Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle

Sanoudou, Despina; Haslett, Judith N.; Kho, Alvin T.; Guo, Shaoqiang; Gazda, Hanna T.; Greenberg, Steven A.; Lidov, Hart G.W.; Kohane, Isaac S.; Kunkel, Louis M.; Beggs, Alan H.

doi:10.1073/pnas.0330960100

Cited by 68 publications

(65 citation statements)

References 48 publications

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“…Gene expression profiling of human and mouse normal and diseased skeletal muscle has generated more detailed insight in the molecular process underlying the different conditions (10)(11)(12)(13)(14). However, although each of these studies has identified a number of genes in various functional categories that are differentially expressed in the disease states, the substantial underlying disease mechanisms remain to be elucidated.…”

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confidence: 99%

Distinctive patterns of microRNA expression in primary muscular disorders

Eisenberg

Eran

Nishino

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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The primary muscle disorders are a diverse group of diseases caused by various defective structural proteins, abnormal signaling molecules, enzymes and proteins involved in posttranslational modifications, and other mechanisms. Although there is increasing clarification of the primary aberrant cellular processes responsible for these conditions, the decisive factors involved in the secondary pathogenic cascades are still mainly obscure. Given the emerging roles of microRNAs (miRNAs) in modulation of cellular phenotypes, we searched for miRNAs regulated during the degenerative process of muscle to gain insight into the specific regulation of genes that are disrupted in pathological muscle conditions. We describe 185 miRNAs that are up- or down-regulated in 10 major muscular disorders in humans [Duchenne muscular dystrophy (DMD), Becker muscular dystrophy, facioscapulohumeral muscular dystrophy, limb-girdle muscular dystrophies types 2A and 2B, Miyoshi myopathy, nemaline myopathy, polymyositis, dermatomyositis, and inclusion body myositis]. Although five miRNAs were found to be consistently regulated in almost all samples analyzed, pointing to possible involvement of a common regulatory mechanism, others were dysregulated only in one disease and not at all in the other disorders. Functional correlation between the predicted targets of these miRNAs and mRNA expression demonstrated tight posttranscriptional regulation at the mRNA level in DMD and Miyoshi myopathy. Together with direct mRNA–miRNA predicted interactions demonstrated in DMD, some of which are involved in known secondary response functions and others that are involved in muscle regeneration, these findings suggest an important role of miRNAs in specific physiological pathways underlying the disease pathology.

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confidence: 99%

Distinctive patterns of microRNA expression in primary muscular disorders

Eisenberg

Eran

Nishino

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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460

518

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“…RNA from placental villous samples (P), and from infantile hemangioma samples (H), RNA target preparation, and hybridization to U95Av2 (12,626 probe sets) GeneChip oligonucleotide microarrays (Affymetrix) were performed as described in ref. 25.…”

Section: Methodsmentioning

confidence: 99%

“…P, H, normal skeletal muscle (N) (25), and brain (B) (26) expression profiles were performed in the microarray facility at Children's Hospital and scaled to a target intensity of 1,500 (MICROARRAY SUITE 5.0, Affymetrix). Normal (L) and cancerous lung data (Sq, SmC, and Car) were obtained from ref.…”

Section: Methodsmentioning

confidence: 99%

Evidence by molecular profiling for a placental origin of infantile hemangioma

Barnes

Huang

Kaipainen

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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The origin of the pathogenic endothelial cells in common infantile hemangioma is unknown. We show here that the transcriptomes of human placenta and infantile hemangioma are sufficiently similar to suggest a placental origin for this tumor, expanding on recent immunophenotypical studies that have suggested this possibility [North, P. E., et al. (2001) Arch. Dermatol. 137, 559 -570]. The transcriptomes of placenta, hemangioma, and eight normal and diseased tissues were compared by hierarchical and nonhierarchical clustering analysis of >7,800 genes. We found that the level of transcriptome similarity between placenta and hemangioma exceeded that of any other tissue compared and paralleled that observed between a given tissue and its derived tumor, such as normal and cancerous lung. The degree of similarity was even greater when a subset of endothelial cell-specific genes was analyzed. Genes preferentially expressed in both placenta and hemangiomas were identified, including 17-␤ hydroxysteroid dehydrogenase type 2 and tissue factor pathway inhibitor 2. These data demonstrate the value of global molecular profiling of tissues as a tool for hypothesis-driven research. Furthermore, it suggests that the unique self-limited growth of infantile hemangioma may, in fact, mirror the lifetime of placental endothelium.angiogenesis ͉ endothelium ͉ microarray ͉ gene array

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“…Several microarray-based studies of gene expression in normal and diseased states have been performed on human skeletal muscles obtained at biopsy or autopsy (1,8,20,21,33) and on murine skeletal muscle obtained immediately postmortem (30,32,37,40). These studies identified a number of genes in various functional categories that are differentially expressed in the disease states, suggesting that major alterations in tissue have far-reaching consequences for gene expression.…”

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confidence: 99%

Transcriptional profile of postmortem skeletal muscle

Sanoudou

Kang

Haslett

et al. 2004

Physiological Genomics

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Autopsy specimens are often used in molecular biological studies of disease pathophysiology. However, few analyses have focused specifically on postmortem changes in skeletal muscles, and almost all of those investigate protein or metabolic changes. Although some structural and enzymatic changes have been described, the sequence of transcriptional events associated with these remains unclear. We analyzed a series of new and preexisting human skeletal muscle data sets on ≃12,500 genes and expressed sequence tags (ESTs) generated by the Affymetrix U95Av2 GeneChips from seven autopsy and seven surgical specimens. Remarkably, postmortem specimens (up to 46 h) revealed a significant and prominent upregulation of transcripts involved with protein biosynthesis. Additional upregulated transcripts are associated with cellular responses to oxidative stress, hypoxia, and ischemia; however, only a subset of genes in these pathways was affected. Overexpression was also seen for apoptosis-related, cell cycle regulation/arrest-related, and signal transduction-related genes. No major gene expression differences were seen between autopsy specimens with <20-h and 34- to 46-h postmortem intervals or between pediatric and adult cases. These data demonstrate that, likely in response to hypoxia and oxidative stress, skeletal muscle undergoes a highly active transcriptional, and possibly, translational phase during the initial 46-h postmortem interval. Knowledge of these changes is important for proper interpretation of gene expression studies utilizing autopsy specimens.

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Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle

Cited by 68 publications

References 48 publications

Distinctive patterns of microRNA expression in primary muscular disorders

Distinctive patterns of microRNA expression in primary muscular disorders

Evidence by molecular profiling for a placental origin of infantile hemangioma

Transcriptional profile of postmortem skeletal muscle

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