A web-accessible complete transcriptome of normal human and DMD muscle.
We present an assessment of the complete transcriptome of human skeletal muscle in Duchenne muscular dystrophy patient muscle and non-dystrophic controls (36 RNAs analyzed from ten Duchenne dystrophy and eight controls; approximately 65,000 gene/expressed sequence tag/probe sets queried on U95 five-GeneChip series and MuscleChip). The use of the multiple chip types allowed us to compare results from different probe sets for the same gene: we found excellent concordance between different probe sets on different microarrays. We found 30% of human genes expressed in muscle at detectable levels. Three percent of these showed differential regulation in dystrophin deficiency. Among 1,882 dysregulated probe sets, 1,324 corresponded to characterized genes/proteins (891 non-redundant transcript units), and 588 to expressed sequence tags or predicted genes. Data interpretation was limited to the insulin-like growth factor pathway members, an investigation of possible de-regulation towards a cardiac lineage, and identification of male- and female-specific transcripts. We found transcriptional upregulation of both IGF-I and IGF-II in dystrophic muscle, however the possible beneficial effects of the growth factors appear offset by transcriptional upregulation of inhibitory IGF-binding proteins and regulators (IGFBP-2, -4, -6 and -7; and PRSS11 [IGFBP-5 protease]). We hypothesize that the beneficial effects of IGF-I or IGF-II supplementation in dystrophic muscle may be the result of dose-dependent sequestration of inhibitory IGF-binding proteins. We also focused on six 'cardiac' genes expressed in muscle (alpha-cardiac actin, CARP, CASQ2, troponin T2 cardiac [TNNT2], CUGBP2, and connexin 43). Comparison to a 27 time point murine muscle regeneration series and mdx muscle profiles showed that CARP and Cx43 were macrophage-associated, and TNNT2 activated-myoblast-associated. Upregulation of cardiac actin and CUGBP2 was not associated with muscle regeneration profiles, suggesting a more specific dysregulation induced by dystrophin deficiency. We found two Y-linked genes expressed solely in male muscle (RPS4Y, DDX3Y), and two autosomal genes expressed much more highly in female muscle (GRO2, ZNF91) (all comparisons P<0.01). Finally, we present the first web-accessible expression profiling database for all data, including image files (.dat), processed image files (.cel), and complete comparison files which are publicly available through a novel queriable web site, that permits query-by-gene across all profiles (http://microarray.cnmcresearch.org/pga). These data enumerate the full range of molecular changes associated downstream of dystrophin deficiency, and provide a web-accessible platform to study the specificity of transcriptional pathway alterations in muscle disease.
Bakay
Marina
M
Research Center for Genetic Medicine, George Washington University School of Medicine, Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010, USA.
Zhao
Po
P
Chen
Josephine
J
Hoffman
Eric P
EP
D000818:Animals; D001706:Biopsy; D002648:Child; D002675:Child, Preschool; D016189:Dystrophin / Q000172:deficiency / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D018969:Insulin-Like Growth Factor Binding Proteins / Q000378:metabolism; D007334:Insulin-Like Growth Factor I / Q000378:metabolism; D007335:Insulin-Like Growth Factor II / Q000378:metabolism; D051379:Mice; D018101:Mice, Inbred mdx; D018482:Muscle, Skeletal / Q000378:metabolism; D009132:Muscles / Q000378:metabolism*; D009137:Muscular Dystrophy, Animal / Q000235:genetics* / Q000378:metabolism; D020388:Muscular Dystrophy, Duchenne / Q000235:genetics* / Q000378:metabolism; D009206:Myocardium / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D015347:RNA Probes; D014158:Transcription, Genetic; D015854:Up-Regulation
D016189:Dystrophin; D018969:Insulin-Like Growth Factor Binding Proteins; D015347:RNA Probes; D007334:Insulin-Like Growth Factor I; D007335:Insulin-Like Growth Factor II