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.
Research Center for Genetic Medicine, George Washington University School of Medicine, Children's National Medical Center, 111 Michigan Avenue NW, Washington, DC 20010, USA.
Marina
M
Bakay
Po
P
Zhao
Josephine
J
Chen
Eric P
EP
Hoffman
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