of Smchd1 and, intriguingly, that the hinge domain also has the capacity to bind DNA and RNA. Our results suggest Smchd1 imparts epigenetic regulation via physical association with chromatin, which may antagonize Ctcf-facilitated chromatin interactions, resulting in coordinated transcriptional control.
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http://dx.doi.org/10.1073/pnas.1504232112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500281PMC
July 2015

Hemizygosity for SMCHD1 in Facioscapulohumeral Muscular Dystrophy Type 2: Consequences for 18p Deletion Syndrome.

Hum Mutat 2015 Jul 20;36(7):679-83. Epub 2015 May 20.

Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.

Facioscapulohumeral muscular dystrophy (FSHD) is most often associated with variegated expression in somatic cells of the normally repressed DUX4 gene within the D4Z4-repeat array. The most common form, FSHD1, is caused by a D4Z4-repeat array contraction to a size of 1-10 units (normal range 10-100 units). The less common form, FSHD2, is characterized by D4Z4 CpG hypomethylation and is most often caused by loss-of-function mutations in the structural maintenance of chromosomes hinge domain 1 (SMCHD1) gene on chromosome 18p. The chromatin modifier SMCHD1 is necessary to maintain a repressed D4Z4 chromatin state. Here, we describe two FSHD2 families with a 1.2-Mb deletion encompassing the SMCHD1 gene. Numerical aberrations of chromosome 18 are relatively common and the majority of 18p deletion syndrome (18p-) cases have, such as these FSHD2 families, only one copy of SMCHD1. Our finding therefore raises the possibility that 18p- cases are at risk of developing FSHD. To address this possibility, we combined genome-wide array analysis data with D4Z4 CpG methylation and repeat array sizes in individuals with 18p- and conclude that approximately 1:8 18p- cases might be at risk of developing FSHD.
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http://dx.doi.org/10.1002/humu.22792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475473PMC
July 2015

Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2.

Hum Mol Genet 2015 Feb 25;24(3):659-69. Epub 2014 Sep 25.

Department of Human Genetics.

Facioscapulohumeral muscular dystrophy (FSHD: MIM#158900) is a common myopathy with marked but largely unexplained clinical inter- and intra-familial variability. It is caused by contractions of the D4Z4 repeat array on chromosome 4 to 1-10 units (FSHD1), or by mutations in the D4Z4-binding chromatin modifier SMCHD1 (FSHD2). Both situations lead to a partial opening of the D4Z4 chromatin structure and transcription of D4Z4-encoded polyadenylated DUX4 mRNA in muscle. We measured D4Z4 CpG methylation in control, FSHD1 and FSHD2 individuals and found a significant correlation with the D4Z4 repeat array size. After correction for repeat array size, we show that the variability in clinical severity in FSHD1 and FSHD2 individuals is dependent on individual differences in susceptibility to D4Z4 hypomethylation. In FSHD1, for individuals with D4Z4 repeat arrays of 1-6 units, the clinical severity mainly depends on the size of the D4Z4 repeat. However, in individuals with arrays of 7-10 units, the clinical severity also depends on other factors that regulate D4Z4 methylation because affected individuals, but not non-penetrant mutation carriers, have a greater reduction of D4Z4 CpG methylation than can be expected based on the size of the pathogenic D4Z4 repeat array. In FSHD2, this epigenetic susceptibility depends on the nature of the SMCHD1 mutation in combination with D4Z4 repeat array size with dominant negative mutations being more deleterious than haploinsufficiency mutations. Our study thus identifies an epigenetic basis for the striking variability in onset and disease progression that is considered a clinical hallmark of FSHD.
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http://dx.doi.org/10.1093/hmg/ddu486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291246PMC
February 2015

DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle.

Hum Mol Genet 2014 Oct 26;23(20):5342-52. Epub 2014 May 26.

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA Department of Neurology, University of Washington, Seattle, WA 98105, USA

Facioscapulohumeral dystrophy (FSHD) is caused by decreased epigenetic repression of the D4Z4 macrosatellite array and recent studies have shown that this results in the expression of low levels of the DUX4 mRNA in skeletal muscle. Several other mechanisms have been suggested for FSHD pathophysiology and it remains unknown whether DUX4 expression can account for most of the molecular changes seen in FSHD. Since DUX4 is a transcription factor, we used RNA-seq to measure gene expression in muscle cells transduced with DUX4, and in muscle cells and biopsies from control and FSHD individuals. We show that DUX4 target gene expression is the major molecular signature in FSHD muscle together with a gene expression signature consistent with an immune cell infiltration. In addition, one unaffected individual without a known FSHD-causing mutation showed the expression of DUX4 target genes. This individual has a sibling with FSHD and also without a known FSHD-causing mutation, suggesting the presence of an unidentified modifier locus for DUX4 expression and FSHD. These findings demonstrate that the expression of DUX4 accounts for the majority of the gene expression changes in FSHD skeletal muscle together with an immune cell infiltration.
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http://dx.doi.org/10.1093/hmg/ddu251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168822PMC
October 2014

Early-onset facioscapulohumeral muscular dystrophy type 1 with some atypical features.

J Child Neurol 2015 Apr 9;30(5):580-7. Epub 2014 Apr 9.

Neuromuscular Unit, Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland.

Facioscapulohumeral muscular dystrophy cases with facial weakness before the age of 5 and signs of shoulder weakness by the age of 10 are defined as early onset. Contraction of the D4Z4 repeat on chromosome 4q35 is causally related to facioscapulohumeral muscular dystrophy type 1, and the residual size of the D4Z4 repeat shows a roughly inverse correlation with the severity of the disease. Contraction of the D4Z4 repeat on chromosome 4q35 is believed to induce a local change in chromatin structure and consequent transcriptional deregulation of 4qter genes. We present early-onset cases in the Polish population that amounted to 21% of our total population with facioscapulohumeral muscular dystrophy. More than 27% of them presented with severe phenotypes (wheelchair dependency). The residual D4Z4 repeat sizes ranged from 1 to 4 units. In addition, even within early-onset facioscapulohumeral muscular dystrophy type 1 phenotypes, some cases had uncommon features (head drop, early disabling contractures, progressive ptosis, and respiratory insufficiency and cardiomyopathy).
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http://dx.doi.org/10.1177/0883073814528281DOI Listing
April 2015

DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix.

Eur J Hum Genet 2014 Sep 22;22(9):1117-23. Epub 2014 Jan 22.

1] UMR 8126, Université Paris Sud, CNRS, Institut de cancérologie Gustave Roussy, Villejuif, France [2] LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, Villejuif, France [3] NK Koltsov Institute of Developmental Biology, RAS, Moscow, Russia.

Mechanisms that regulate attachment of the scaffold/matrix attachment regions (S/MARs) to the nuclear matrix remain largely unknown. We have studied the effect of simple sequence length polymorphism (SSLP), DNA methylation and chromatin organization in an S/MAR implicated in facioscapulohumeral dystrophy (FSHD), a hereditary disease linked to a partial deletion of the D4Z4 repeat array on chromosome 4q. This FSHD-related nuclear matrix attachment region (FR-MAR) loses its efficiency in myoblasts from FSHD patients. Three criteria were found to be important for high-affinity interaction between the FR-MAR and the nuclear matrix: the presence of a specific SSLP haplotype in chromosomal DNA, the methylation of one specific CpG within the FR-MAR and the absence of histone H3 acetylated on lysine 9 in the relevant chromatin fragment.
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http://dx.doi.org/10.1038/ejhg.2013.306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135416PMC
September 2014