Comprehensive expression profiling by muscle tissue class and identification of the molecular niche of extraocular muscle

• Published in: The FASEB journal 2003-07, Vol.17 (10), p.1370-1372
• Main Authors: Khanna, Sangeeta, Merriam, Anita P., Gong, Bendi, Leahy, Patrick, Porter, John D.
• Format: Article
• Language: English
• Subjects: Animals; cardiac muscle; DNA microarray; Eye - anatomy & histology; Gene Expression Profiling; Genetic Predisposition to Disease; Hindlimb - anatomy & histology; Muscle Proteins - genetics; Muscle Proteins - metabolism; Muscle, Skeletal - metabolism; Muscle, Smooth - metabolism; Muscular Diseases - genetics; Myocardium - metabolism; Oligonucleotide Array Sequence Analysis; Organ Specificity; proteomics; Rats; skeletal muscle; smooth muscle; Transcription, Genetic
• ISSN: 0892-6638; 1530-6860
• DOI: 10.1096/fj.02-1108fje

ABSTRACT Muscle tissue is an elegant model for biologic integration of structure with function and is frequently affected by a variety of inherited diseases. Traditional muscle classes‐‐skeletal, cardiac, and smooth‐‐share basic aspects of contractile and energetics mechanisms but also have distinctive role‐specific adaptations. We used large‐scale oligonucleotide microarrays to broaden knowledge of the adaptive expression patterns underlying muscle tissue differences and to identify transcript subsets that are most likely to represent candidate disease genes. Using stringent analysis criteria, we found ≥95 transcripts, which were preferentially expressed by each muscle class and were validated by inclusion of known muscle class‐specific and inherited disease‐related genes. Differentially expressed transcripts not previously identified as class‐specific extend understanding of muscle class transcriptomes and may represent novel muscle‐specific disease genes. We also analyzed the expression profile of extraocular muscle, which is divergent from other skeletal muscles, in the broader context of all major muscle classes. Data show that the extraocular muscle phenotype results from the combination of tissue‐specific transcripts, novel expression levels of skeletal muscle transcripts, and partial sharing of gene expression patterns with cardiac and smooth muscle. These, and additional proteomic data, establish that extraocular muscle does not constitute a distinctive muscle class but that it does occupy a novel niche within the skeletal muscle class.