Global gene expression profiles associated with retinoic acid‐induced differentiation of embryonal carcinoma cells

Abstract

We have evaluated the effects of retinoic acid (RA) treatment of F9 embryonal carcinoma (EC) cells, which induces differentiation into primitive endoderm, on gene expression patterns. F9 cells were exposed to RA in culture, and global expression patterns were examined with cDNA-based microarrays at early (8 hr) and later times (24 hr) after exposure. Of the 1,176 known transcripts examined, we identified 57 genes (4.8%) that were responsive to RA at 8 and/or 24 hr: 35 were induced, 20 were repressed, and 2 were differentially regulated at these time points. To determine if our results were dependent on the array technology employed, we also evaluated the response to RA at 24 hr with oligonucleotide-based arrays. With these more dense arrays (12,488 genes), we identified an additional 353 RA-regulated genes (2.8%): 173 were upregulated and 180 were downregulated. Thus, a total of 410 genes regulated by RA were identified with roughly equivalent numbers induced or repressed. Although the expression of many genes found on both array platforms was consistent, the results for some genes were disparate. Quantitative PCR studies on a subset of these genes supported the results obtained with the cDNA arrays. Our results confirmed the regulation of several known RA-responsive genes and we also identified a number of genes not previously known to be RA-responsive. Those novel genes that were induced presumably contribute to the cellular processes required for a shift from proliferation to differentiation, whereas those new genes that were downregulated may possibly contribute to the maintenance of cell proliferation.

Retinoic Acid and the Development of the Endoderm

“…In addition to the changes in gene expression noted above, EC and ES cells have shed considerable light on the fact that ExEn differentiation is accompanied by significant changes in gene expression, and this has been reported in several gene-profiling studies [152,[162][163][164][165][166][167][168][169][170][171][172], including both positive and negative regulation imposed on the RA receptors themselves [173,174]. Although assembling these changes in gene regulation into a hierarchy or network has until recent been problematic, integrative genomics have nevertheless revealed the diversity of distinct regulatory programs involved in RA signaling during F9 cell differentiation [175].…”

Retinoic acid induces TGFβ-dependent autocrine fibroblast growth

“…Comparison of T-RA-regulated genes in fibroblasts with those regulated during parietal endoderm differentiation of F9 embryonal carcinoma cells Eifert et al, 2006) or neuronal differentiation of P19 cells (Wei et al, 2002) reveals only a limited number of common targets and in some cases, T-RA even has an opposite effect as TEF (thyrotroph embryonic factor) is induced during F9 differentiation, but repressed in fibroblasts. Otherwise, the repertoire of T-RA-regulated genes in F9/P19 cells and fibroblasts is distinct.…”

Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)

“…Among these genes are the "stimulated by RA" (Stra) genes such as Bhlhb40 (Stra13) (51), Tcfap2C (Stra2) (52), and Meis2 (Stra10) (53), and zinc finger proteins (Zfp598 and Zfp503) (8,10). Note that three RAREs are associated to the Meis2 gene but that only two were occupied by RAR/RXR heterodimers in F9 cells.…”