Simultaneous measurement of the size and methylation of chromosome 4qA-D4Z4 repeats in facioscapulohumeral muscular dystrophy by long-read sequencing

• DOI: 10.1186/s12967-022-03743-7
• Publication Date: 2022-11-08T22:03:01Z
• Authors: Yosuke Hiramuki; Yuriko Kure; Yoshihiko Saito; Megumu Ogawa; Keiko Ishikawa; Madoka Mori-Yoshi...; Yasushi Oya; Yuji Takahashi; Dae-Seong Kim; Noriko Arai; Chiaki Mori; Tsuyoshi Matsumura; Tadanori Hamano; Kenichiro Nakamura; Koji Ikezoe; Shinichiro Hayashi; Yuichi Goto; Satoru Noguchi; Ichizo Nishino
• Keywords: Homeodomain Proteins; 0301 basic medicine; D4Z4; DUX4; Chromosomal Proteins, Non-Histone; Research; R; DNA Methylation; Muscular Dystrophy, Facioscapulohumeral; Chromosomes; 03 medical and health sciences; Facioscapulohumeral muscular dystrophy; Nanopore sequencer; CpG methylation; Medicine; Humans; CRISPR/Cas9

Abstract Background Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant muscular disorder characterized by asymmetric muscle wasting and weakness. FSHD can be subdivided into two types: FSHD1, caused by contraction of the D4Z4 repeat on chromosome 4q35, and FSHD2, caused by mild contraction of the D4Z4 repeat plus aberrant hypomethylation mediated by genetic variants in SMCHD1, DNMT3B, or LRIF1. Genetic diagnosis of FSHD is challenging because of the complex procedures required.

Methods We applied Nanopore CRISPR/Cas9-targeted resequencing for the diagnosis of FSHD by simultaneous detection of D4Z4 repeat length and methylation status at nucleotide level in genetically-confirmed and suspected patients.

Results We found significant hypomethylation of contracted 4q-D4Z4 repeats in FSHD1, and both 4q- and 10q-D4Z4 repeats in FSHD2. We also found that the hypomethylation in the contracted D4Z4 in FSHD1 is moderately correlated with patient phenotypes.

Conclusions Our method contributes to the development for the diagnosis of FSHD using Nanopore long-read sequencing. This finding might give insight into the mechanisms by which repeat contraction causes disease pathogenesis.