A multistage sequencing strategy pinpoints novel candidate alleles for Emery-Dreifuss muscular dystrophy and supports gene misregulation as its pathomechanism

Abstract

Background: As genome-wide approaches prove difficult with genetically heterogeneous orphan diseases, we developed a new approach to identify candidate genes. We applied this to Emery-Dreifuss muscular dystrophy (EDMD), characterised by early onset contractures, slowly progressive muscular wasting, and life-threatening heart conduction disturbances with wide intra-and inter-familial clinical variability. Roughly half of EDMD patients are linked to six genes encoding nuclear envelope proteins, but the disease mechanism remains unclear because the affected proteins function in both cell mechanics and genome regulation. Methods: A primer library was generated to test for mutations in 301 genes from four categories: (I) all known EDMD-linked genes; (II) genes mutated in related muscular dystrophies; (III) candidates generated by exome sequencing in five families; (IV) functional candidatesother muscle nuclear envelope proteins functioning in mechanical/genome processes affected in EDMD. This was used to sequence 56 unlinked patients with EDMD-like phenotype. Findings: Twenty-one patients could be clearly assigned: 18 with mutations in genes of similar muscular dystrophies; 3 with previously missed mutations in EDMD-linked genes. The other categories yielded novel candidate genes, most encoding nuclear envelope proteins with functions in gene regulation. Interpretation: Our multi-pronged approach identified new disease alleles and many new candidate EDMD genes. Their known functions strongly argue the EDMD pathomechanism is from altered gene regulation and mechanotransduction due to connectivity of candidates from the nuclear envelope to the plasma membrane. This approach highlights the value of testing for related diseases using primer libraries and may be applied for other genetically heterogeneous orphan diseases. Funding: The Wellcome Trust, Muscular Dystrophy UK, Medical Research Council, European Community's Seventh Framework Programme "Integrated European Àomics research project for diagnosis and therapy in rare neuromuscular and neurodegenerative diseases (NEUROMICS)".

The Molecular Basis and Biologic Significance of the β-Dystroglycan-Emerin Interaction

“…Furthermore, B-lymphocyte cell cultures derived from a patient with EDMD showed decreased protein level of β-DG. We speculate that deficiency of β-DG may lead by itself to some of the observed EDMD phenotype, as over 60% of EDMD patients remain to be associated with a genetic defect [ 35 ].…”

Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs

“…According to the way we modeled the effects and selected the top genes identified were the genes that had most significant interactions effects with other genes in relation to changes in FCR. From the top 20 genes ( Supplementary Data 3), the most interesting genes based on previous literature and function were: several transcription regulators: ETV1 (an androgen receptor activated gene), LF1 (transcription factor) and KDM4C (transcription activator and growth related gene) (Bray and Kafatos, 1991;Cai et al, 2007;Gregory and Cheung, 2014); two mitochondrial genes, KMO and MRPS11 (Meinke et al, 2019); two genes related to muscular atrophy -GEMIN7 and PLPP7 (Baccon et al, 2002;Meinke et al, 2019); one gene implicated in heart development BIN1 (Nicot et al, 2007), two lipid metabolism/obesity related genes ACOT11 and GPD1 (Adams et al, 2001;Park et al, 2006); and finally 3 genes associated with specific traits in pig IL2RG (Immune system in pigs) (Suzuki et al, 2012), GGPS1 (meat quality) and PPARA (weak association with fat percentage) (Szczerbal et al, 2007). Interestingly, MRPS11 was also differentially expressed in the DEA.…”

An Omics View of Emery–Dreifuss Muscular Dystrophy

“…Full exome sequencing is routinely used in clinical diagnostic laboratories to identify pathogenic variants in a given patient at a reasonable cost [ 17 , 18 , 19 , 20 ]. A new next-generation sequencing approach to identify potential new candidate EDMD genes has also recently been tested [ 21 ].…”