International Immunology, Vol. 14, No. 12, pp. 1383-1395,
December 2002
© 2002 Japanese Society for Immunology
Serial analysis of gene expression in murine fetal thymocyte cell lines
1 Molecular Pathology Division, Department of Cellular Pathology and Genetics, Armed Forces Institute of Pathology, Rockville, MD 20850, USA 2 Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA 19104, USA 3 Present address: Department of Animal Science, University of Vermont, Burlington, VT 05405-0148, USA 4 Present address: Cancer Biology, Telethon Institute for Child Health Research, Subiaco, WA 6008 Australia
Correspondence to: J. K. Taubenberger; E-mail: taubenbe{at}afip.osd.mil
Transmitting editor: A. Singer
FTL-1, -3 and -10 are three murine day 14 fetal thymocyte cell lines produced in order to model developmental stages within early (CD3–CD4–CD8–) thymocyte differentiation. In this study, we used the serial analysis of gene expression (SAGE) method to perform a systematic analysis of transcripts present in these three cell lines. A total of 77,313 SAGE tags were sequence identified from the three cell lines, representing 24,645 unique transcripts. Differentially expressed mRNA transcripts representing different gene classes were identified, including T cell functional genes, cytokine receptors, adhesion molecules and transcription factors. These results may serve as a model of the transcriptome of early thymocyte differentiation. A large number of unknown expressed sequence tags were also found to be differentially expressed. In order to validate the SAGE data, selected differentially expressed transcripts identified by SAGE were analyzed by quantitative RT-PCR in normal murine double-negative stage DN1–4 thymocytes. Expression of the transcription factors RUNX2 and PHD finger protein 2 and of the IGF type 1 receptor was shown to have differentially regulated expression patterns in sorted DN1–4 cells. These genes, and others identified by this analysis, are likely to play important roles in the development of T cells.
Keywords: differentiation, gene expression, serial analysis of gene expression, T cells, thymocytes, transcription factors
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