Genomics

Dataset Information

42

Comparative gene expression profiling between cultured and tissue human skeletal muscle


ABSTRACT: Culturing myotubes from skeletal muscle (SM) biopsies enables investigating transcriptional defects and assaying therapeutic strategies. This study compares the transcriptome of aneurally cultured human SM cells versus that of tissue biopsies. We determined the transcriptomic differences between tissue and cultured SM samples from five individuals. In cultured myotubes compared to the tissue, 1216 genes were regulated: 583 down and 633 up. Downregulated genes were mainly associated with cytoplasm, particularly mitochondria, and involved in metabolism and the muscle-system/contraction process. Upregulated genes were predominantly related to cytoplasm, endoplasmic reticulum, and extracellular matrix. The most significantly regulated pathway was mitochondrial dysfunction. Apoptosis genes were also modulated. Among the most downregulated genes were genes encoding metabolic proteins AMPD1, PYGM, CPT1B and UCP3, muscle-system proteins TMOD4, MYBPC1, MYOZ1 and XIRP2, the proteolytic CAPN3 and the myogenic regulator MYF6. Within the most upregulated group were genes encoding senescence/apoptosis-related proteins CDKN1A and KIAA1199 and potential regulatory factors HIF1A, TOP2A and CCDC80. In conclusion, cultured muscle cells display reductive metabolic and muscle-system transcriptome adaptations as observed in muscle atrophy and they activate tissue-remodeling and senescence/apoptosis processes. Novel candidate regulators in SM dysfunction are revealed Overall design: 5 biopsies, 5 cell cultures obtained from the biopsies, paired samples. The supplementary file 'GSE17503_non-normalized_data.txt' contains non-normalized data for Samples GSM436162, GSM436164, and GSM436432-GSM436439.

INSTRUMENT(S): Illumina humanRef-8 v2.0 expression beadchip

ORGANISM(S): Homo Sapiens

SUBMITTER: Frederic Raymond  

PROVIDER: GSE17503 | GEO | 2010-02-22

SECONDARY ACCESSION(S): PRJNA118915

REPOSITORIES: GEO

Dataset's files

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GSE17503_RAW.tar Raw
GSE17503_non-normalized_data.txt.gz Txt
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Publications

Comparative gene expression profiling between human cultured myotubes and skeletal muscle tissue.

Raymond Frederic F   Métairon Sylviane S   Kussmann Martin M   Colomer Jaume J   Nascimento Andres A   Mormeneo Emma E   García-Martínez Cèlia C   Gómez-Foix Anna M AM  

BMC genomics 20100222


<h4>Background</h4>A high-sensitivity DNA microarray platform requiring nanograms of RNA input facilitates the application of transcriptome analysis to individual skeletal muscle (SM) tissue samples. Culturing myotubes from SM-biopsies enables investigating transcriptional defects and assaying therapeutic strategies. This study compares the transcriptome of aneurally cultured human SM cells versus that of tissue biopsies.<h4>Results</h4>We used the Illumina expression BeadChips to determine the  ...[more]

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