Open Access Research article

Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression

Vincent A Funari1, Allen Day2, Deborah Krakow123, Zachary A Cohn1, Zugen Chen2, Stanley F Nelson24 and Daniel H Cohn124*

Author Affiliations

1 Medical Genetics Institute, Cedars-Sinai Medical Center, SSB-3, 8700 Beverly Blvd, Los Angeles, CA 90048, USA

2 Departments of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA

3 Departments of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA

4 Departments of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA

For all author emails, please log on.

BMC Genomics 2007, 8:165  doi:10.1186/1471-2164-8-165

Published: 12 June 2007



Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18–22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed Celsius.


161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as cartilage collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis.


Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated.