title: Global Gene Expression Profiling and Alternative Splicing Events during the Chondrogenic Differentiation of Human Cartilage Endplate-Derived Stem Cells.
abstract: Low back pain (LBP) is a very prevalent disease and degenerative disc diseases (DDDs) usually account for the LBP. However, the pathogenesis of DDDs is complicated and difficult to elucidate. Alternative splicing is a sophisticated regulatory process which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. In addition, the cartilage endplate-derived stem cells have been discovered and identified by our research group. In this paper, we continue to investigate gene expression profiling and alternative splicing events during chondrogenic differentiation of cartilage endplate-derived stem cells. We adopted Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) to compare the transcriptional and splicing changes between the control and differentiated samples. RT-PCR and quantitative PCR are used to validate the microarray results. The GO and KEGG pathway analysis was also performed. After bioinformatics analysis of the data, we detected 1953 differentially expressed genes. In terms of alternative splicing, the Splicing Index algorithm was used to select alternatively spliced genes. We detected 4411 alternatively spliced genes. GO and KEGG pathway analysis also revealed several functionally involved biological processes and signaling pathways. To our knowledge, this is the first study to investigate the alternative splicing mechanisms in chondrogenic differentiation of stem cells on a genome-wide scale.
authors.affiliation: Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Shang
authors.affiliation: Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Fan
authors.affiliation: Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Shangguan
authors.affiliation: Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Orthopedics, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D000328:Adult; D000368:Aged; D017398:Alternative Splicing / Q000235:genetics*; D002356:Cartilage / Q000166:cytology / Q000378:metabolism; D002454:Cell Differentiation / Q000235:genetics*; D002478:Cells, Cultured; D019902:Chondrocytes / Q000166:cytology / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007405:Intervertebral Disc Displacement / Q000235:genetics; D008297:Male; D008875:Middle Aged; D013168:Spondylolisthesis / Q000235:genetics; D013234:Stem Cells / Q000166:cytology; D059467:Transcriptome / Q000235:genetics*