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Gene expression profiling of ventilation induced muscle wasting in rat plantaris

ABSTRACT: gene expression profiling of ventilation induced muscle wasting in rat plantaris

PROVIDER: PRJEB12368 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1210840.fastq.gz	Fastqsanger.gz
	ERR1210850.fastq.gz	Fastqsanger.gz
	ERR1210841.fastq.gz	Fastqsanger.gz
	ERR1210851.fastq.gz	Fastqsanger.gz
	ERR1210842.fastq.gz	Fastqsanger.gz

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Project description:Existing data suggest that NF-kappaB signaling is a key regulator of cancer-induced skeletal muscle wasting. However, identification of the components of this signaling pathway and of the NF-M-NM-:B transcription factors that regulate wasting is far from complete. In muscles of C26 tumor bearing mice, overexpression of d.n. IKKM-NM-2 blocked muscle wasting by 69%, the IM-NM-:BM-NM-1-super repressor blocked wasting by 41%. In contrast, overexpression of d.n. IKKM-NM-1 or d.n. NIK did not block C26-induced wasting. Surprisingly, overexpression of d.n. p65 or d.n. c-Rel did not significantly block muscle wasting. Genome-wide mRNA expression arrays showed upregulation of many genes previously implicated in muscle atrophy. To test if these upregulated genes were direct targets of NF-M-NM-:B transcription factors, we compared genome-wide p65 or p50 binding to DNA in control and cachectic muscle using ChIP-sequencing. Bioinformatic analysis of ChIP-seq data from control and C26 muscles showed increased p65 and p50 binding to a few regulatory and structural genes but only two of these genes were upregulated with atrophy. The p65 and p50 ChIP-seq data are consistent with our finding of no significant change in protein binding to an NF-M-NM-:B oligo in a gel shift assay. Taken together, these data support the idea that although inhibition of IM-NM-:BM-NM-1, and particularly IKKM-NM-2, blocks cancer-induced wasting, the alternative NF-M-NM-:B signaling pathway is not required. In addition, the downstream NF-M-NM-:B transcription factors do not regulate the transcriptional changes. These data are consistent with the growing body of literature showing that there are NF-M-NM-:B-independent substrates of IKKM-NM-2 and IM-NM-:BM-NM-1 that regulate physiological processes. To compare gene expression changes in atrophied muscles from C26 tumor bearing mice, gastrocnemius/plantaris muscles were harvested from 4 C26 tumor-bearing mice, and 3 control non tumor-bearing mice. Total RNA were isolated and pooled (2-3 muslces in the same group per RNA sample ) to make equal amount of total RNA per sample. Three pooled total RNA samples from healthy control muscles and 3 pooled total RNA from muscles of C26 tumor bearing mice were labelled and hybridized on 6 Mouse Affyemtrix Gene 1.0 ST arrays. Two-side t-tests and multiple test corrections were performed to identify differentially expressed genes due to C26 tumor bearing induced cachexia.

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Gene expression profiling of ventilation induced muscle wasting in rat plantaris

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