The first comprehensive -- but preliminary -- list of Foxp3 targets in mice could provide clues to how the protein helps regulate the immune system
By Chandra Shekhar | January 22, 2007
The first comprehensive catalogue of mouse genes targeted by the transcriptional factor Foxp3 appears in two papers published in this week's Nature. The lists from both studies don't always match, but the combined findings represent a key step in understanding how the protein helps regulatory T-cells maintain immune system tolerance and prevent autoimmune diseases.
"The papers provide the first look at relating the transcriptional DNA-binding activity of Foxp3 with specific target genes," said Fred Ramsdell of ZymoGenetics in Seattle, who was not involved in either study. "This is something the field has been looking to do for the past five years."
Expressed primarily in regulatory T-cells, Foxp3 is essential to both their development and normal function. Loss-of-function Foxp3 mutations in mice and humans result in fatal autoimmune diseases.
A research team led by Alexander Rudensky of the University of Washington in Seattle, with Ye Zheng as first author, used ex vivo T-cells from mice with Foxp3 knocked out or tagged with GFP. Using a chromatin immunoprecipitation (ChIP) protocol, the team located nearly 1,300 Foxp3 binding sites on the mouse genome, from which it identified 702 Foxp3-bound genes. "Unlike other transcription factors, Foxp3 binds to only a few sites in the genome," observed Rudensky. "But its binding results in very efficient changes in gene expression."
Another study, led by Richard Young of the Whitehead Institute in Cambridge, Mass. and Harald von Boehmer of the Dana-Farber Cancer Institute in Boston, also used ChIP to identify Foxp3 binding sites. Out of more than 1,500 binding sites, they identified 1,119 genes bound by Foxp3. Instead of ex vivo T-cells, however, the researchers used T-cell hybridomas transfected with Foxp3. This made it easier to observe the effects of T-cell receptor stimulation, explained study's first author, Alexander Marson. "Foxp3 exerts a much stronger influence on its target genes in stimulated cells than in unstimulated cells," he noted.
Ethan Shevach of the National Institutes of Health in Bethesda, Md., who was not involved in either study, said he preferred the use of normal T-cells -- as in the Zheng et al. study -- to hybridomas. "There is no evidence that the cell [Marson et al] transfect with Foxp3 is a regulatory T-cell," Shevach said.
Some of the direct targets of Foxp3 identified in the two studies -- such as members of the irf family -- are transcription factors in their own right, indicating a second layer of regulation mediated by Foxp3. The target lists also include a number of genes for cell surface molecules, such as CD28, and signal transduction, such as Cdc42. "Some of these targets are red herrings," cautioned Shevach. "Foxp3 may bind to them, but they may have nothing to do with regulatory cell function."
The results from the two studies differ significantly. For instance, Zheng et al. noted that ctla4 -- an important T-cell inhibitor -- was bound and strongly upregulated by Foxp3, but Marson et al. did not observe this. Conversely, while both studies found that Foxp3 bound to the receptor for IL2, a key player in immune response, only Marson et al. found IL2 itself to be a target. Further, while Zheng et al. determined that Foxp3 activated more genes than it suppressed, Marson et al. came to the opposite conclusion. "What I found most striking was the amount of non-overlap between the two datasets," said Steve Ziegler of the Benaroya Research Institute in Seattle. "This may reflect the fact that they used two different systems for their chip-on-chip analysis."
Despite the discrepancies, experts said the studies would be a major help in research into immune tolerance. "Foxp3 is located in the nucleus and is hard to get at," said Ziegler. "Downstream targets of it may be more accessible and give us more tractable surrogate markers of regulatory T-cells."
Links within this article
Y. Zheng, et al., "Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells," Nature, Jan 2007.
A. Marson, et al., "Foxp3 occupancy and regulation of key target genes during T-cell stimulation," Nature, Jan 2007.
T.P. Toma, "Self-tolerance gene?" The Scientist, January 9, 2003
M. Greener, "Hot on tolerance's trail: The hunt for human Foxp3," The Scientist, May 23, 2005
F. Ramsdell, "Foxp3 and natural regulatory T cells: Key to a cell lineage?" Immunity, August 2003.
Harald von Boehmer
I am not a scientist, but I am a M.S. sufferer, who has used all of the ABC et al drugs. Dr. Young's statement, "...in autoimmune disorders, most of the genes are less active..." This seems to contradict the efficacy of T cell modulating drugs, but it does suggests inanition in the Foxp3 function.