Identifying diagnostic DNA methylation profiles for facioscapulohumeral muscular dystrophy in blood and saliva using bisulfite sequencing.
BACKGROUND
Facioscapulohumeral muscular dystrophy (FSHD) is linked to chromatin relaxation due to epigenetic changes at the 4q35 D4Z4 macrosatellite array. Molecular diagnostic criteria for FSHD are complex and involve analysis of high molecular weight (HMW) genomic DNA isolated from lymphocytes, followed by multiple restriction digestions, pulse-field gel electrophoresis (PFGE), and Southern blotting. A subject is genetically diagnosed as FSHD1 if one of the 4q alleles shows a contraction in the D4Z4 array to below 11 repeats, while maintaining at least 1 repeat, and the contraction is in cis with a disease-permissive A-type subtelomere. FSHD2 is contraction-independent and cannot be diagnosed or excluded by this common genetic diagnostic procedure. However, FSHD1 and FSHD2 are linked by epigenetic deregulation, assayed as DNA hypomethylation, of the D4Z4 array on FSHD-permissive alleles. We have developed a PCR-based assay that identifies the epigenetic signature for both types of FSHD, distinguishing FSHD1 from FSHD2, and can be performed on genomic DNA isolated from blood, saliva, or cultured cells.


RESULTS
Samples were obtained from healthy controls or patients clinically diagnosed with FSHD, and include both FSHD1 and FSHD2. The genomic DNAs were subjected to bisulfite sequencing analysis for the distal 4q D4Z4 repeat with an A-type subtelomere and the DUX4 5' promoter region. We compared genomic DNA isolated from saliva and blood from the same individuals and found similar epigenetic signatures. DNA hypomethylation was restricted to the contracted 4qA chromosome in FSHD1 patients while healthy control subjects were hypermethylated. Candidates for FSHD2 showed extreme DNA hypomethylation on the 4qA DUX4 gene body as well as all analyzed DUX4 5' sequences. Importantly, our assay does not amplify the D4Z4 arrays with non-permissive B-type subtelomeres and accurately excludes the arrays with non-permissive A-type subtelomeres.


CONCLUSIONS
We have developed an assay to identify changes in DNA methylation on the pathogenic distal 4q D4Z4 repeat. We show that the DNA methylation profile of saliva reflects FSHD status. This assay can distinguish FSHD from healthy controls, differentiate FSHD1 from FSHD2, does not require HMW genomic DNA or PFGE, and can be performed on either cultured cells, tissue, blood, or saliva samples.
The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA.
Takako I
TI
Jones
The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Key Lab of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 P.R. China.
Chi
C
Yan
The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA.
Peter C
PC
Sapp
The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA.
Diane
D
McKenna-Yasek
Department of Pediatrics, Division of Pediatric Neurology, University of Florida College of Medicine, 1600 SW Archer Road, Gainesville, FL 32607 USA.
Peter B
PB
Kang
The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Department of Neurology, Hospital of the University of Pennsylvania, 3400 Spruce St, 3 Gates, Philadelphia, PA 19104 USA.
Colin
C
Quinn
The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA.
Johnny S
JS
Salameh
The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA.
Oliver D
OD
King
The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA.
Peter L
PL
Jones
Bisulfite sequencing; D4Z4; DNA methylation; DUX4; Disease diagnostics; Epigenetics; FSHD1; FSHD2; Facioscapulohumeral muscular dystrophy