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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles in muscle tissue from FSHD patients

ABSTRACT: Muscle biopsies from biceps and deltoid were taken from 5 patients with FSHD, 5 asymptomatic carriers and 5 normal controls. The genome-wide expression patterns were compared using Affymetrix U133 Plus 2.0 chips. Keywords: Facioscapulohumeral, FSHD, muscular dystrophy Gene expression profiles were generated for 15 individuals (5 affected patients, 5 asymptomatic carriers and 5 healthy controls)

ORGANISM(S): Homo sapiens

SUBMITTER: Alvin Kho

PROVIDER: E-GEOD-15090 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers.

Arashiro Patricia P Eisenberg Iris I Kho Alvin T AT Cerqueira Antonia M P AM Canovas Marta M Silva Helga C A HC Pavanello Rita C M RC Verjovski-Almeida Sergio S Kunkel Louis M LM Zatz Mayana M

Proceedings of the National Academy of Sciences of the United States of America 20090401 15

Facioscapulohumeral muscular dystrophy (FSHD) is a progressive muscle disorder that has been associated with a contraction of 3.3-kb repeats on chromosome 4q35. FSHD is characterized by a wide clinical inter- and intrafamilial variability, ranging from wheelchair-bound patients to asymptomatic carriers. Our study is unique in comparing the gene expression profiles from related affected, asymptomatic carrier, and control individuals. Our results suggest that the expression of genes on chromosome ...[more]

PMID: 19339494

Similar Datasets

Gene expression profiles in muscle tissue from FSHD patients

Project description:Muscle biopsies from biceps and deltoid were taken from 5 patients with FSHD, 5 asymptomatic carriers and 5 normal controls. The genome-wide expression patterns were compared using Affymetrix U133 Plus 2.0 chips. Keywords: Facioscapulohumeral, FSHD, muscular dystrophy

2009-03-04 | GSE15090 | GEO

Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers

Project description:Facioscapulohumeral muscular dystrophy (FSHD) is a progressive neuromuscular disorder caused by contractions of repetitive elements within the macrosatellite D4Z4 on chromosome 4q35. In order to develop mRNA-based biomarkers of affected muscles, we used GeneChip Gene 1.0 ST arrays for global analysis of gene expression in muscle biopsy specimens obtained from FSHD subjects and their unaffected first degree relatives. FSHD typically affects biceps muscles more severely than deltoid muscles. To examine muscle-specific expression changes associated with FSHD while controlling for background genetic variation, we analyzed RNA extracted from both biceps and deltoids of FSHD subjects and unaffected first-degree relatives.

2012-09-19 | E-GEOD-36398 | biostudies-arrayexpress

Transcription profiling of human Facioscapulohumeral muscular dystrophy (FSHD) muscle profiles

Project description:Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant disorder linked to contractions of the D4Z4 repeat array in the subtelomeric region of chromosome 4q. By comparing genome-wide gene expression data from muscle biopsies of patients with FSHD to those of 11 other neuromuscular disorders, we intend to identify disease-specific changes which are more likely to be involved in the early stages of the disease progression. The data will help to identify pathological mechanisms involved in FSHD. Experiment Overall Design: Comparison of the profiles of FSHD to 13 other conditions for disease-specific changes. The 13 conditions are NHM (Normal healthy muscle) n=15; JDM (Juvenile dermatomyositis) n=25; HSP (Human spastic paraplegia) n=4; FSHD (facioscapulohumeral dystrophy) unaffected n=5, affected n=9; FKRP (Fukutin related protein deficiency) n=7; ED-L (Emery-Dreifuss muscular dystrophy, lamin A/C deficiency) n=4; ED-E (Emery-Dreifuss muscular dystrophy, emerin deficiency) n=4; DYSF (dysferlinopathy) n=10; DMD (Duchenne Muscular Dystrophy) n=10; CALP (Calpain-3 deficiency) n=10; BMD (Becker Muscular Dystrophy) n=5; AQM (Acute quadriplegic myopathy) n=5; ALS (Amyotrophic lateral sclerosis) n=9.

2008-06-16 | E-GEOD-9397 | biostudies-arrayexpress

FSHD Muscle Profiles

2007-10-23 | GSE9397 | GEO

D2O proteome dynamics in FSHD vs UASb myoblasts

Project description:Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight to disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; D2O) labelling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from 2 individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4483 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of ‘older’ less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.

2023-06-27 | PXD038818 | Pride

MOE silencing of DUX4 in FSHD and UASB myoblasts

2023-06-27 | PXD042374 | Pride

DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle

Project description:Facioscapulohumeral dystrophy (FSHD) is caused by decreased epigenetic repression of the D4Z4 macrosatellite array and recent studies have shown that this results in the expression of low levels of the DUX4 mRNA in skeletal muscle. Several other mechanisms have been suggested for FSHD pathophysiology and it remains unknown whether DUX4 expression can account for most of the molecular changes seen in FSHD. Since DUX4 is a transcription factor, we used RNA-seq to measure gene expression in muscle cells transduced with DUX4, and in muscle cells and biopsies from control and FSHD individuals. We show that DUX4 target gene expression is the major molecular signature in FSHD muscle together with a gene expression signature consistent with an immune cell infiltration. In addition, one unaffected individual without a known FSHD-causing mutation showed expression of DUX4 target genes. This individual has a sibling with FSHD and also without a known FSHD-causing mutation, suggesting the presence of yet unidentified modifier locus for DUX4 expression and FSHD. These findings demonstrate that expression of DUX4 accounts for the majority of the gene expression changes in FSHD skeletal muscle together with an immune cell infiltration. RNA-seq for muscle cells and biopsies from control and FSHD individuals.

2014-07-03 | E-GEOD-56787 | biostudies-arrayexpress

Correction of the FSHD myoblast differentiation defect by fusion with healthy myoblasts

Project description:Facioscapulohumeral dystrophy (FSHD) is a neuromuscular disease characterized by progressive asymmetric muscle weakness. Myoblasts isolated from FSHD muscles exhibit morphological differentiation defects and show a distinct transcription profile. These abnormalities may be linked to the muscle weakness in FSHD patients. Here, we have tested whether fusion of FSHD myoblasts (obtained from 2 patients) with primary myoblasts isolated from 2 healthy individuals could correct the differentiation defects. Our results show that the number of hybrid myotubes with normal phenotype increased with the percentage of normal myoblasts initially cultured. We demonstrated that a minimum of 50% of normal nuclei is required for a phenotypic correction of the FSHD phenotype. To test the correction on the functional level we analyzed transcriptomic profiles of phenotypically corrected hybrid myotubes. These myotubes were cultured in DMEM with 10% FBS. The present study concerns gene expression of FSHD, normal and hybrid myotubes after RNA extraction (TriPrep NucleoSpin ® kit) according to manufacturer’s instructions. Gene expression was performed in single color on Agilent 8x60K Human whole genome (design 039494) minimum in duplicates in each condition. Transcriptomic profiles of phenotypically corrected hybrid myotubes showed that the expression of deregulated genes in FSHD myotubes became almost normal. We thus propose that while phenotypical and functional correction of FSHD is feasible, it requires more than 50% of normal myoblasts, it creates limitations for cell therapy in the FSHD context.

2015-08-17 | E-MTAB-3658 | biostudies-arrayexpress

Rbfox1 downregulation and altered Calpain 3 splicing by FRG1 in a mouse model of facioscapulohumeral muscular dystrophy (FSHD).

Project description:FRG1 over-expression results in an FSHD-like phenotype in mice. Muscles (vastus lateralis and biceps brachii) from wild type and FRG1 over-expressing mice were compared at 4 and 13 weeks of age by splicing sensitive microarray.

2012-12-01 | GSE32073 | GEO

Rbfox1 downregulation and altered Calpain 3 splicing by FRG1 in a mouse model of facioscapulohumeral muscular dystrophy (FSHD).

2012-12-01 | E-GEOD-32073 | biostudies-arrayexpress