Identification of an Alu element‐mediated deletion in the promoter region of GNE in siblings with GNE myopathy

Abstract

Background GNE myopathy is a rare genetic disease characterized by progressive muscle atrophy and weakness. It is caused by biallelic mutations in the GNE gene that encodes for the bifunctional enzyme, uridine diphosphate (UDP)‐N‐acetylglucosamine (GlcNAc) 2‐epimerase/N‐acetylmannosamine (ManNAc) kinase. Typical characteristics of GNE myopathy include progressive myopathy, first involving anterior tibialis muscle and sparing the quadriceps, and rimmed vacuoles on muscle biopsy. Identifying biallelic mutations by sequencing of the GNE gene confirms the diagnosis of GNE myopathy. In a subset of patients, diagnostic confirmation is challenged by the identification of mutations in only one allele, suggesting mutations in deep intronic regions or regulatory regions.MethodsWe performed targeted sequencing and copy number variant (CNV) analysis of GNE in two siblings who clinically presented with GNE myopathy. Further molecular and biochemical studies were done to characterize the effect of a previously uncharacterized GNE mutation.ResultsWe report two siblings of Indian descent with characteristic features of GNE myopathy, including progressive skeletal muscle weakness initially involving the anterior tibialis, and rimmed vacuoles on muscle biopsy, in which a heterozygous mutation, p.Val727Met, was identified in both affected siblings, but no other deleterious variants in either coding region or exon–intron boundaries of the gene. Subsequent insertion/deletion analysis identified a novel 11.3‐kb deletion (Chr9 [GRCh37]: g.36257583_36268910del) encompassing the GNE promoter region, with breakpoints residing in Alu repeats. Gene expression analysis revealed reduced GNE mRNA and protein levels, confirming decreased expression of the deleted allele harboring the deletion.ConclusionsWe have identified GNE as one of the genes susceptible to Alu‐mediated recombination. Our findings suggest that the deletion may encompass the promoter or another region necessary for GNE expression. In patients with typical manifestations of GNE myopathy and a single GNE variant identified, copy number variant (CNV) analysis may be useful in arriving at the diagnosis.

Clinical utility of RNA sequencing to resolve unusual GNE myopathy with a novel promoter deletion

“…The second causal variant was inferred from the combination of aCGH and RNA-seq that definitively diagnosed the case as GNE-related myopathy, and led to identification of multiple gene expression perturbations. This study shows the involvement of quadriceps muscle directly with both rimmed vacuoles and inflammation, unlike previous reports of individual cases and cohorts, 22,23,26,27 enhancing the molecular-pathological spectrum of GNE-myopathy that is important to understand for patient stratification in clinical trials.…”

“…Recently, a~11.3-kb deletion encompassing exon 2 was found in a patient along with a single V727M variant. 22 In our study, aCGH revealed a novel 7.08 kb deletion (g.36,259,402 to g.36,266,483) (SCV000599234) upstream of the GNE gene (different from deletions identified in Zhu et al 23 ) (Fig. 2B).…”

“…Previously, Zhu et al showed that large promoter region deletions in GNE are common in already clinically diagnosed GNE‐myopathy patients, and Garland et al showed that a combination of such deletions and a V727M missense variant causes a more severe reduction in GNE expression than the combination of V727M and another missense variant. Here, we show that such variant combinations are associated with unique GNE‐related myopathy pathology and the clinical/molecular diagnostic hurdles faced.…”

“…Generally, inflammation is not associated with HIBM, in which quadriceps muscles are relatively spared of any rimmed vacuolar pathology compared with other muscle types, as seen in studies of smaller numbers of individuals with inclusion-body myositis (IBM) 22 and in larger study cohorts. 25 The presence of both inflammation and rimmed vacuoles in the quadriceps muscle of this patient is not characteristic of either primary inflammatory or rimmed vacuolar myopathies.…”

GNE Myopathy: Etiology, Diagnosis, and Therapeutic Challenges

“…There are ethnic GNE founder mutations found in Middle Eastern (Met743Thr), Japanese (Cys44Ser, Asp207Val, and Val603Leu), Roma Bulgarian (Ile618Thr) and Indian/Asian (Val727Met) populations ( Table 1). Besides founder mutations, there are more than 200 GNE gene mutations reported in over 950 GNE myopathy patients worldwide, in either the epimerase or the kinase encoding domains of the enzyme [20,31,76,77], several proven to result in decreased enzyme activity [31,33,57]. Most pathogenic mutations that cause GNE myopathy are missense, but nonsense mutations, insertion/deletions, and intronic (splice site) variants have also been described [76,77].…”