Gene expression profile of human chondrocyte HCS-2/8 cell line by EST sequencing analysis

ArticleinGene 330(1):85-92 · May 2004with24 Reads
Impact Factor: 2.14 · DOI: 10.1016/j.gene.2004.01.007 · Source: PubMed
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.

    • "Results DICAM belongs to Ig superfamily and has homology with JAM family DICAM was first identified as adipocyte specific protein 3 (ASP3) in a subtracted adipocyte library (Tsuruga, 2001). We identified DICAM in HCS-2/8 human chondrocyte library (Jung et al., 2004). Human and mouse DICAM were located in chromosome 1p36 and chromosome 4 (83.0 cM) respectively, and composed of 10 exons (Fig. 1A). "
    [Show abstract] [Hide abstract] 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.
    Full-text · Article · Sep 2008 · Journal of Cellular Physiology
    0Comments 8Citations
    • "Numerous genes involved in skeletal development have been discovered through in vitro and in vivo studies [6,7]. Expressed sequence tag (EST) libraries, prepared from both normal and diseased human cartilage have been created8910 as have cDNA libraries [11]. Another similar set of libraries from Serial Analysis of Gene Expression (SAGE) also provides cartilage specific expression libraries. "
    [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.
    Full-text · Article · Feb 2007 · BMC Genetics
    0Comments 0Citations
    • "Unfortunately, no corresponding data are available for the 12 –20 week fetal cartilage library (Pogue et al., 2004). A comparison with an equivalent classification by Jung et al. (2004) for an EST profile (3350 sequences) of the human chondrocyte HCS-2/8 cell line revealed differences (Table 1). Although functional categorisation of genes is somewhat arbitrary and therefore comparison between these data has to be interpreted carefully, it is remarkable that the number of genes involved in metabolism and gene/ protein expression is similar between all three libraries, while in contrast much more genes involved in cell division and cell structure/motility are expressed in the cell line. "
    [Show abstract] [Hide abstract] ABSTRACT: The differentiation of mesenchymal stem cells into hypertrophic chondrocytes is an integral and multistep process important in pattern formation, endochondral ossification, and postnatal growth of the skeleton. In recent years, novel genes involved in these processes have been identified, but still only little is known about the large-scale gene expression profile during skeletal development. We initiated an expressed sequence tag (EST) project aiming at the identification of genes and pathways involved in this complex process. Candidate genes are expected to be of value for diagnosis and treatment of monogenic and multigenic heritable disorders of the skeleton. Here, we describe the sequences of 4,748 clones from a human growth plate cartilage cDNA library generated from 20 weeks prenatal-2 years postnatal specimens. In silico analysis of these sequences revealed 1,688 individual transcription units, corresponding to known (1,274) and to novel, yet uncharacterised potential genes (414). The tissue specificity of the library was reflected by its corresponding EST profile representing a total of approximately 10% proteins already shown to be involved in cartilage/bone development or homeostasis. The EST profile also reflects the developmental stage of the tissue with significant differences in the expression of matrix proteins compared to corresponding EST profiles from 8-12 and 12-20 week human fetal cartilage. Calculation of the relative frequency of transcripts in our cDNA library, as compared to their abundance in other EST datasets, revealed a set of approximately 200 genes, including 81 novel, yet uncharacterised genes, showing increased expression. These genes represent candidates for the large number of osteochondrodysplasias for which the causative gene defects have not yet been identified.
    Full-text · Article · Jan 2006 · Matrix Biology
    0Comments 12Citations
Show more