Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2

Patrizia Calandra, Isabella Cascino, Richard J L F Lemmers, Giuliana Galluzzi, Emanuela Teveroni, Mauro Monforte, Giorgio Tasca, Enzo Ricci, Fabiola Moretti, Silvère M. van der Maarel, Giancarlo Deidda

Research output: Contribution to journalArticle

Abstract

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.
Original languageEnglish
JournalJournal of Medical Genetics
DOIs
Publication statusPublished - Feb 1 2016

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Facioscapulohumeral Muscular Dystrophy
Polyadenylation
Alleles
DNA
Methylation
Epigenomics
DNA Methylation
Skeletal Muscle
Transcription Factors
Chromosomes
Mutation
Genes

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Calandra, P., Cascino, I., Lemmers, R. J. L. F., Galluzzi, G., Teveroni, E., Monforte, M., ... Deidda, G. (2016). Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2. Journal of Medical Genetics. https://doi.org/10.1136/jmedgenet-2015-103436

Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2. / Calandra, Patrizia; Cascino, Isabella; Lemmers, Richard J L F; Galluzzi, Giuliana; Teveroni, Emanuela; Monforte, Mauro; Tasca, Giorgio; Ricci, Enzo; Moretti, Fabiola; van der Maarel, Silvère M.; Deidda, Giancarlo.

In: Journal of Medical Genetics, 01.02.2016.

Research output: Contribution to journalArticle

Calandra, P, Cascino, I, Lemmers, RJLF, Galluzzi, G, Teveroni, E, Monforte, M, Tasca, G, Ricci, E, Moretti, F, van der Maarel, SM & Deidda, G 2016, 'Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2', Journal of Medical Genetics. https://doi.org/10.1136/jmedgenet-2015-103436
Calandra P, Cascino I, Lemmers RJLF, Galluzzi G, Teveroni E, Monforte M et al. Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2. Journal of Medical Genetics. 2016 Feb 1. https://doi.org/10.1136/jmedgenet-2015-103436
Calandra, Patrizia ; Cascino, Isabella ; Lemmers, Richard J L F ; Galluzzi, Giuliana ; Teveroni, Emanuela ; Monforte, Mauro ; Tasca, Giorgio ; Ricci, Enzo ; Moretti, Fabiola ; van der Maarel, Silvère M. ; Deidda, Giancarlo. / Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2. In: Journal of Medical Genetics. 2016.
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abstract = "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.",
author = "Patrizia Calandra and Isabella Cascino and Lemmers, {Richard J L F} and Giuliana Galluzzi and Emanuela Teveroni and Mauro Monforte and Giorgio Tasca and Enzo Ricci and Fabiola Moretti and {van der Maarel}, {Silv{\`e}re M.} and Giancarlo Deidda",
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T1 - Allele-specific DNA hypomethylation characterises FSHD1 and FSHD2

AU - Calandra, Patrizia

AU - Cascino, Isabella

AU - Lemmers, Richard J L F

AU - Galluzzi, Giuliana

AU - Teveroni, Emanuela

AU - Monforte, Mauro

AU - Tasca, Giorgio

AU - Ricci, Enzo

AU - Moretti, Fabiola

AU - van der Maarel, Silvère M.

AU - Deidda, Giancarlo

PY - 2016/2/1

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N2 - 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.

AB - 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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