A Novel Start Codon Variant in SMCHD1 from a Chinese Family Causes Facioscapulohumeral Muscular Dystrophy Type 2
Facioscapulohumeral muscular dystrophy type 2 (FSHD2) is an epigenetic myopathy characterized by progressive muscle weakness in specific body regions, including the face, shoulder girdle, and upper limbs. The condition is caused by variants in genes encoding chromatin regulators, such as SMCHD1, which lead to the derepression of the D4Z4-encoded DUX4 retrogene in skeletal muscle. While FSHD2 has been associated with causative variants in SMCHD1 in various populations, no cases have been reported in Chinese patients until now. This study presents the first Chinese FSHD2 family with D4Z4 hypomethylation and identifies a novel start codon variant (c.1 A>G) in SMCHD1.
The study involved four patients from a single family. The proband (II.3) was a 47-year-old man initially diagnosed with ankylosing spondylitis (AS) due to muscle weakness in the bilateral upper limbs and lower back pain at the age of 26. By 36, he developed marked muscle dystrophy, exercise intolerance, and a stooped posture. Upon reevaluation, the diagnosis of AS was reconsidered due to normal HLA-B27 and sacroiliac joint X-ray results. Physical examination revealed core signs of FSHD, including facial muscle weakness and left-right asymmetry of scapular winging. The patient also exhibited a “bent spine,” classifying him as category D1 according to the clinical comprehensive evaluation form (CCEF) with an FSHD clinical score (CS) of 7 points. Electromyography (EMG) showed typical myopathic changes and slight spontaneous activity. Muscle 3.0-T magnetic resonance imaging (MRI) revealed atrophy and mild fatty infiltration. A muscular biopsy at 34 showed mild dystrophic changes with mild-moderate variation in fiber size, perivascular lymphocyte infiltrates, and interstitial fibrosis.
The proband’s mother (I.2) had facial and bilateral upper limb muscle weakness but committed suicide in her 50s, leaving limited clinical data. The proband’s half-sister (II.6), aged 42, also exhibited core FSHD signs, including facial muscle weakness and scapular winging. She was classified as category A2 of the CCEF with an FSHD CS of 8 points. EMG results showed typical myopathic changes, and muscle MRI revealed severe atrophy and moderate fatty infiltration. Her recent histopathology showed an end-stage appearance with marked variation in fiber size, endomysial fibrosis, and endomysial adipose tissue infiltration. Additionally, she developed impaired vision in her left eye at 42, diagnosed as acute optic neuritis after excluding retinal exudative retinopathy.
Both of patient II.6’s sons (III.4 and III.5) were also affected by FSHD. The older son (III.4), aged 18, presented mild facial muscle weakness and clavicular flattening without limitation of upper limb muscle abduction, classified as category B2 with an FSHD CS of 1 point. The younger son (III.5), aged 7, showed mild scapular winging at rest without facial muscle impairment, classified as category B1 with an FSHD CS of 1 point. Creatine kinase levels were elevated two-fold in III.5.
Southern blotting analysis revealed that the proband (II.3) had two D4Z4 arrays on chromosome 4q: one with 11 units (41 kb) and the 4A161PAS haplotype, and another with >10 units and the 4B163 haplotype. This array was also detected in his asymptomatic biological sisters (II.1 and II.2) and symptomatic half-sister (II.6), suggesting inheritance from their mother (I.2). The array was transmitted from patient II.6 to her two symptomatic sons (III.4 and III.5). The proband’s daughter (III.2) was asymptomatic, carrying two 4q D4Z4 arrays, both >10 units with the 4B163 haplotype.
D4Z4 methylation levels in five family members (II.3, II.6, III.2, III.4, and III.5) were at least 2 SD below the average levels in both the DR1 (52 ± 8%) and polyadenylation signal (PAS) (64 ± 7%) regions in the general population. Nearly complete hypomethylation was observed in FSHD1 and FSHD2 patients compared to normal controls, with no significant difference between FSHD1 and FSHD2 patients.
A novel heterozygous variant (c.1 A>G) in SMCHD1 was identified in the five family members with D4Z4 hypomethylation. This variant was absent in 500 non-FSHD controls and had not been previously reported. According to guidelines for interpreting sequence variants, the c.1 A>G variant in SMCHD1 was considered a loss-of-function mutation, providing strong evidence for pathogenicity. Cosegregation analysis indicated that the novel SMCHD1 variant was initially inherited from the patient I.2, along with the D4Z4 array of 11 units with the 4qA haplotype.
The mRNA level of SMCHD1 was decreased in peripheral blood leukocytes (PBLs) from the three variant carriers (II.3, II.6, and III.2) and in fibroblasts from II.3 compared to normal controls. Protein expression levels of SMCHD1 were also decreased in fibroblasts from II.3 and muscle tissue from II.6. DUX4 mRNA levels were increased in PBLs from II.3, II.6, and III.2, as well as in muscle tissue from II.6. The DUX4 transcript of NM_001306068.3 was detected in patient II.6, and the 4A161L haplotype was relatively highly expressed in muscle tissue. These findings suggest that the defective expression of DUX4 may result from the loss of function of the novel SMCHD1 variant.
The proband (II.3) exhibited atypical features, including initial lower back pain and a “bent spine,” which are inconsistent with the core phenotypes of FSHD. Pain has been reported in other FSHD studies, and the “bent spine” classified the proband as category D1 according to CCEF. These results highlight the need for genetic analysis and follow-up in individuals with minor or atypical FSHD signs to evaluate disease onset and expression risks.
Patient II.6 exhibited unexplained acute optic neuritis, which may or may not be related to FSHD. Pathogenic SMCHD1 variants have been reported in Bosma arhinia microphthalmia syndrome, which presents severe hypoplasia or absence of the external nose, but there are no reports of acute optic neuritis in FSHD or SMCHD1 variant carriers. Thus, acute optic neuritis in patient II.6 may be coincidental and not attributable to FSHD2.
Muscle MRI of patients II.3 and II.6 demonstrated imaging changes consistent with asymmetric atrophy, with fat infiltration in II.6’s MRI consistent with her histology. Muscle MRI may be useful for selecting a muscle for biopsy and could be used in FSHD longitudinal studies due to its non-invasive, pain-free nature and lack of age or disease severity limitations.
The digenic inheritance pattern has been reported to explain the causal mechanism of FSHD2, involving putative dominant-negative SMCHD1 mutations and haploinsufficiency mutations. In this FSHD2 family, the c.1 A>G variant on the start codon of SMCHD1 led to decreased SMCHD1 expression and subsequently increased DUX4 expression. Combined with D4Z4 hypomethylation, these findings provide evidence for a haploinsufficiency mechanism in FSHD2.
This study is the first to identify four FSHD2 patients from a Chinese family based on strict criteria: a novel heterozygous variant (c.1 A>G) in the start codon of the SMCHD1 gene cosegregating with D4Z4 hypomethylation and an intermediate size for the D4Z4 array of 11 units on the 4qA chromosome.
doi.org/10.1097/CM9.0000000000001425
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