title: Gene co-expression network analysis of dysferlinopathy: Altered cellular processes and functional prediction of TOR1AIP1, a novel muscular dystrophy gene.
abstract: Dysferlinopathy, caused by a dysferlin gene mutation, is a clinically heterogeneous autosomal recessive muscle disease characterized by progressive muscle degeneration. The dysferlin protein's functions and dysferlinopathy disease pathogenesis are not fully explored, and there is no specific treatment available that can alter the disease progression. This study uses publicly available dysferlinopathy patient microarray data to construct a gene co-expression network and investigates significant cellular pathways and their key players in dysferlinopathy pathogenesis. Extracellular matrix deposition, inflammation, mitochondrial abnormalities and protein degradation were found to be important in dysferlinopathy. Out of the hub genes, OXR1 and TIMP1 were selected through literature search as candidate genes for possible biomarker and molecular therapeutic target studies. A recently identified muscular dystrophy gene TOR1AIP1 was detected as a hub gene in dysferlinopathy. Co-expression and protein sequence feature analysis were adopted to predict TOR1AIP1's function. Our results suggest that LAP1 protein encoded by TOR1AIP1 may play a role in protein degradation possibly through transcriptional regulation in muscle tissue. These findings extend dysferlinopathy pathogenesis by presenting key genes and also suggest a novel function for a poorly characterized gene.
authors.affiliation: Department of Medical Biology, Faculty of Medicine, Hacettepe University, Sihhiye, 06100, Ankara, Turkey. Electronic address: ayseececalidaylan@gmail.com.
authors.forename: Ayse Ece
authors.initials: AE
authors.lastname: Cali-Daylan
authors.affiliation: Department of Medical Biology, Faculty of Medicine, Hacettepe University, Sihhiye, 06100, Ankara, Turkey.
authors.forename: Pervin
authors.initials: P
authors.lastname: Dincer
mesh_terms: D000073939:Dysferlin / Q000235:genetics*; D015870:Gene Expression / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D050883:HSC70 Heat-Shock Proteins / Q000235:genetics*; D006801:Humans; D018832:Molecular Chaperones / Q000235:genetics*; D049288:Muscular Dystrophies, Limb-Girdle / Q000235:genetics*
chemical_list: C114839:DYSF protein, human; D000073939:Dysferlin; D050883:HSC70 Heat-Shock Proteins; C494371:HSPA8 protein, human; D018832:Molecular Chaperones; C108175:TOR1A protein, human
keywords: Co-expression; Dysferlin; Muscle dystrophy; TOR1AIP1