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Series GSE85017 Query DataSets for GSE85017
Status Public on Jan 09, 2017
Title Role of Alternative splicing in human skeletal muscle and cancer cachexia
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Alternative splicing (AS) is a post-transcriptional gene regulatory mechanism that contributes to proteome diversity. Aberrant splicing mechanisms (mutations, polymorphisms, insertion/deletion etc.) contribute to various cancers and muscle related conditions such as Duchenne muscular dystrophy. However, dysregulation of AS in Cancer Cachexia (CC) patients remains unexplored. Our objectives were (i) to profile alternatively spliced genes (ASGs) on a genome-wide scale, and (ii) to identify DE alternatively spliced genes (DASGs) associated with CC. Rectus abdominis muscle biopsies obtained from cancer patients were stratified into cachectic cases (n=21, classified based on International consensus diagnostic framework for CC) and non-cachectic controls (n=19, weight stable cancer patients). Human Transcriptome array 2.0 was used for profiling ASGs using the total RNA isolated from muscle biopsies. Representative DASG signatures were validated using semi-quantitative RT-PCR. We identified 8960 ASGs, of which 922 DASGs (772 up-regulated, 150 down-regulated) were identified at > 1.4 fold-change and p < 0.05. Representative DASGs when validated by semi-quantitative RT-PCR also showed similar trends, confirming the primary findings from the genome-wide arrays. Identified DASGs were associated with myogenesis, adipogenesis, protein ubiquitination and inflammation. Up to 10% of the DASGs exhibited cassette exon (exon included or skipped) as a predominant form of AS event. We also observed other forms of AS events such as intron retention, alternate promoters. Overall, we have, for the first time conducted global profiling of muscle tissue to identify DASGs associated with CC. The mechanistic roles of the identified DASGs in CC pathophysiology using model systems is warranted, as well as replication of findings in independent cohorts.
 
Overall design Identification of Differentially expressed Alternatively spliced genes associated with cancer cachexia
 
Contributor(s) Damaraju S, Narasimhan A, Greiner R, Bathe OF, Baracos VE
Citation(s) 28058815, 28984045
Submission date Jul 31, 2016
Last update date Jun 11, 2019
Contact name Sambasivarao Damaraju
E-mail(s) sdamaraj@ualberta.ca
Phone 7804328869
Organization name University of Alberta
Department Laboratory medicine and pathology
Street address 11560 University Ave
City Edmonton
State/province Alberta
ZIP/Postal code T6G1Z2
Country Canada
 
Platforms (1)
GPL17585 [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [probe set (exon) version]
Samples (40)
GSM2256249 Cachectic cases [3003]
GSM2256250 Cachectic cases [3005]
GSM2256251 Cachectic cases [4093]
Relations
BioProject PRJNA335911

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE85017_RAW.tar 976.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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