Gene expression profile of human chondrocyte HCS-2/8 cell line by EST sequencing analysis.
ABSTRACT Large-scale single-pass sequencing of randomly selected cDNA clones from cell type specific libraries has proven to be a powerful approach for the discovery of novel gene functions, identification of novel gene family members, and definition of gene expression profiles. HCS-2/8 chondrocyte has been used as a cell culture model to study chondrocyte differentiation. Here we performed 3350 single-pass sequencing reactions obtained from the 5' ends of cDNAs from HCS-2/8 cells. To define the expression profiles of HCS-2/8 chondrocytes, we analyzed the identity of these representative cDNA sequences using database searches (BLAST). The sequences represent 1927 unique genes with known function (i.e., unigene clusters), 38 transcripts that are similar to genes with known function, 739 expressed genes with unknown function (i.e., expressed sequence tags), and 18 cDNAs which have not previously been sequenced. Interestingly, many transcripts were expressed from chromosome 12 compared with total genes, while the fewer numbers of cDNAs were derived from genes on chromosomes 14, 18 and Y. The chondrocytic phenotype of HCS-2/8 cells is reflected by abundant expression of genes related to cell structure and motility and the 20 most frequently expressed unigenes reflect a chondrocyte-related gene expression signature. Thus, our data establish a representative set of more than 2000 genes expressed in a chondrocytic cell line. This finding provides a framework for understanding cell growth and differentiation of chondrocytes and their metabolic function in the formation and remodeling of cartilage.
- SourceAvailable from: Kenneth M C Cheung[show abstract] [hide abstract]
ABSTRACT: Diseases of cartilage, such as arthritis and degenerative disc disease, affect the majority of the general population, particularly with ageing. Discovery and understanding of the genes and pathways involved in cartilage biology will greatly assist research on the development, degeneration and disorders of cartilage. We have established the Integrated Cartilage Gene Database (iCartiGD) of genes that are known, based on results from high throughput experiments, to be expressed in cartilage. Information about these genes is extracted automatically from public databases and presented as a single page report via a web-browser. A variety of flexible search options are provided and the chromosomal distribution of cartilage associated genes can be presented. iCartiGD provides a comprehensive source of information on genes known to be expressed in cartilage. It will remain current due to its automatic update capability and provide researchers with an easily accessible resource for studies involving cartilage. Genetic studies of the development and disorders of cartilage will benefit from this database.BMC Genetics 02/2007; 8:4. · 2.81 Impact Factor
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ABSTRACT: Immunoglobulin (Ig) superfamily members are abundant with diverse functions including cell adhesion in various tissues. Here, we identified and characterized a novel adhesion molecule that belongs to the CTX protein family and named as DICAM (Dual Ig domain containing cell adhesion molecule). DICAM is a type I transmembrane protein with two V-type Ig domains in the extracellular region and a short cytoplasmic tail of 442 amino acids. DICAM is found to be expressed ubiquitously in various organs and cell lines. Subcellular localization of DICAM was observed in the cell-cell contact region and nucleus of cultured epithelial cells. Cell-cell contact region was colocalized with tight junction protein, ZO-1. The DICAM increased MDCK cell adhesion to 60% levels of fibronectin. DICAM mediated cell adhesion was specific for the alphavbeta3 integrin; other integrins, alpha2, alpha5, beta1, alpha2beta1, alpha5beta1, were not involved in cell adhesion. In identifying the interacting domain of DICAM with alphavbeta3, the Ig domain 2 showed higher cell adhesion activity than that of Ig domain 1. Although RGD motif in Ig domain 2 was engaged in cell adhesion, it was not participated in DICAM-alphavbeta3 mediated cell adhesion. Furthermore, differentially expressing DICAM stable cells showed well correlated cell to cell adhesion capability with integrin beta3-overexpressing cells. Collectively, these results indicate that DICAM, a novel dual Ig domain containing adhesion molecule, mediates cell adhesion via alphavbeta3 integrin.Journal of Cellular Physiology 10/2008; 216(3):603-14. · 4.22 Impact Factor
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ABSTRACT: Although the rabbit is commonly used as an animal model for the in vivo study of cartilage formation or regeneration, genetic approaches to the rabbit cartilage are rare. We constructed an expressed sequence tag (EST) library from rabbit cartilage tissue for the first time to establish the foundations for genetic study on rabbit cartilage. From our results, we identified 2387 unique genes among 4885 clones, corresponding to 1839 matched to characterized genes including 1618 genes with known function and 548 uncharacterized and novel genes. Gene expression profiles based on EST frequency show that type II collagen (COL2A1) and type X collagen (COL10A1) among collagen clones, proteoglycan 4 (PRG4) and decorin (DCN) among proteoglycan clones, and cartilage oligomeric matrix protein (COMP) and matrix Gla protein (MGP) among other extracellular matrix clones, are highly expressed in rabbit cartilage. In addition, gene expression analysis based on real-time PCR of these major extracellular matrix constituents showed that expression of col2a1 and col10a1 remains constant whereas the expression of prg4, dcn, and comp reveals substantial change with rabbit age. This EST library will provide a valuable resource with which to identify genes involved in the biochemical and physiological functions of rabbit cartilage, and will contribute to establishing the rabbit as an animal model for cartilage research.Gene 09/2008; 424(1-2):147-52. · 2.20 Impact Factor